Contacts of the helix formed by residues 95 - 119 (chain C) in PDB entry 5DIR
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 GLU 95 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 4.2 10.8 - - + +
92C LYS* 3.4 48.0 + - + +
93C LYS 3.3 3.0 - - - -
94C GLY* 1.3 75.6 - - - +
96C THR* 1.3 62.8 + - - +
97C TRP 3.5 2.8 + - - -
98C LEU* 3.5 24.7 + - + +
99C ALA* 3.3 21.1 + - - +
156C ASP* 5.8 0.2 - - - +
159C ARG* 3.2 32.7 + - - +
90D ARG* 3.5 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TRP* 5.6 12.5 + - + +
94C GLY* 3.3 20.2 + - - +
95C GLU* 1.3 72.7 - - - +
97C TRP* 1.3 67.1 + - - +
99C ALA* 3.3 6.7 + - - +
100C ILE* 3.1 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C GLU* 3.5 0.8 - - + -
96C THR* 1.3 83.5 + - - +
98C LEU* 1.3 66.2 + - - +
100C ILE* 3.4 7.2 + - + +
101C ALA* 3.4 15.8 + - - +
152C MET* 3.0 72.2 + - + +
155C LEU* 4.5 24.1 + - + -
156C ASP* 4.1 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C TRP* 3.9 35.2 - - + +
91C LEU* 3.9 21.3 - - + -
95C GLU* 3.5 34.3 + - + +
96C THR 3.4 0.2 - - - -
97C TRP* 1.3 82.6 - - + +
99C ALA* 1.3 62.8 + - - +
101C ALA* 3.3 4.2 + - + +
102C LEU* 3.2 37.6 + - + +
153C LEU* 4.5 11.2 - - + -
156C ASP* 4.0 32.7 + - + +
90D ARG* 4.5 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TRP* 4.6 21.8 - - + +
88C LEU* 4.0 11.5 - - + +
91C LEU* 3.6 21.0 - - + +
95C GLU 3.3 12.6 + - - +
96C THR* 3.6 12.1 - - - +
97C TRP 3.3 0.2 - - - -
98C LEU* 1.3 78.7 - - - +
100C ILE* 1.3 61.8 + - - +
102C LEU* 3.3 4.3 + - - +
103C ALA* 3.1 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TRP* 5.3 7.4 - - + +
15C ILE* 4.0 30.2 - - + +
96C THR* 3.1 25.2 + - - +
97C TRP* 3.7 11.0 - - + +
98C LEU 3.3 0.2 - - - -
99C ALA* 1.3 77.3 - - + +
101C ALA* 1.3 63.6 + - - +
103C ALA* 3.4 3.0 + - - +
104C LEU* 3.1 37.5 + - + +
152C MET* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C TRP 3.4 6.3 + - - +
98C LEU* 3.3 10.9 + - - +
99C ALA 3.3 0.4 - - - -
100C ILE* 1.3 80.3 - - - +
102C LEU* 1.3 61.6 - - - +
104C LEU* 3.5 0.6 + - - -
105C VAL* 3.1 28.9 + - - +
149C GLY* 3.5 10.3 - - - +
152C MET* 3.5 34.7 - - + +
153C LEU* 3.5 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 3.9 17.4 - - + +
87C TRP* 3.7 55.9 - - + -
88C LEU* 3.9 34.8 - - + +
91C LEU* 4.3 9.4 - - + -
98C LEU* 3.2 20.5 + - + +
99C ALA 3.8 5.8 - - - +
100C ILE 3.3 0.2 - - - -
101C ALA* 1.3 74.8 - - - +
103C ALA* 1.3 56.2 + - - +
105C VAL* 3.1 6.2 + - - +
106C LEU* 2.8 39.0 + - + +
153C LEU* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TRP 5.5 1.8 - - - +
13C LEU* 5.3 6.7 - - - -
15C ILE* 3.9 25.4 - - + -
16C THR* 2.8 33.6 + - - +
88C LEU* 4.7 8.8 - - + +
99C ALA 3.1 16.5 + - - +
100C ILE* 3.4 5.6 + - - +
102C LEU* 1.3 76.6 - - - +
104C LEU* 1.3 57.0 + - - +
106C LEU* 4.4 3.1 - - - -
