Contacts of the helix formed by residues 91 - 113 (chain A) in PDB entry 2GC5
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 PRO 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ASN* 4.4 0.2 - - - +
89A PRO 3.5 8.5 - - - +
90A ILE* 1.3 88.1 - - + +
92A ASP* 1.3 66.1 + - - +
93A ALA* 3.2 4.5 - - + +
94A ALA* 3.2 16.2 + - + +
95A LEU* 2.9 20.6 + - - +
131A TYR* 3.7 14.4 - - - +
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Residues in contact with ASP 92 (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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3A TYR* 3.5 29.4 - - + -
78A ARG* 2.7 47.1 + - - -
80A ASN* 2.7 20.7 + - - +
91A PRO* 1.3 71.3 - - - +
93A ALA* 1.3 58.0 + - - +
95A LEU* 3.3 5.0 + - - +
96A VAL* 3.0 32.2 + - - +
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Residues in contact with ALA 93 (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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91A PRO* 3.2 4.5 - - + +
92A ASP* 1.3 75.1 - - - +
94A ALA* 1.3 61.2 + - - +
96A VAL* 3.4 10.4 + - - +
97A ASN* 3.0 36.5 + - - +
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Residues in contact with ALA 94 (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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90A ILE* 3.8 15.9 - - + +
91A PRO* 3.2 26.1 + - + +
93A ALA* 1.3 77.8 - - - +
95A LEU* 1.3 56.4 + - - +
97A ASN* 3.4 7.2 + - - +
98A ALA* 2.8 30.8 + - - +
131A TYR* 4.3 12.8 - - + +
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Residues in contact with LEU 95 (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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3A TYR* 3.9 24.5 - - + -
6A THR* 4.4 3.6 - - + -
7A VAL* 4.3 8.3 - - + -
10A ILE* 4.4 2.7 - - + -
79A PHE* 3.8 37.0 - - + -
80A ASN* 4.3 8.3 - - - +
83A ILE* 5.2 0.9 - - + -
90A ILE* 3.7 27.5 - - + +
91A PRO 2.9 12.7 + - - +
92A ASP* 3.3 9.8 + - - +
94A ALA* 1.3 72.8 - - - +
96A VAL* 1.3 60.0 + - - +
98A ALA* 3.2 0.8 + - - -
99A VAL* 2.8 52.5 + - + +
127A LEU* 4.3 15.9 - - + -
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Residues in contact with VAL 96 (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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1A MET* 3.4 22.2 - - - +
2A ASN* 3.8 2.7 - - - +
3A TYR* 3.6 36.1 - - + +
6A THR* 4.0 12.5 + - - +
92A ASP 3.0 21.3 + - - +
93A ALA* 3.5 11.0 - - - +
95A LEU* 1.3 76.4 - - - +
97A ASN* 1.3 66.1 + - - +
99A VAL* 3.5 2.4 + - - +
100A ALA* 3.0 29.0 + - + +
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Residues in contact with ASN 97 (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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93A ALA* 3.0 24.1 + - - +
94A ALA* 3.9 6.5 - - - +
96A VAL* 1.3 84.8 - - - +
98A ALA* 1.3 57.1 + - - +
100A ALA* 3.4 8.0 + - - +
101A PHE* 3.1 28.6 + - - +
130A TRP* 5.3 1.5 - - - -
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Residues in contact with ALA 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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90A ILE* 4.6 4.5 - - + -
94A ALA 2.8 19.7 + - - +
95A LEU* 3.7 4.9 - - - +
97A ASN* 1.3 75.0 - - - +
99A VAL* 1.3 65.4 + - - +
101A PHE* 3.2 2.6 + - - +
102A VAL* 3.0 28.4 + - - +
127A LEU* 3.8 26.5 - - + -
130A TRP* 3.9 26.5 - - + -
131A TYR* 5.1 4.0 - - + -
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Residues in contact with VAL 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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1A MET* 3.6 28.7 - - + -
6A THR* 3.1 31.6 - - + -
9A TYR* 3.6 20.6 - - + -
10A ILE* 3.7 23.8 - - + -
95A LEU* 2.8 16.1 + - + +
96A VAL 3.8 1.6 - - - +
98A ALA* 1.3 75.5 - - - +
100A ALA* 1.3 58.8 + - - +
103A ARG* 2.8 28.6 + - - +
123A PHE* 4.0 4.6 - - + -
127A LEU* 3.7 16.8 - - + -
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Residues in contact with ALA 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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1A MET* 5.6 3.1 - - + -
96A VAL* 3.0 19.6 + - + +
97A ASN* 3.5 10.3 - - - +
98A ALA 3.2 0.2 - - - -
99A VAL* 1.3 78.9 - - - +
101A PHE* 1.3 56.0 + - - +
103A ARG* 3.5 8.7 - - - +
104A ALA* 3.0 28.6 + - - +
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Residues in contact with PHE 101 (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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31A ALA 5.6 2.0 - - - -
32A LEU* 3.7 23.3 - - + -
97A ASN 3.1 16.4 + - - +
98A ALA 3.2 4.2 + - - +
100A ALA* 1.3 74.1 - - - +
102A VAL* 1.3 64.0 + - + +
104A ALA* 3.4 7.8 + - + +
105A ALA* 3.2 20.3 + - + +
108A ARG* 5.1 8.6 + - - -
130A TRP* 3.2 53.6 - + + -
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Residues in contact with VAL 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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28A LEU* 3.9 24.6 - - + +
