Contacts of the helix formed by residues 88 - 107 (chain D) in PDB entry 3LOC
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 ALA 88 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR* 3.7 39.5 - - - +
131B GLY* 4.0 10.9 - - - -
86D ASP 4.0 0.4 + - - -
87D PHE* 1.3 70.6 - - - +
89D PRO* 1.3 72.1 - - + +
90D LEU* 3.3 1.7 + - + +
91D ALA* 3.3 9.4 + - + +
92D ALA* 3.1 21.3 + - - +
152D LYS* 5.2 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE 3.4 5.6 - - - +
88D ALA* 1.3 82.6 - - + +
90D LEU* 1.3 60.7 + - + +
92D ALA* 3.2 5.9 + - + +
93D ILE* 2.8 37.1 + - + +
147D TRP* 3.5 60.3 - - + +
152D LYS* 4.1 30.3 - - + +
153D LEU* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASP* 4.1 17.5 - - - +
130B THR* 5.9 1.6 - - - +
88D ALA* 3.4 0.8 - - + -
89D PRO* 1.3 74.9 - - + +
91D ALA* 1.3 61.5 + - - +
93D ILE* 4.6 0.7 - - - -
94D LYS* 2.9 36.5 + - - +
152D LYS 4.9 4.3 - - - +
153D LEU* 3.5 29.4 - - + -
205D ILE* 3.7 18.4 - - + +
208D ILE* 4.0 18.4 - - + -
209D ARG* 3.3 48.2 - - + +
210D PRO* 4.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASP* 4.2 26.2 - - + +
130B THR* 5.1 0.8 + - - +
131B GLY* 4.6 6.5 - - - -
88D ALA* 3.3 21.7 + - + +
90D LEU* 1.3 77.6 - - - +
92D ALA* 1.3 56.7 + - - +
94D LYS* 3.6 7.5 + - - +
95D GLU* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 4.0 27.6 - - + -
87D PHE* 4.2 24.5 - - + -
88D ALA 3.1 14.1 + - - +
89D PRO* 3.6 8.5 - - + +
91D ALA* 1.3 76.7 - - - +
93D ILE* 1.3 58.4 + - - +
95D GLU* 3.2 11.6 + - - +
96D TYR* 2.8 28.9 + - - +
147D TRP* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 4.2 18.8 - - + -
89D PRO* 2.8 23.6 + - + +
90D LEU 4.0 2.5 - - - +
92D ALA* 1.3 73.1 - - - +
94D LYS* 1.3 67.3 + - - +
96D TYR* 3.1 6.8 + - + +
97D ILE* 2.8 29.4 + - + +
144D ILE* 5.5 3.4 - - + -
147D TRP* 5.3 2.9 - - + +
153D LEU* 4.6 11.2 - - + -
161D LEU* 3.8 18.2 - - + -
165D ILE* 3.9 24.2 - - + -
204D ILE* 4.7 2.9 - - + -
205D ILE* 3.8 17.0 - - + -
208D ILE* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 5.7 2.6 + - - -
124B LEU 5.1 7.9 + - - -
127B ASP* 3.1 40.7 + - + +
90D LEU 2.9 19.3 + - - +
91D ALA* 3.7 6.7 - - - +
93D ILE* 1.3 74.2 - - - +
95D GLU* 1.3 63.5 + - - +
97D ILE* 3.2 2.1 + - - +
98D ARG* 3.0 12.0 + - - +
201D GLN* 2.9 49.1 + - - +
205D ILE* 3.6 30.7 - - + +
209D ARG* 5.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ALA 3.0 20.3 + - - +
92D ALA* 3.5 9.3 - - - +
93D ILE 3.1 0.2 - - - -
94D LYS* 1.3 76.9 - - - +
96D TYR* 1.3 51.1 + - - +
98D ARG* 3.2 10.0 + - + +
99D LEU* 2.8 60.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TRP 4.0 17.2 + - - -
77D LEU* 5.0 1.4 - - - +
79D PRO* 3.7 19.7 - - + -
80D LEU* 3.6 42.9 - - + +
83D PHE* 4.1 21.1 - + + -
92D ALA 2.8 17.5 + - - +
93D ILE* 3.3 10.3 - - + +
95D GLU* 1.3 71.3 - - - +
97D ILE* 1.3 62.6 + - - +
99D LEU* 3.2 5.5 + - - +
100D LYS* 2.9 40.8 + - + +
162D ILE* 5.2 5.8 - - + -
165D ILE* 3.8 33.4 - - + -
166D TRP* 2.9 29.7 + + - -
212D URA 4.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 2.8 30.6 + - + +
94D LYS* 3.4 7.9 - - - +
96D TYR* 1.3 73.2 - - - +
98D ARG* 1.3 65.5 + - - +
100D LYS* 3.4 4.0 + - - +
101D LEU* 3.2 33.2 + - + +
165D ILE* 4.2 22.9 - - + -
