Contacts of the helix formed by residues 89 - 115 (chain D) in PDB entry 2F3M
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 89 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLU* 1.3 83.3 - - + +
90D GLU* 1.3 65.9 + - - +
91D GLU* 2.9 18.9 + - - +
92D GLU* 3.1 32.2 + - + +
93D LYS* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C HIS* 5.2 7.6 - - + +
78C TYR* 3.9 13.2 - - + -
81C ARG* 3.1 48.3 + - - +
89D THR* 1.3 74.3 + - - +
91D GLU* 1.3 65.5 + - - +
93D LYS* 3.1 17.6 + - - +
94D ILE* 3.1 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C HIS* 3.4 32.1 + - - +
89D THR* 2.9 8.5 + - - +
90D GLU* 1.3 78.9 - - - +
92D GLU* 1.3 62.0 + - + +
94D ILE* 3.4 9.2 + - - +
95D ARG* 3.2 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D GLY* 3.7 7.6 - - - -
88D GLU* 2.9 36.2 + - - +
89D THR* 3.1 38.1 + - + +
91D GLU* 1.3 78.0 - - + +
93D LYS* 1.3 58.3 + - - +
95D ARG* 3.4 3.1 + - - +
96D VAL* 2.9 33.6 + - - +
148D ALA* 3.9 29.4 - - + +
149D GLY* 5.4 1.8 - - - -
150D ASN 5.3 2.1 + - - -
151D LYS* 4.7 16.2 + - - +
153D THR* 4.7 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ARG* 4.0 35.4 - - - +
93C LYS* 6.2 0.4 - - - +
86D CYS* 4.3 9.9 - - - +
87D GLY 3.6 22.2 - - - +
88D GLU 3.9 8.1 + - - +
89D THR 3.2 15.4 + - - +
90D GLU* 3.1 13.5 + - - +
92D GLU* 1.3 76.9 - - - +
94D ILE* 1.3 54.3 + - - +
96D VAL* 3.2 7.7 + - + +
97D ASP* 2.8 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C HIS* 3.3 38.4 - - + +
68C LYS 5.7 0.4 - - - +
69C ILE* 4.2 16.2 - - + -
74C ALA* 6.4 0.4 - - + -
78C TYR* 3.8 20.9 - - + -
81C ARG* 3.8 19.7 - - - +
90D GLU* 3.1 20.4 + - + +
91D GLU* 3.7 13.2 - - - +
93D LYS* 1.3 73.6 - - - +
95D ARG* 1.3 67.9 + - + +
97D ASP* 3.1 6.2 + - - +
98D ILE* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D GLU* 3.2 32.6 + - - +
92D GLU 3.7 5.8 - - - +
94D ILE* 1.3 82.1 - - + +
96D VAL* 1.3 63.0 + - - +
98D ILE* 3.7 4.1 - - + +
99D LEU* 3.0 30.5 + - - +
140D PHE* 2.8 69.4 + - + -
141D LEU* 4.6 1.0 - - - +
144D ARG* 3.3 35.3 - - - +
147D PHE 2.8 34.3 + - - +
148D ALA* 3.5 21.8 + - - -
155D VAL* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D CYS* 4.0 23.1 - - - +
87D GLY* 4.7 1.1 - - - -
92D GLU 2.9 19.5 + - - +
93D LYS* 3.2 10.3 + - - +
95D ARG* 1.3 75.2 - - - +
97D ASP* 1.3 65.4 + - - +
100D GLU* 2.8 34.9 + - - +
148D ALA* 4.4 7.4 - - + -
153D THR* 4.3 10.3 - - - +
154D PHE* 3.6 33.0 - - + -
155D VAL* 3.5 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN 5.6 0.2 - - - -
74C ALA* 3.9 20.5 - - + +
77C CYS* 3.7 17.8 - - - +
81C ARG* 3.0 32.4 + - - -
100C GLU* 5.9 2.5 - - - -
93D LYS* 2.8 22.2 + - - +
94D ILE* 3.6 5.4 - - - +
96D VAL* 1.3 78.5 - - - +
98D ILE* 1.3 60.9 + - - +
100D GLU* 3.5 15.4 - - - +
101D ASN* 2.7 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASP* 5.2 10.5 - - + +
56C PHE* 4.0 28.0 - - + -
68C LYS 4.5 10.3 - - - +
69C ILE* 4.6 3.4 - - + -
70C THR* 3.9 37.5 - - - +
71C GLN* 3.8 5.5 - - + +
74C ALA* 4.2 9.6 - - + -
94D ILE* 2.9 38.5 + - + +