32A LEU* 4.1 23.1 - - + -
98A ALA 3.0 16.8 + - - +
101A PHE* 1.3 76.2 - - + +
103A ARG* 1.3 61.1 + - - +
105A ALA* 3.4 2.9 + - - +
106A LEU* 2.9 26.9 + - - +
123A PHE* 3.4 36.6 - - + +
127A LEU* 4.0 28.5 - - + +
130A TRP* 4.9 6.5 - - + -
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Residues in contact with ARG 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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1A MET* 4.0 35.0 - - - +
9A TYR* 3.4 45.5 - - + +
99A VAL 2.8 19.7 + - - +
100A ALA* 3.5 7.4 - - - +
102A VAL* 1.3 76.2 - - - +
104A ALA* 1.3 57.9 + - - +
106A LEU* 3.0 6.1 + - - +
107A GLU* 2.8 57.5 + - + +
123A PHE* 4.0 2.5 - - - -
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Residues in contact with ALA 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 ALA 3.0 17.5 + - - +
101A PHE* 3.7 9.2 - - + +
102A VAL 3.3 0.2 - - - -
103A ARG* 1.3 75.9 - - - +
105A ALA* 1.3 62.7 + - - +
107A GLU* 3.3 10.0 + - - +
108A ARG* 3.0 39.6 + - - +
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Residues in contact with ALA 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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28A LEU* 4.1 4.5 - - + -
31A ALA* 3.9 14.9 - - + +
32A LEU* 3.7 27.1 - - + -
101A PHE* 3.2 7.3 + - + +
102A VAL 3.5 8.7 - - - +
104A ALA* 1.3 76.5 - - - +
106A LEU* 1.3 62.8 + - - +
108A ARG* 3.3 29.9 + - - +
109A LEU* 3.1 27.5 + - - +
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Residues in contact with LEU 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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9A TYR* 3.8 14.1 - - - +
13A PHE* 3.6 32.3 - - + -
28A LEU* 4.3 13.2 - - + +
102A VAL 2.9 15.4 + - - +
103A ARG* 3.3 8.5 - - - +
105A ALA* 1.3 75.5 - - - +
107A GLU* 1.3 59.6 + - + +
109A LEU* 3.2 6.7 + - - +
110A GLN* 3.0 54.5 + - - +
116A PHE* 3.6 33.7 - - + +
117A ASN* 4.4 6.7 - - - +
118A VAL* 4.8 8.7 - - + -
123A PHE* 4.8 4.0 - - + -
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Residues in contact with GLU 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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9A TYR* 5.8 0.4 - - - +
103A ARG* 2.8 60.8 + - + +
104A ALA* 3.7 9.0 - - - +
106A LEU* 1.3 78.0 - - + +
108A ARG* 1.3 60.5 + - - +
110A GLN* 3.2 19.2 + - - +
111A GLN* 3.1 25.1 + - - +
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Residues in contact with ARG 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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31A ALA* 3.7 23.8 + - + +
101A PHE* 5.1 8.9 + - - -
104A ALA* 3.0 20.7 + - - +
105A ALA* 3.4 44.4 - - - +
107A GLU* 1.3 75.7 - - - +
109A LEU* 1.3 60.9 + - + +
111A GLN* 3.3 30.6 + - - +
112A GLN* 3.5 16.9 + - - +
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Residues in contact with LEU 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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27A THR* 3.6 46.0 - - + +
28A LEU* 3.9 12.6 - - + -
30A HIS* 5.9 3.4 - - - +
31A ALA* 3.8 20.6 - - + -
105A ALA 3.1 15.0 + - - +
106A LEU* 3.2 8.5 + - - +
108A ARG* 1.3 73.2 - - + +
110A GLN* 1.3 57.7 + - - +
111A GLN 3.1 4.7 - - - -
112A GLN* 3.1 25.8 + - + +
113A GLN* 2.8 32.1 + - + +
116A PHE* 3.8 24.2 - - + -
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Residues in contact with GLN 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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106A LEU* 3.0 43.2 + - + +
107A GLU* 3.2 22.8 + - - +
109A LEU* 1.3 76.1 - - - +
111A GLN* 1.3 59.1 + - - +
112A GLN 3.4 0.2 - - - -
113A GLN 3.3 8.7 - - - +
114A ALA* 3.3 30.0 - - - +
116A PHE* 3.0 30.7 - - + +
117A ASN* 4.0 13.5 + - - -
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Residues in contact with GLN 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 GLU 3.1 9.8 + - - +
108A ARG* 3.3 28.6 - - - +
109A LEU 3.1 0.2 - - - -
110A GLN* 1.3 79.6 - - - +
112A GLN* 1.3 57.6 + - - +
114A ALA 5.3 0.3 + - - -
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Residues in contact with GLN 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 ARG* 3.5 14.1 + - - +
109A LEU* 3.3 33.9 - - + +
111A GLN* 1.3 80.2 - - - +
113A GLN* 1.3 57.6 + - + +
114A ALA 4.0 1.3 + - - -
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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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27A THR* 5.0 8.5 + - - +
109A LEU* 2.8 12.0 + - - +
110A GLN* 3.3 14.7 - - - -
112A GLN* 1.3 79.3 - - + +
114A ALA* 1.3 64.9 + - - +
115A ASP 4.5 3.1 - - - +
116A PHE* 3.0 52.1 + - + +
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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