Contacts of the strand formed by residues 81 - 94 (chain A) in PDB entry 2G1O
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 GLY 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A TYR* 2.9 41.0 + - - +
79A SER 3.7 0.4 - - - -
80A THR* 1.3 78.9 + - - +
82A THR* 1.3 63.5 + - - -
113A PRO* 4.3 14.4 - - - -
114A PHE* 4.6 5.8 - - - -
885A 2IG 5.4 0.7 - - - -
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Residues in contact with THR 82 (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 THR* 3.7 23.8 - - + -
76A LEU 3.2 14.1 - - - +
77A ARG* 4.0 20.4 + - + +
78A TYR* 4.7 2.0 + - - -
81A GLY* 1.3 76.6 + - - -
83A VAL* 1.3 71.8 + - - +
84A SER* 5.5 1.1 - - - -
110A PRO* 3.2 32.7 - - - +
114A PHE* 3.7 2.4 - - - -
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Residues in contact with VAL 83 (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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40A TRP* 3.8 26.9 - - + -
75A THR* 3.5 4.5 - - - +
76A LEU* 2.8 62.3 + - + +
78A TYR* 4.0 6.1 - - + -
82A THR* 1.3 82.5 - - - +
84A SER* 1.3 61.6 + - - +
106A VAL* 3.7 18.4 - - + -
108A GLU 3.5 11.0 - - - +
109A MET* 4.7 2.0 - - + -
114A PHE* 3.5 29.2 - - + -
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Residues in contact with SER 84 (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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74A LEU 3.5 5.8 + - - -
75A THR* 3.2 23.2 + - - -
82A THR* 5.5 1.1 - - - -
83A VAL* 1.3 78.3 - - - +
85A GLY* 1.3 55.4 + - - +
106A VAL* 3.2 10.2 - - - -
107A THR* 2.8 30.3 + - - -
108A GLU* 3.1 40.7 + - - -
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Residues in contact with GLY 85 (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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73A GLU* 3.3 10.9 - - - +
74A LEU* 2.9 33.1 + - - +
84A SER* 1.3 80.0 + - - +
86A PHE* 1.3 63.4 + - - +
105A GLU 3.2 12.8 - - - -
106A VAL* 4.1 0.7 - - - -
107A THR* 3.7 13.5 - - - -
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Residues in contact with PHE 86 (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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43A SER* 4.1 0.7 - - - -
45A LYS* 3.5 40.4 - - + -
67A TYR* 5.1 6.3 - - - -
69A HIS* 6.2 1.3 - + - -
71A GLY* 3.5 24.0 - - - +
72A THR 3.1 12.3 - - - +
73A GLU* 4.4 3.4 - - + -
74A LEU* 3.5 7.5 - - - +
85A GLY* 1.3 76.8 - - - +
87A LEU* 1.3 69.2 + - - +
88A SER* 3.6 17.5 - - - -
105A GLU* 2.7 63.1 + - + -
107A THR* 3.6 28.3 - - + -
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Residues in contact with LEU 87 (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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38A ASN* 5.2 0.7 - - - +
70A ASN* 3.8 14.3 + - - +
71A GLY 3.0 23.2 + - - -
72A THR* 2.7 37.0 + - + +
74A LEU* 3.6 34.8 - - + -
86A PHE* 1.3 75.8 - - - +
88A SER* 1.3 65.3 + - - +
102A MET* 3.2 25.6 - - + -
103A PHE* 3.2 17.3 - - - +
133A GLY* 5.2 5.2 - - - +
135A VAL* 3.6 24.7 - - + -
985A NAG 5.3 6.1 - - - +
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Residues in contact with SER 88 (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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67A TYR* 3.5 18.3 + - - -
68A LYS 3.9 5.6 - - - -
