Contacts of the helix formed by residues 97 - 113 (chain A) in PDB entry 1G3I
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 ASP 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A GLU* 3.3 18.5 + - - +
96A VAL* 1.3 81.7 - - - +
98A SER* 1.3 64.9 + - - +
99A ILE 3.0 0.9 + - - -
100A ILE* 3.1 6.7 + - - +
101A ARG* 3.1 42.3 + - - +
284A PRO* 6.0 0.3 - - - +
285A LEU* 3.9 13.5 - - - +
291A VAL* 3.3 32.2 - - + +
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS* 4.3 11.3 + - - -
86A PHE* 3.8 11.6 - - - -
95A GLU* 2.5 31.7 + - - +
96A VAL 2.9 0.4 - - - -
97A ASP* 1.3 80.6 - - - +
99A ILE* 1.3 66.1 + - - +
101A ARG* 3.5 16.4 - - - +
102A ASP* 2.7 38.8 + - - -
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 4.4 4.9 - - + +
81A VAL* 3.8 33.9 - - + -
85A LYS* 6.3 0.2 - - - +
86A PHE* 3.7 30.1 - - + -
96A VAL 3.0 14.9 + - - +
98A SER* 1.3 79.4 + - - +
100A ILE* 1.3 69.7 + - + +
102A ASP* 3.5 6.2 + - - +
103A LEU* 3.0 18.9 + - - +
254A VAL* 3.8 35.2 - - + -
256A ILE* 5.1 4.3 - - + -
282A LEU* 3.9 25.1 - - + -
285A LEU* 4.0 8.7 - - + -
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP 3.1 3.2 + - - +
99A ILE* 1.3 79.7 - - + +
101A ARG* 1.3 66.6 + - - +
103A LEU* 3.0 11.3 + - + +
104A THR* 2.9 26.2 + - - +
248A VAL* 4.8 8.1 - - + -
254A VAL* 4.9 1.1 - - + -
285A LEU* 3.8 23.3 - - + -
291A VAL* 3.3 19.1 - - + -
298A VAL* 3.1 34.1 - - + -
299A LYS 5.8 0.2 - - - -
300A THR* 3.4 33.7 - - + -
303A ILE* 4.6 14.1 - - + -
305A PHE* 4.7 6.5 - - + -
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU* 4.0 24.0 + - - +
97A ASP* 3.1 37.9 + - - +
98A SER* 3.0 17.9 + - - +
100A ILE* 1.3 75.7 - - - +
102A ASP* 1.3 68.4 + - - +
104A THR* 2.9 16.5 + - - -
105A ASP* 3.0 15.1 + - - +
291A VAL* 4.4 2.0 - - - +
292A SER* 3.1 28.1 + - - +
293A THR* 3.7 24.7 - - + +
294A LYS* 5.0 4.3 - - + +
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 4.6 21.1 - - + +
81A VAL* 5.8 2.9 - - - +
85A LYS* 4.4 14.9 + - - -
98A SER* 2.7 31.7 + - - +
99A ILE* 3.8 4.4 - - - +
101A ARG* 1.3 76.0 - - - +
103A LEU* 1.3 62.7 + - - +
105A ASP* 3.2 13.7 + - - +
106A SER* 3.0 21.5 + - - -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 3.5 34.8 - - + +
78A PHE 4.0 2.7 - - - +
79A ILE* 3.3 26.6 - - + +
99A ILE 3.0 15.4 + - - +
100A ILE* 3.2 15.0 - - + +
101A ARG 3.0 0.2 - - - -
102A ASP* 1.3 76.2 - - - +
104A THR* 1.3 65.8 + - - +
106A SER* 2.9 17.0 + - - -
107A ALA* 3.0 11.8 + - - +
248A VAL* 3.6 28.3 - - + -
252A GLY* 4.3 4.9 - - - -
253A ILE 4.0 3.1 - - - +
254A VAL* 3.9 16.8 - - + -
303A ILE* 3.9 17.0 - - + -
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Residues in contact with THR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ILE* 2.9 13.8 + - - +
101A ARG 3.2 7.6 - - - -
103A LEU* 1.3 77.5 - - - +
105A ASP* 1.3 60.4 + - - +
107A ALA* 3.2 16.2 + - + +
108A MET* 3.4 9.2 + - - +
244A ALA* 4.6 2.0 - - + +
245A ILE* 5.1 6.1 - - + +
248A VAL* 3.3 15.8 - - + +
293A THR* 3.0 33.9 - - + +
295A HIS* 3.7 24.5 - - + -
298A VAL* 3.4 21.7 - - + +
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ARG* 3.0 12.6 + - - +