95D ARG* 3.7 7.2 - - + +
97D ASP* 1.3 75.2 - - - +
99D LEU* 1.3 53.9 + - - +
101D ASN* 3.0 6.4 + - - +
102D GLN* 2.7 36.0 + - + +
140D PHE* 5.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 4.1 9.6 - - + -
95D ARG 3.0 15.4 + - - +
98D ILE* 1.3 73.4 - - - +
100D GLU* 1.3 64.6 + - - +
102D GLN* 3.9 4.5 - - + -
103D THR* 2.9 31.6 + - + +
137D TYR* 4.0 27.6 - - + -
140D PHE* 3.6 33.7 - - + -
147D PHE* 3.2 39.3 - - + +
155D VAL* 3.9 25.8 - - + -
159D VAL* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ASP* 5.7 2.4 - - - +
100C GLU* 5.0 14.7 - - - +
101C ASN* 5.0 2.9 + - - -
73D ASN* 3.2 58.0 + - - +
77D CYS* 5.0 3.8 - - - +
96D VAL* 2.8 18.5 + - - +
97D ASP* 3.5 23.5 + - - +
98D ILE 3.2 0.2 - - - -
99D LEU* 1.3 78.2 - - - +
101D ASN* 1.3 68.5 + - - +
103D THR* 3.4 10.2 + - - -
104D MET* 3.8 4.5 - - - +
154D PHE* 3.9 22.9 - - + -
155D VAL* 3.8 11.2 - - + +
158D LEU* 4.2 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLN* 3.5 27.7 - - + +
73C ASN* 3.9 35.3 + - - +
74C ALA 4.1 8.5 - - - +
100C GLU* 5.1 2.9 + - - +
101C ASN* 4.7 7.6 - - - +
73D ASN* 4.7 3.9 + - - +
97D ASP* 2.7 24.4 + - - +
98D ILE 3.0 2.4 + - - +
100D GLU* 1.3 88.4 + - - +
102D GLN* 1.3 64.3 + - - +
103D THR 3.3 0.2 - - - -
104D MET* 3.4 6.2 + - - +
105D ASP* 3.1 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 3.3 58.1 - - + +
58C ASN* 4.8 4.4 + - - +
71C GLN* 3.2 24.2 + - - +
98D ILE* 2.7 26.4 + - + +
99D LEU* 3.9 9.9 - - + +
101D ASN* 1.3 74.3 - - - +
103D THR* 1.3 62.9 + - - +
105D ASP* 3.1 7.1 + - - +
106D ASN* 3.1 50.8 + - - +
136D LEU* 5.5 2.6 - - - +
137D TYR* 3.8 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LEU* 2.9 24.0 + - - +
100D GLU 3.4 6.6 + - - -
102D GLN* 1.3 74.8 - - - +
104D MET* 1.3 60.9 + - - +
105D ASP 3.2 0.2 + - - -
106D ASN* 3.2 2.6 + - - +
107D HIS* 2.8 36.7 + - - +
137D TYR* 3.6 19.7 - - + +
158D LEU* 3.6 24.8 - - + +
159D VAL* 3.9 39.3 - - + +
162D VAL* 3.8 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ASP* 5.5 2.9 - - - +
108C MET* 6.1 0.4 - - + -
12D LEU* 4.5 23.3 - - + -
72D SER* 5.3 4.5 - - - -
73D ASN* 4.5 12.1 - - - +
100D GLU 3.8 12.1 + - - +
101D ASN* 3.4 10.7 + - - +
102D GLN 3.3 0.2 - - - -
103D THR* 1.3 82.0 + - - +
105D ASP* 1.3 60.3 + - - +
107D HIS* 3.6 8.5 - - + +
108D MET* 2.9 59.9 + - + +
158D LEU* 6.5 0.4 - - - -
4218D GTD 3.8 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN* 4.5 2.8 + - - -
71C GLN* 2.8 23.1 + - - +
104C MET* 5.4 3.1 - - - +
3218C GTD 3.5 27.3 + - - +
101D ASN* 3.1 16.1 + - - +
102D GLN* 3.4 12.3 - - - +
103D THR 3.1 0.2 - - - -
104D MET* 1.3 76.4 - - - +
106D ASN* 1.3 61.2 + - - +
107D HIS 3.2 0.3 + - - -
108D MET* 3.2 18.3 + - - +
109D GLN* 2.9 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D GLN* 3.1 27.5 + - - +
103D THR 3.8 5.8 - - - +
105D ASP* 1.3 76.2 - - - +
107D HIS* 1.3 60.3 + - - +
109D GLN* 2.9 25.6 + - - +
110D LEU* 3.2 21.7 + - - +
126D TYR* 4.1 4.2 + - - -
133D LYS* 4.0 23.8 + - + +
137D TYR* 2.4 37.6 + - - +