70A ASN* 4.5 3.1 + - - +
86A PHE* 3.6 6.9 - - - -
87A LEU* 1.3 77.9 + - - +
89A GLN* 1.3 61.7 + - - +
102A MET* 3.3 7.5 - - - +
103A PHE* 2.8 44.0 + - - -
105A GLU* 2.7 38.2 + - - -
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Residues in contact with GLN 89 (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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67A TYR* 3.4 4.3 - - - -
68A LYS* 2.8 66.2 + - + +
70A ASN* 6.0 0.2 - - + -
88A SER* 1.3 76.6 - - - +
90A ASP* 1.3 66.7 + - - +
100A THR* 3.5 26.8 + - + +
101A GLN 3.3 20.0 - - - +
102A MET* 4.0 22.2 - - + +
103A PHE* 3.9 2.0 - - - -
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Residues in contact with ASP 90 (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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21A ILE* 4.1 4.7 - - + -
22A GLY* 3.1 15.9 - - - -
59A PHE* 3.6 5.7 - - + -
64A SER* 2.5 30.5 + - - -
66A SER* 2.7 34.9 + - - +
67A TYR* 3.5 7.1 - - - +
68A LYS* 5.9 0.2 - - - -
89A GLN* 1.3 79.9 - - - +
91A ILE* 1.3 79.1 + - - +
92A ILE* 3.6 2.9 + - - +
100A THR* 4.4 4.9 - - - -
101A GLN* 3.0 30.8 + - - +
103A PHE* 3.8 17.6 - - + -
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Residues in contact with ILE 91 (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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20A GLY 3.5 1.4 - - - +
21A ILE* 3.4 2.9 - - - -
22A GLY 2.9 28.8 + - - +
23A THR* 3.1 24.0 - - + +
66A SER* 3.8 11.7 - - - +
90A ASP* 1.3 92.3 + - - +
92A ILE* 1.3 61.0 + - - +
98A THR* 4.3 20.4 - - + -
99A VAL 3.5 6.1 - - - +
100A THR* 4.1 18.8 - - + +
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Residues in contact with ILE 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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19A ILE* 4.1 15.5 - - + -
20A GLY 3.1 6.7 - - - +
21A ILE* 4.0 21.1 - - + -
39A VAL* 4.1 21.1 - - + -
90A ASP 4.2 3.4 - - - +
91A ILE* 1.3 76.3 - - - +
93A THR* 1.3 72.6 + - - +
94A VAL* 3.9 15.1 + - + -
97A ILE 3.9 0.3 - - - +
98A THR* 3.4 5.3 - - - -
99A VAL* 2.8 38.5 + - + +
101A GLN* 3.4 36.1 - - + -
103A PHE* 4.2 10.8 - - + -
138A ILE* 4.2 7.0 - - + -
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Residues in contact with THR 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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18A GLU 5.8 0.2 - - - +
19A ILE* 3.3 14.6 - - - +
20A GLY* 2.7 39.5 + - - +
25A PRO* 6.1 3.8 - - + +
91A ILE 4.2 0.2 + - - -
92A ILE* 1.3 73.1 - - - +
94A VAL* 1.3 63.9 + - - +
95A GLY* 4.3 7.2 - - - +
96A GLY 5.1 5.5 + - - +
97A ILE 3.5 4.0 + - - +
98A THR* 3.7 16.8 + - - +
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Residues in contact with VAL 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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3A SER* 4.3 5.2 - - - -
5A VAL* 4.2 10.9 - - + +
18A GLU 5.4 0.2 - - - +
19A ILE* 4.7 7.2 - - + -
32A PHE* 4.1 26.9 - - + -
92A ILE* 3.9 10.5 - - + +
93A THR* 1.3 81.0 - - - +
95A GLY* 1.3 66.9 - - - +
96A GLY 3.1 1.3 + - - -
97A ILE* 2.9 24.1 + - + +
99A VAL* 5.1 2.0 - - + -
138A ILE* 3.7 31.0 - - + -
142A ILE* 4.8 8.1 - - + -
173A LEU* 3.8 26.2 - - + +
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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