102A ASP* 3.3 18.1 - - - +
103A LEU 3.1 0.2 - - - -
104A THR* 1.3 75.5 - - - +
106A SER* 1.3 63.7 + - - +
108A MET* 3.1 19.6 + - - +
109A LYS* 3.6 4.3 + - - +
294A LYS* 3.2 24.8 + - - +
295A HIS* 3.1 26.0 + - - -
292B SER* 4.9 5.0 - - - -
297B MET* 3.9 28.8 - - + +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 4.5 3.2 - - - +
78A PHE 4.0 27.0 + - - -
79A ILE* 5.9 1.1 - - - -
102A ASP 3.0 11.3 + - - -
103A LEU* 2.9 10.8 + - - -
105A ASP* 1.3 70.5 - - - +
107A ALA* 1.3 63.4 + - - +
108A MET 3.0 5.7 + - - -
109A LYS* 3.3 15.2 + - - +
110A LEU* 3.0 23.0 + - - +
297B MET* 6.2 1.1 - - - -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 3.9 17.4 - - + +
103A LEU 3.0 5.8 + - - +
104A THR 3.2 13.2 + - - +
106A SER* 1.3 76.4 - - - +
108A MET* 1.3 63.7 + - - +
110A LEU* 3.7 7.1 - - - +
111A VAL* 3.0 28.3 + - - +
244A ALA* 3.6 19.2 - - + +
247A ALA* 4.2 1.6 - - + -
248A VAL* 3.5 26.7 - - + -
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Residues in contact with MET 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A THR 3.4 3.1 + - - +
105A ASP 3.1 11.5 + - - +
106A SER 3.0 0.8 - - - -
107A ALA* 1.3 73.8 - - - +
109A LYS* 1.3 52.0 + - - +
110A LEU 2.6 15.9 + - - -
111A VAL* 2.7 3.0 + - - -
112A ARG* 2.6 34.2 + - + +
240A LEU* 3.9 34.3 - - + -
241A LYS* 4.1 18.4 - - + -
244A ALA* 3.7 20.4 - - - -
295A HIS* 3.3 50.5 - - + +
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASP 3.6 4.7 + - - +
106A SER* 3.3 15.0 + - - +
108A MET* 1.3 77.1 - - - +
110A LEU* 1.3 62.6 + - - +
112A ARG* 4.0 9.2 - - - -
113A GLN* 3.2 26.3 + - + +
290B THR* 4.1 14.9 + - - +
297B MET* 5.5 16.6 - - + -
299B LYS* 3.3 37.6 - - + +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASN* 3.7 35.9 - - - +
76A ALA 3.9 8.5 - - - +
77A PRO* 3.8 38.6 - - + -
106A SER* 3.0 17.2 + - - +
107A ALA 3.7 4.9 - - - +
108A MET 2.6 4.9 + - - -
109A LYS* 1.3 78.1 - - - +
111A VAL* 1.3 62.7 + - + +
113A GLN 3.5 2.1 - - - +
114A GLN* 2.9 33.8 + - + +
247A ALA* 5.9 0.9 - - + -
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA 3.0 17.6 + - - +
108A MET* 2.7 6.9 + - - +
110A LEU* 1.3 72.7 - - + +
112A ARG* 1.3 69.1 + - - +
114A GLN* 3.0 24.3 + - + +
115A GLU* 3.1 14.4 + - + +
240A LEU* 3.4 28.9 - - + +
243A LYS* 4.4 24.2 - - + +
244A ALA* 4.0 20.4 - - + +
247A ALA* 4.4 12.1 - - + -
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Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A MET* 2.6 29.5 + - + +
109A LYS* 4.1 5.6 - - - -
111A VAL* 1.3 71.1 - - - +
113A GLN* 1.3 58.7 + - + +
114A GLN 2.3 19.2 + - - -
115A GLU* 2.7 17.7 + - - +
116A ILE* 3.6 27.6 + - + +
235A ILE* 5.2 18.4 - - - +
237A PRO* 6.3 0.6 - - - +
240A LEU* 3.9 35.9 - - + +
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LYS* 3.2 21.9 + - + +
110A LEU 3.5 2.9 - - - +
112A ARG* 1.3 78.3 - - + +
114A GLN* 1.3 61.7 + - - +
115A GLU 3.8 0.2 - - - -
116A ILE* 3.3 32.7 - - - +
117A ALA* 4.4 17.4 - - + +
242B GLN* 6.0 2.0 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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