162D VAL* 4.6 13.5 - - + -
166D HIS* 4.8 6.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLY* 4.3 13.9 - - - -
12D LEU* 3.8 30.3 - - + +
103D THR 2.8 17.1 + - - +
104D MET* 3.6 12.8 - - + +
106D ASN* 1.3 74.3 - - - +
108D MET* 1.3 69.8 + - + +
110D LEU* 3.1 9.4 + - - +
111D GLY 2.9 18.2 + - - -
161D ASP* 4.1 8.6 + - - -
162D VAL* 4.2 12.0 - - + +
165D LEU* 3.9 27.3 - - + +
166D HIS* 6.3 0.2 - - - -
207D VAL* 6.0 0.7 - - + -
208D PHE* 4.0 17.5 - + - -
4218D GTD 3.9 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C MET* 5.8 1.8 - - + -
108C MET* 3.7 40.6 - - + +
104D MET* 2.9 51.8 + - + +
105D ASP* 3.8 18.4 - - - +
107D HIS* 1.3 74.1 - - + +
109D GLN* 1.3 53.7 + - - +
111D GLY 3.1 1.0 + - - -
112D MET* 2.7 49.1 + - + +
4218D GTD 4.0 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ASP* 2.9 27.6 + - - +
106D ASN* 2.9 34.0 + - - +
107D HIS 3.1 0.4 - - - -
108D MET* 1.3 76.3 - - + +
110D LEU* 1.3 63.5 + - - +
112D MET* 3.2 36.6 + - + +
113D ILE* 3.5 7.8 + - - +
126D TYR* 3.9 10.4 - - + -
133D LYS* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ASN 3.2 7.6 + - - +
107D HIS* 3.1 10.2 + - - +
109D GLN* 1.3 77.1 - - - +
111D GLY* 1.3 64.4 - - - +
112D MET 3.1 0.7 + - - -
113D ILE* 3.2 9.8 + - + +
114D CYS* 3.1 35.6 + - - -
126D TYR* 3.2 36.0 + - + +
165D LEU* 4.2 34.1 - - + +
166D HIS* 4.0 18.2 - - + +
169D PHE* 4.3 15.3 - - + -
208D PHE* 4.1 20.4 - - + -
214D TRP* 5.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D HIS 2.9 10.6 + - - -
108D MET 3.4 4.0 - - - -
110D LEU* 1.3 77.6 - - - +
112D MET* 1.3 61.5 + - - +
114D CYS* 4.0 2.0 - - - -
115D TYR* 2.9 33.6 + - - +
208D PHE* 3.9 19.7 - - - -
4218D GTD 3.5 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D MET* 2.7 26.2 + - + +
109D GLN* 3.4 35.4 - - + +
110D LEU 3.1 0.6 - - - -
111D GLY* 1.3 76.9 - - - +
113D ILE* 1.3 64.3 + - + +
115D TYR* 4.0 2.9 - - - +
116D ASN* 3.3 22.4 + - - +
4218D GTD 5.0 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLN 3.9 10.3 - - - +
110D LEU* 3.2 11.2 + - - +
112D MET* 1.3 78.0 - - + +
114D CYS* 1.3 62.2 + - - +
115D TYR 3.0 4.7 - - - -
116D ASN* 2.8 33.0 + - - +
119D PHE* 3.3 31.7 - - + +
122D LEU* 4.3 24.0 - - + -
123D LYS* 4.5 12.6 - - - +
126D TYR* 3.7 43.5 - - + -
169D PHE* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LEU* 3.1 29.7 + - - +
111D GLY 4.4 1.6 - - - +
112D MET 3.5 0.2 - - - -
113D ILE* 1.3 80.5 - - - +
115D TYR* 1.3 59.1 + - - +
119D PHE* 3.7 24.0 - - - -
169D PHE* 4.0 1.8 - - - -
208D PHE* 3.6 27.8 - - + -
212D ALA* 3.5 5.2 - - - +
213D VAL* 2.8 27.1 + - - -
214D TRP* 3.4 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D GLY* 2.9 29.8 + - - +
112D MET* 4.0 3.6 - - - +
113D ILE 3.0 1.0 - - - -
114D CYS* 1.3 79.3 - - - +
116D ASN* 1.3 61.0 + - - +
117D PRO* 3.4 9.0 - - - +
208D PHE* 3.5 25.2 - + + +
209D SER* 3.1 34.5 + - - -
211D MET* 4.1 35.1 - - + +
212D ALA* 4.2 11.9 - - + +
213D VAL* 4.9 4.2 - - - +
4218D GTD 3.0 57.4 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il