107C GLY* 2.8 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 3.9 13.5 - - + -
19C VAL* 3.6 26.0 - - + -
100C ILE* 3.1 27.8 + - + +
101C ALA 3.7 4.7 - - - +
103C ALA* 1.3 77.0 - - - +
105C VAL* 1.3 58.0 + - - +
107C GLY* 3.3 1.0 + - - -
108C GLY 2.8 24.4 + - - -
145C ALA* 3.3 27.2 - - + +
148C VAL* 4.0 28.3 - - + -
149C GLY* 4.3 3.4 - - - +
152C MET* 4.1 13.9 - - - -
204C OLC 6.3 4.7 - - + -
301F OLC 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C VAL* 5.6 0.2 - - + -
84C LEU* 3.7 22.4 - - + -
101C ALA 3.1 17.9 + - - +
102C LEU* 3.1 6.1 + - - +
104C LEU* 1.3 72.5 - - - +
106C LEU* 1.3 60.4 + - - +
108C GLY* 3.4 0.5 + - - -
109C ALA* 2.8 27.9 + - - +
146C ILE* 3.9 21.1 - - + +
149C GLY* 3.7 25.6 - - - +
150C ALA* 3.8 6.5 - - + +
153C LEU* 4.6 6.3 - - + -
201F MLE 4.2 20.4 - - + -
302F OLC 5.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 6.2 1.1 - - + -
16C THR* 3.6 19.1 - - + +
81C SER* 4.5 10.3 - - - +
84C LEU* 4.1 16.6 - - + +
85C VAL* 3.7 32.5 - - + +
88C LEU* 4.5 17.9 - - + -
102C LEU* 2.8 17.1 + - + +
103C ALA* 3.8 3.8 - - - +
105C VAL* 1.3 76.6 - - - +
107C GLY* 1.3 57.5 + - - +
109C ALA* 3.2 4.9 + - - +
110C LEU* 2.9 55.2 + - + +
202C OLC 5.9 0.4 - - + -
203C OLC 4.4 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C THR* 3.7 26.2 - - - +
19C VAL* 3.7 14.6 - - - +
20C PHE* 4.2 7.0 - - - -
23C ASP* 5.6 0.3 - - - +
103C ALA 2.8 17.4 + - - -
104C LEU 3.7 1.3 - - - -
106C LEU* 1.3 78.2 - - - +
108C GLY* 1.3 60.2 + - - +
110C LEU* 3.5 3.1 + - - +
111C GLY* 3.1 20.1 + - - -
142C ALA* 5.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C VAL* 3.8 2.1 - - - +
104C LEU 2.8 13.3 + - - -
107C GLY* 1.3 72.6 - - - +
109C ALA* 1.3 65.1 + - - +
111C GLY 3.4 0.2 + - - -
112C ASN* 3.4 11.8 + - - -
142C ALA* 3.3 48.5 - - - +
145C ALA* 4.4 1.1 - - - -
146C ILE* 3.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ALA* 4.3 5.9 - - + +
81C SER* 3.6 18.6 - - - +
84C LEU* 5.3 3.1 - - + -
105C VAL* 2.8 19.3 + - + +
106C LEU* 3.4 8.1 - - - +
108C GLY* 1.3 77.2 - - - +
110C LEU* 1.3 57.8 + - - +
112C ASN* 3.6 2.1 + - - +
113C LEU* 3.1 28.0 + - - +
146C ILE* 3.8 7.3 - - - +
201F MLE 3.9 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C THR* 4.4 3.1 - - + -
20C PHE* 3.5 10.7 - - + -
81C SER* 3.8 19.3 - - - +
106C LEU* 2.9 39.1 + - + +
107C GLY* 4.1 2.0 - - - +
109C ALA* 1.3 74.8 - - - +
111C GLY* 1.3 60.5 + - - +
113C LEU* 3.5 14.7 - - + +
114C TYR* 2.9 31.5 + - - +
202C OLC 3.6 60.5 - - + +
203C OLC 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 3.7 10.0 - - - -
23C ASP* 3.4 23.3 - - - -
24C GLN* 3.0 26.4 + - - -
107C GLY 3.1 13.9 + - - -
108C GLY 3.4 3.3 + - - -
109C ALA 3.3 0.4 - - - -
110C LEU* 1.3 78.0 - - - +
112C ASN* 1.3 60.0 + - - +
115C ASP* 3.3 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LYS* 3.1 21.1 + - - -
