Contacts of the helix formed by residues 89 - 107 (chain C) in PDB entry 1GG3
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 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A ARG* 2.9 26.7 + - - -
38C GLU* 3.2 34.0 + - - +
39C GLU* 2.9 8.3 + - + +
87C LEU* 3.2 1.5 + - - +
88C THR* 1.3 94.1 - - + +
90C ASP* 1.3 64.0 + - - +
91C ILE* 2.9 33.2 - - + +
92C THR* 3.4 19.8 + - - +
93C ARG* 3.1 24.1 + - - +
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Residues in contact with ASP 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 4.4 17.8 - - - +
89C GLU* 1.3 73.3 - - - +
91C ILE* 1.3 56.2 + - + +
92C THR 2.9 1.8 - - - -
93C ARG* 2.5 36.3 + - - +
94C TYR* 2.7 34.9 + - - +
171C ALA* 3.0 32.4 - - + +
174C ASP* 4.8 1.2 - - - +
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Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 4.1 31.1 + - + +
262A ARG* 4.2 15.3 - - - +
35C ASN 4.4 9.2 - - - +
36C LEU* 4.3 9.4 - - + +
37C LEU* 4.5 5.8 - - + -
89C GLU* 2.9 49.6 - - + +
90C ASP* 1.3 73.7 - - - +
92C THR* 1.3 69.8 + - - +
94C TYR* 3.0 6.6 + - + +
95C TYR* 2.9 50.4 + - + +
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Residues in contact with THR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.0 13.5 - - + +
39C GLU* 2.4 51.2 + - + +
42C PHE* 5.0 4.7 - - + -
44C LEU* 4.9 14.2 - - + +
87C LEU* 3.3 24.2 - - + -
89C GLU* 3.4 14.8 + - - +
91C ILE* 1.3 84.3 - - - +
93C ARG* 1.3 56.6 + - - +
95C TYR* 3.3 2.9 + - - +
96C LEU* 2.9 27.1 + - + +
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Residues in contact with ARG 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C PRO 3.3 13.0 + - - +
85C ALA* 3.1 16.1 + - - -
87C LEU* 2.6 41.4 + - + -
88C THR 4.8 0.6 - - - -
89C GLU* 3.1 14.9 + - - +
90C ASP* 2.5 41.4 + - - +
92C THR* 1.3 72.6 - - - +
94C TYR* 1.3 67.1 + - - +
96C LEU* 3.5 8.9 - - - +
97C CYS* 2.8 30.1 + - - -
171C ALA 5.5 2.4 + - - -
174C ASP* 4.2 8.7 - - + -
175C LEU* 4.0 25.6 - - - +
178C LEU* 3.5 24.2 - - + -
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Residues in contact with TYR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 4.9 8.0 + - - +
67A ARG* 3.5 47.5 - - + +
68A GLY* 4.2 17.3 - - - -
9C ASP* 5.2 4.7 + - - +
90C ASP 2.7 17.0 + - - +
91C ILE* 3.4 12.8 - - + +
93C ARG* 1.3 73.8 - - - +
95C TYR* 1.3 85.4 - + - +
97C CYS* 3.2 4.0 + - + +
98C LEU* 2.9 50.1 + - + +
126C SER* 6.0 4.3 - - - -
127C GLU* 4.5 16.0 + - - -
170C PRO* 6.5 0.2 - - + -
174C ASP* 3.3 22.9 + - - +
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 2.8 43.3 + - - -
8C LEU* 3.7 21.7 - - + +
9C ASP* 6.0 1.6 - - - -
35C ASN* 3.1 31.6 + - + +
37C LEU* 3.4 37.9 - - + -
44C LEU* 4.5 11.7 - - + -
75C PHE* 5.0 0.9 - + - -
77C VAL* 5.0 2.0 - - - -
91C ILE* 2.9 32.3 + - + +
92C THR 3.8 3.6 - - - +
94C TYR* 1.3 94.1 - + - +
96C LEU* 1.3 64.4 + - - +
97C CYS 3.1 1.6 - - - -
98C LEU* 3.1 16.6 + - + +
99C GLN* 3.0 23.9 + - - +
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 5.7 0.2 - - - +
77C VAL* 4.4 17.2 - - + +
80C TYR* 4.2 18.2 - - + -
81C PRO* 3.5 26.0 - - + -
84C PRO* 3.5 32.1 - - + -
87C LEU* 3.9 9.4 - - + -
92C THR* 2.9 17.5 + - + +
93C ARG* 3.5 8.3 - - - +
95C TYR* 1.3 76.7 - - - +
97C CYS* 1.3 57.1 + - - +
99C GLN* 3.5 1.2 + - - +
100C LEU* 3.1 44.2 + - + +
178C LEU* 4.1 7.6 - - + -
187C TYR* 4.2 4.3 - - - +
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Residues in contact with CYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ARG 2.8 24.2 + - - +
94C TYR* 3.5 6.1 - - + +
96C LEU* 1.3 75.3 - - - +
98C LEU* 1.3 61.1 + - - +
99C GLN 3.1 1.6 - - - -
100C LEU* 3.9 3.7 - - - +
101C ARG* 2.8 43.3 + - - +
174C ASP* 3.8 31.0 - - - +
177C PHE* 4.1 15.9 - - + -
178C LEU* 3.4 31.4 - - - -
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.5 44.9 - - + +
