Contacts of the strand formed by residues 97 - 108 (chain B) 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 ILE 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B SER* 3.5 26.9 - - - -
92B ILE 3.4 0.2 - - - +
93B THR* 3.3 4.9 - - - +
94B VAL* 2.7 41.2 + - + +
95B GLY 3.2 3.2 - - - -
96B GLY* 1.3 81.2 - - - +
98B THR* 1.3 72.9 + - - +
99B VAL* 4.6 1.3 - - + -
142B ILE* 4.1 37.9 - - + -
145B GLN* 3.8 19.1 - - - +
147B VAL* 4.6 11.2 - - + -
148B LEU* 4.1 15.0 - - + -
173B LEU* 4.9 4.9 - - + -
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ILE* 3.8 25.4 - - + -
92B ILE 3.1 4.0 - - - -
93B THR* 4.1 12.6 - - + +
96B GLY 5.2 3.4 - - - +
97B ILE* 1.3 82.8 - - - +
99B VAL* 1.3 60.8 + - - +
145B GLN* 3.4 18.6 + - - +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 4.3 2.0 - - - +
92B ILE* 3.0 32.6 + - + +
94B VAL* 4.7 1.8 - - + -
97B ILE* 4.6 2.7 - - + -
98B THR* 1.3 76.7 - - - +
100B THR* 1.3 72.1 + - - +
101B GLN* 3.1 5.7 + - - +
138B ILE* 3.5 26.9 - - + -
141B ASN* 3.5 33.0 - - + +
142B ILE* 3.6 24.2 - - + +
145B GLN* 3.8 14.1 - - - +
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Residues in contact with THR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B SER 6.2 0.2 - - - +
89B GLN* 3.6 36.6 + - + +
90B ASP* 3.6 11.7 - - - +
91B ILE* 4.0 16.9 - - + +
99B VAL* 1.3 80.0 - - - +
101B GLN* 1.3 59.2 + - - +
141B ASN* 3.6 10.6 - - - +
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 4.5 10.0 + - + +
89B GLN* 4.2 4.0 - - - -
90B ASP 2.8 32.4 + - - +
92B ILE* 3.6 28.5 - - + -
99B VAL* 3.1 6.0 + - - +
100B THR* 1.3 74.5 - - - +
102B MET* 1.3 81.4 + - - +
103B PHE* 3.5 8.0 - - - +
135B VAL* 4.8 0.3 - - - +
136B THR 2.9 19.2 - - - +
137B PRO* 3.7 1.0 - - - +
138B ILE* 3.2 42.8 + - + +
141B ASN* 2.7 32.5 + - - +
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Residues in contact with MET 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 4.7 3.5 + - - +
70B ASN* 3.6 29.2 - - + +
87B LEU* 3.7 29.6 - - + -
88B SER 3.2 10.1 - - - +
89B GLN* 3.5 42.0 - - - +
101B GLN* 1.3 89.9 - - - +
103B PHE* 1.3 59.9 + - - +
135B VAL* 3.4 32.6 - - + +
136B THR 5.4 0.7 - - - +
141B ASN* 5.0 1.0 + - - -
986B NAG 3.7 17.3 - - - +
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.7 19.1 - - + -
39B VAL* 3.3 32.1 - - + +
40B TRP* 5.0 0.2 - - - -
41B VAL* 4.1 20.0 - - + -
59B PHE* 3.5 39.5 - + - -
87B LEU* 3.3 10.3 - - - +
88B SER* 2.9 47.3 + - - +
90B ASP* 3.7 28.0 - - + -
92B ILE* 4.6 10.1 - - + -
101B GLN 3.5 11.4 - - - -
102B MET* 1.3 74.5 - - - +
104B GLY* 1.3 72.2 + - - +
105B GLU* 4.1 10.1 - - + -
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL 2.8 16.1 + - - -
40B TRP* 3.3 9.2 - - - +
41B VAL 3.2 25.8 + - - +
74B LEU* 4.8 18.1 - - - +
86B PHE 3.7 7.9 - - - -
87B LEU* 4.5 0.9 - - - -
103B PHE* 1.3 81.3 - - - +
105B GLU* 1.3 61.5 + - - -
106B VAL* 3.4 2.0 + - - -
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Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B VAL* 3.9 4.0 - - - -
43B SER* 2.7 31.7 + - - -
45B LYS* 4.5 7.3 + - - -
59B PHE* 3.8 23.2 - - + +
61B ALA* 4.1 3.0 - - - +
67B TYR* 3.5 15.4 - - - -
74B LEU* 6.2 0.2 - - - -
85B GLY* 3.0 4.4 - - - -
86B PHE* 2.8 63.3 + - + +
88B SER* 2.5 37.9 + - - +
103B PHE* 4.1 10.8 - - + -
104B GLY* 1.3 70.7 - - - -
106B VAL* 1.3 63.0 + - - +
107B THR 3.5 0.3 + - - -
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TRP* 3.2 35.4 - - + -
41B VAL 3.0 16.4 + - - +
42B PRO* 4.0 0.3 - - - +
43B SER* 2.9 25.8 + - - +
46B CYS* 3.9 4.5 - - - +
53B CYS* 5.4 0.4 - - - -
74B LEU* 5.9 2.5 - - + -
76B LEU* 5.6 1.3 - - + -
83B VAL* 3.6 24.2 - - + -
84B SER 3.3 8.5 - - - +
85B GLY* 4.1 0.2 - - - -
104B GLY* 3.4 1.1 + - - -
105B GLU* 1.3 71.9 - - - +
107B THR* 1.3 61.2 + - - +
108B GLU 3.6 24.2 - - - +
109B MET* 3.3 26.0 - - + -
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Residues in contact with THR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B SER* 4.3 2.0 - - - -
45B LYS* 3.9 26.5 - - + +
46B CYS* 3.7 18.5 - - - +
47B SER 5.1 0.7 + - - -
50B TYR* 3.6 11.1 - - - -
84B SER 2.8 8.2 + - - -
85B GLY* 3.6 13.7 - - - -
86B PHE* 3.4 34.5 - - + -
105B GLU 3.5 0.4 + - - +
106B VAL* 1.3 77.6 - - - +
108B GLU* 1.3 67.0 + - - +
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TYR* 3.2 30.4 + - + +
83B VAL* 3.5 22.1 - - - +
84B SER* 3.4 33.4 + - - +
106B VAL* 3.6 3.0 - - - +
107B THR* 1.3 85.4 - - - +
109B MET* 1.3 59.8 + - - +
110B PRO* 3.3 13.6 - - + +
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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