169D THR* 3.8 7.0 - - + +
197D VAL 4.5 0.9 - - - +
200D VAL* 3.4 41.7 - - + +
201D GLN* 3.8 26.0 - - + +
204D ILE* 4.0 19.1 - - + -
205D ILE* 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LYS 3.0 12.6 + - - +
95D GLU* 3.6 12.6 - - + +
97D ILE* 1.3 78.6 - - - +
99D LEU* 1.3 68.3 + - + +
101D LEU* 3.1 5.2 + - - +
102D GLU* 3.1 39.6 + - + +
193D PHE* 4.5 9.0 - - - -
194D ASN* 2.4 32.5 + - - +
197D VAL* 3.2 43.5 - - + +
198D GLU* 5.7 3.2 - - - +
201D GLN* 3.9 16.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
79D PRO* 4.3 31.6 - - + -
95D GLU* 2.8 42.8 + - + +
96D TYR 3.7 3.6 - - - +
98D ARG* 1.3 79.5 - - + +
100D LYS* 1.3 60.6 + - - +
102D GLU* 3.3 32.7 + - - +
103D VAL* 3.2 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TRP* 3.2 46.3 + - + +
79D PRO* 5.7 1.8 - - + -
96D TYR* 2.9 37.7 + - + +
97D ILE* 3.6 6.1 - - - +
99D LEU* 1.3 76.9 - - - +
101D LEU* 1.3 58.6 + - - +
103D VAL* 3.3 8.6 + - + +
104D SER* 3.0 27.9 + - - -
165D ILE* 4.6 4.7 - - + -
166D TRP* 3.9 11.7 - - - -
169D THR* 3.5 25.7 + - + +
170D GLN* 2.6 32.1 + - - +
212D URA 2.7 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ILE* 3.2 20.0 + - + +
98D ARG 3.1 7.8 + - - +
100D LYS* 1.3 73.4 - - - +
102D GLU* 1.3 61.3 + - - +
104D SER* 3.1 5.2 + - - -
105D ARG 2.9 24.8 + - - -
169D THR* 3.8 31.4 - - + +
172D TYR* 4.0 13.5 - - + -
187D LEU* 3.9 7.8 - - + +
193D PHE* 3.7 19.8 - - + -
196D THR* 3.9 18.4 - - + -
197D VAL* 3.7 37.0 - - + +
200D VAL* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ARG* 3.1 35.2 + - - +
99D LEU* 3.3 35.1 - - - +
101D LEU* 1.3 76.1 - - - +
103D VAL* 1.3 57.2 + - + +
105D ARG* 3.1 27.8 + - - +
106D ASP* 2.8 39.1 + - - +
193D PHE* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ILE* 5.8 2.5 - - + -
75D ILE* 3.8 32.1 - - + +
76D TRP* 3.5 35.0 - - + +
79D PRO* 6.5 1.6 - - + -
99D LEU* 3.2 16.9 + - + +
100D LYS* 3.5 10.1 - - + +
101D LEU 3.2 0.2 - - - -
102D GLU* 1.3 75.7 - - + +
104D SER* 1.3 56.5 + - - +
107D TYR* 2.8 55.4 + - + +
111D SER* 6.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TRP* 5.8 1.8 + - - +
100D LYS* 3.0 12.2 + - - -
101D LEU* 3.2 12.3 - - - -
103D VAL* 1.3 79.6 - - - +
105D ARG* 1.3 60.6 + - - +
107D TYR 5.2 0.7 - - - -
108D PRO* 3.6 22.5 - - - +
111D SER* 5.1 4.2 + - - -
169D THR 2.6 33.0 + - - -
170D GLN* 3.7 10.0 - - - +
173D ALA* 3.7 17.8 - - - +
187D LEU* 3.7 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU 2.9 12.1 + - - +
102D GLU* 3.1 26.8 + - - +
104D SER* 1.3 78.4 - - - +
106D ASP* 1.3 92.5 + - - +
108D PRO* 3.7 10.8 - - - +
187D LEU* 3.4 43.5 + - + +
188D ARG* 4.9 23.1 + - + +
193D PHE* 3.6 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D GLU* 2.8 22.7 + - - +
105D ARG* 1.3 113.4 + - - +
107D TYR* 1.3 82.0 + - + +
108D PRO* 3.2 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 6.0 4.5 - - + -
72D ILE* 6.2 0.4 - - + -
75D ILE* 4.6 32.6 - - + +
103D VAL* 2.8 44.1 + - + +
106D ASP* 1.3 94.4 - - + +
108D PRO* 1.3 63.6 - - - +
109D GLN 3.4 2.2 - - - -
110D ALA* 3.2 16.4 + - + +
111D SER* 3.2 19.6 + - - -
----------------------------------------------------------
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