108C GLY 3.4 9.4 + - - +
109C ALA 4.3 1.1 - - - +
111C GLY* 1.3 73.3 - - - +
113C LEU* 1.3 61.8 + - - +
115C ASP* 3.2 7.7 + - - +
116C ARG* 3.0 42.5 + - - +
122C VAL* 3.5 12.4 - - + +
140C ASN* 3.3 8.0 + - - -
142C ALA* 3.3 16.3 - - - +
143C ASP* 3.0 26.7 + - - -
146C ILE* 4.2 1.8 - - - +
201F MLE 3.1 27.0 + - - +
202F IIL 3.8 1.2 - - - -
203F SER 3.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA* 3.5 40.6 - - + +
77C ALA* 4.0 12.8 - - + +
78C ILE* 4.0 12.6 - - + +
109C ALA 3.1 18.9 + - - +
110C LEU* 3.5 22.9 - - + +
111C GLY 3.3 0.2 - - - -
112C ASN* 1.3 76.7 - - - +
114C TYR* 1.3 62.9 + - - +
116C ARG* 3.1 8.9 + - - +
117C MET* 3.0 36.8 + - + +
202C OLC 4.2 12.6 - - + -
203C OLC 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 3.9 16.2 - + + -
24C GLN* 3.3 35.4 - - + +
110C LEU 2.9 17.7 + - - +
111C GLY 3.5 4.3 - - - +
113C LEU* 1.3 76.1 - - - +
115C ASP* 1.3 66.8 + - - +
117C MET* 4.1 0.2 - - - +
118C VAL* 3.0 60.5 + - + +
119C LEU* 5.6 3.4 - - + -
202C OLC 3.6 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.6 20.1 + - - +
27C LYS* 2.5 37.3 + - - +
111C GLY 3.3 7.1 + - - -
112C ASN* 3.2 9.8 + - - +
113C LEU 3.1 0.8 - - - -
114C TYR* 1.3 83.9 - - - +
116C ARG* 1.3 58.3 + - - +
119C LEU* 2.8 52.5 + - + +
120C GLY 3.1 5.0 + - - -
121C HIS 3.2 15.9 - - - +
122C VAL* 3.9 6.9 - - - +
123C VAL 3.6 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASN 5.2 2.2 + - - -
55C THR 6.3 1.0 - - - -
56C GLY* 5.9 0.8 - - - +
69C GLN 4.3 1.2 + - - -
70C ARG* 2.9 60.4 + - + +
73C PHE* 3.5 36.2 + - - +
74C ALA* 3.9 12.8 - - + +
77C ALA* 5.8 1.2 - - - +
112C ASN* 3.0 23.2 + - - +
113C LEU* 3.1 8.5 + - - +
115C ASP* 1.3 77.1 - - - +
117C MET* 1.3 58.7 + - - +
120C GLY* 3.3 3.8 - - - -
121C HIS* 4.0 12.6 - - - +
122C VAL* 3.6 20.9 - - + +
201F MLE 3.5 20.8 + - - -
202F IIL 3.0 12.5 + - - -
203F SER 2.8 28.9 + - - -
204F ALO 4.1 0.2 - - - -
205F 5BV 3.6 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 2.9 13.0 + - - +
71C TRP* 3.9 18.6 - - + -
74C ALA* 3.8 24.5 - - + -
78C ILE* 5.1 9.4 - - + -
113C LEU* 3.0 26.0 + - + +
114C TYR 4.1 0.7 - - - +
115C ASP 3.2 0.2 - - - -
116C ARG* 1.3 78.2 - - - +
118C VAL* 1.3 58.9 + - - +
202C OLC 3.7 29.4 - - + -
203C OLC 2.8 82.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 4.7 1.4 + - - -
114C TYR* 3.0 56.4 + - + +
117C MET* 1.3 79.8 - - - +
119C LEU* 1.3 75.0 + - + +
202C OLC 3.7 53.2 + - + +
203C OLC 4.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LYS* 6.3 0.4 - - + -
31C GLN* 5.5 6.1 - - + +
70C ARG* 4.9 1.1 - - - -
114C TYR* 5.6 3.6 - - + -
115C ASP* 2.8 42.6 + - - +
118C VAL* 1.3 88.9 - - + +
120C GLY* 1.3 54.2 + - - +
121C HIS* 3.3 39.2 + - + +
123C VAL* 3.7 25.8 - - + -
----------------------------------------------------------
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