Contacts of the strand formed by residues 86 - 92 (chain B) in PDB entry 2GZD
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 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B LYS 3.4 6.0 + - - -
14B VAL* 3.4 8.7 - - - -
15B VAL* 3.2 19.9 + - - +
84B ALA* 3.5 9.6 - - - +
85B VAL* 1.3 81.9 - - - +
87B ALA* 1.3 60.2 + - - +
117B ILE* 3.8 4.7 - - - -
118B VAL 3.2 10.5 - - - -
168B ILE* 4.0 4.0 - - - -
172B ILE* 3.8 15.3 - - - -
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Residues in contact with ALA 87 (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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14B VAL* 5.1 0.2 - - - -
15B VAL* 3.2 15.5 - - + +
17B ILE* 4.7 7.0 - - + -
86B GLY* 1.3 73.9 - - - +
88B LEU* 1.3 60.4 + - - +
89B LEU 3.5 0.9 + - - -
109B LEU* 3.8 23.6 - - + -
117B ILE* 3.6 18.8 - - + -
118B VAL 2.9 7.7 + - - +
119B ILE* 3.5 6.4 - - + +
120B MSE 2.9 26.0 + - - -
168B ILE* 3.4 7.2 - - - +
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Residues in contact with LEU 88 (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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14B VAL* 4.6 10.9 - - + +
15B VAL 2.9 7.8 + - - +
16B LEU* 3.4 29.6 - - + -
17B ILE* 2.9 27.8 + - - +
27B LEU* 5.2 4.9 - - + -
87B ALA* 1.3 70.4 - - - +
89B LEU* 1.3 58.8 + - - +
90B VAL* 3.5 9.6 + - + +
120B MSE 3.5 26.9 - - + +
122B VAL* 3.8 24.0 - - + -
164B ALA* 5.0 7.6 - - + +
165B PHE* 3.5 35.7 - - + -
168B ILE* 4.3 13.7 - - + -
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Residues in contact with LEU 89 (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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17B ILE* 3.6 18.8 - - + +
87B ALA 3.5 2.2 + - - -
88B LEU* 1.3 70.1 - - - +
90B VAL* 1.3 66.4 + - - +
102B VAL* 3.7 39.0 - - + +
105B TRP* 3.5 40.6 - - + -
106B LEU* 3.9 21.3 - - + +
109B LEU* 4.6 2.2 - - + -
119B ILE* 4.2 13.5 - - + -
120B MSE 2.9 13.4 + - - +
121B LEU* 3.4 18.2 - - + +
122B VAL 3.0 23.0 + - - -
148B LEU* 5.5 1.6 - - + -
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Residues in contact with VAL 90 (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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16B LEU* 4.2 11.4 - - + -
17B ILE 2.7 16.0 + - - +
18B GLY* 3.4 20.4 - - - -
19B ASP 4.1 1.6 + - - -
22B VAL* 3.5 27.3 - - + +
24B LYS* 4.2 5.6 - - + -
27B LEU* 3.7 34.3 - - + -
88B LEU* 3.6 20.0 - - + +
89B LEU* 1.3 78.8 - - - +
91B TYR* 1.3 66.2 + - - +
98B THR 4.9 1.2 - - - +
122B VAL* 3.4 12.8 - - + +
124B ASN* 3.9 18.2 - - + -
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Residues in contact with TYR 91 (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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22B VAL* 3.8 10.8 - - - -
90B VAL* 1.3 74.8 - - - +
92B ASP* 1.3 67.2 + - - +
93B ILE* 3.7 21.5 - - + +
98B THR 3.5 26.0 - - - +
99B TYR* 3.9 22.0 - + + -
102B VAL* 4.0 9.0 - - + -
121B LEU* 3.5 38.8 - - + -
122B VAL 3.0 9.1 + - - -
123B GLY* 3.5 16.0 - - - -
124B ASN* 2.7 37.2 + - - +
134B VAL* 4.0 18.6 - - + +
139B ALA* 3.2 23.2 - - - +
150B PHE* 3.3 12.1 - - - -
152B GLU* 4.4 1.7 + - - -
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Residues in contact with ASP 92 (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 GLY 4.1 3.2 - - - +
22B VAL* 3.7 17.2 - - + +
91B TYR* 1.3 81.3 - - - +
93B ILE* 1.3 63.5 + - - +
94B ALA* 3.1 23.3 + - - +
95B LYS* 3.2 32.7 + - + +
98B THR* 3.1 24.0 + - + +
124B ASN 3.7 4.0 - - - -
125B LYS* 3.0 42.6 + - - +
128B LEU* 5.3 0.7 - - - +
134B VAL* 3.9 0.7 - - - +
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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