9C ASP* 3.7 17.9 - - + +
94C TYR* 2.9 48.3 + - + +
95C TYR* 3.5 17.7 - - + +
97C CYS* 1.3 77.8 - - - +
99C GLN* 1.3 56.0 + - - +
101C ARG* 3.7 34.0 - - - +
102C GLN* 3.1 24.1 + - - +
127C GLU* 4.6 2.2 - - - +
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Residues in contact with GLN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.4 10.2 - - + +
76C ASN* 3.0 32.5 + - - +
77C VAL* 2.6 48.0 + - + -
80C TYR* 3.5 23.5 + - + +
95C TYR 3.0 16.2 + - - +
96C LEU 3.6 4.9 - - - +
97C CYS 3.1 0.2 - - - -
98C LEU* 1.3 73.2 - - - +
100C LEU* 1.3 54.6 + - - +
101C ARG 3.1 1.3 - - - -
102C GLN* 2.7 16.5 + - - +
103C ASP* 2.6 54.8 + - - +
108C ARG* 3.9 7.1 - - - +
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C TYR* 3.8 17.0 - - + -
96C LEU* 3.1 37.0 + - + +
97C CYS 3.9 2.9 - - - +
99C GLN* 1.3 77.7 - - - +
101C ARG* 1.3 58.1 + - - +
103C ASP* 3.0 10.6 + - - +
104C ILE* 2.8 35.8 + - - +
109C LEU* 4.1 18.8 - - + -
177C PHE* 4.1 17.7 - - + -
178C LEU* 3.6 21.8 - - + -
181C ALA* 4.3 5.6 - - + -
187C TYR* 3.5 35.0 - - + -
188C GLY 5.0 1.6 - - - +
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C TYR* 6.0 0.2 - - - -
97C CYS* 2.8 33.8 + - - +
98C LEU* 3.7 24.0 - - - +
100C LEU* 1.3 77.8 - - - +
102C GLN* 1.3 61.0 + - - +
104C ILE* 3.5 8.5 + - - +
105C VAL* 3.2 32.6 + - + +
123C THR* 3.4 33.4 + - - +
126C SER* 5.5 1.2 + - - -
127C GLU* 3.1 40.6 + - - +
144C PHE* 4.4 12.9 - - - +
145C LYS 5.0 12.1 + - - +
146C LEU* 5.4 0.2 - - - +
177C PHE* 4.0 18.2 - - + -
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Residues in contact with GLN 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU 5.0 0.7 - - - +
8C LEU* 3.1 36.8 - - + +
10C ASP* 4.1 18.9 + - - +
76C ASN* 5.5 2.5 - - - +
98C LEU 3.1 9.2 + - - +
99C GLN* 2.7 28.6 + - - +
101C ARG* 1.3 79.5 - - - +
103C ASP* 1.3 62.3 + - - +
105C VAL* 3.9 7.4 + - - +
106C ALA* 3.6 17.7 + - - +
108C ARG* 4.1 9.2 + - - +
145C LYS* 5.5 6.3 - - - +
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Residues in contact with ASP 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C TYR* 2.6 42.1 + - - -
99C GLN* 2.6 20.9 + - - +
100C LEU* 3.4 18.0 - - - +
102C GLN* 1.3 73.1 - - - +
104C ILE* 1.3 64.0 + - - +
106C ALA* 3.1 19.1 + - - +
108C ARG* 2.7 59.8 + - + +
109C LEU* 3.9 15.4 - - + +
188C GLY 5.4 1.2 + - - -
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C LEU 2.8 20.4 + - - +
101C ARG* 3.7 7.6 - - - +
103C ASP* 1.3 73.9 - - - +
105C VAL* 1.3 65.9 + - + +
106C ALA 3.0 1.4 + - - -
107C GLY* 3.5 8.1 + - - -
109C LEU* 3.3 49.3 - - + +
111C CYS* 5.3 5.4 - - - -
116C LEU* 3.8 17.9 - - + -
119C LEU* 3.9 26.7 - - + -
146C LEU 3.7 25.4 - - - +
147C ALA* 4.4 0.7 - - - -
148C PRO* 3.7 11.3 - - - +
177C PHE* 4.3 14.8 - - + -
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.2 19.2 + - + +
102C GLN* 4.4 8.7 - - - +
104C ILE* 1.3 77.2 - - + +
106C ALA* 1.3 62.6 + - - +
145C LYS* 3.3 57.4 - - + +
146C LEU 4.4 2.2 - - - -
147C ALA 4.2 12.8 - - - +
148C PRO* 3.6 19.7 - - + +
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLN 3.6 6.7 + - - +
103C ASP 3.1 11.6 + - - +
104C ILE 3.0 1.0 + - - -
105C VAL* 1.3 81.9 - - - +
107C GLY* 1.3 59.9 + - - +
108C ARG* 3.4 33.2 - - - +
148C PRO* 4.4 6.5 - - - +
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Residues in contact with GLY 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ASP 3.3 1.6 + - - -
104C ILE 3.5 6.2 + - - -
106C ALA* 1.3 75.7 - - - +
108C ARG* 1.3 68.1 + - - +
109C LEU 3.1 10.8 + - - -
110C PRO* 4.1 10.7 - - - +
148C PRO* 5.2 5.4 - - - -
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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) + - + + + + + -
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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