Contacts of the strand formed by residues 80 - 86 (chain B) in PDB entry 3SEA
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 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B LYS 3.4 3.2 + - - -
9B ILE* 3.3 19.3 - - - +
10B ALA 3.1 13.3 + - - -
78B ILE* 3.0 18.0 + - - +
79B ASN* 1.3 80.3 - - - +
81B TYR* 1.3 66.4 + - - -
113B PRO* 3.4 15.7 - - - -
163B ILE* 4.2 3.8 - - - -
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Residues in contact with TYR 81 (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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10B ALA* 3.5 13.9 - - + -
12B LEU* 3.7 22.7 - - + -
70B PHE* 4.9 0.2 - + - -
74B TYR 2.5 29.7 + - - -
75B SER* 3.6 13.2 - - - -
78B ILE* 3.4 27.3 + - + +
80B GLY* 1.3 75.2 - - - -
82B ILE* 1.3 62.2 + - - +
83B LEU* 3.7 15.7 - - + -
103B LEU* 3.6 28.1 - - + +
107B VAL* 4.0 3.6 - - - +
112B ILE* 3.5 40.8 - - + -
113B PRO 2.9 11.1 + - - +
114B ILE* 3.3 7.6 - - + +
115B MET 2.8 26.7 + - - -
163B ILE* 3.5 4.6 - - - +
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Residues in contact with ILE 82 (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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9B ILE* 3.7 19.3 - - + -
10B ALA 3.0 8.8 + - - +
11B ILE* 3.4 11.8 - - + +
12B LEU 2.8 26.9 + - - +
22B LEU* 5.8 0.9 - - + -
81B TYR* 1.3 74.6 - - - +
83B LEU* 1.3 61.0 + - - +
84B VAL* 3.9 13.6 + - + -
115B MET* 3.6 15.3 - - + -
117B VAL* 3.6 29.6 - - + -
159B VAL* 3.8 15.0 - - + -
160B PHE* 3.4 40.6 - - + -
163B ILE* 4.1 12.1 - - + -
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Residues in contact with LEU 83 (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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12B LEU* 3.5 22.9 - - + -
81B TYR* 3.7 23.8 - - + -
82B ILE* 1.3 77.5 - - - +
84B VAL* 1.3 61.1 + - - +
96B ILE* 3.4 25.1 - - + -
99B ILE* 4.3 4.0 - - + -
100B HIS* 3.6 42.6 - - + +
103B LEU* 4.3 7.0 - - + -
114B ILE* 4.4 7.6 - - + -
115B MET 2.9 13.4 + - - +
116B LEU* 3.5 7.6 - - - +
117B VAL 2.9 23.4 + - - -
141B TRP* 3.9 18.2 - - + -
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Residues in contact with VAL 84 (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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11B ILE* 3.9 28.5 - - + -
12B LEU 2.8 12.0 + - - +
13B GLY* 3.6 11.6 - - - -
14B TYR 4.1 2.6 + - - -
17B VAL* 3.7 24.0 - - + +
19B LYS* 4.2 7.6 - - + +
22B LEU* 4.8 10.8 - - + -
82B ILE* 3.9 15.0 - - + -
83B LEU* 1.3 76.5 - - - +
85B TYR* 1.3 74.9 + - - +
92B SER 5.0 0.5 - - - +
96B ILE* 3.5 15.9 - - - +
117B VAL* 3.4 14.4 - - + +
119B ASN* 3.8 17.3 - - + -
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Residues in contact with TYR 85 (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 VAL* 3.9 10.1 - - - -
84B VAL* 1.3 82.0 - - - +
86B SER* 1.3 81.2 + - - +
87B VAL* 4.1 10.5 - - + -
92B SER* 3.5 27.1 - - - +
93B PHE* 3.7 34.3 - + + -
96B ILE* 4.5 4.7 - - + -
116B LEU* 3.8 30.3 - - + -
117B VAL 2.9 13.9 + - - +
118B GLY* 3.5 24.0 - - - -
119B ASN* 2.8 23.2 + - - +
129B ILE* 3.9 16.0 - - + +
130B SER 4.6 0.7 + - - -
134B GLY* 3.5 12.0 + - - -
145B PHE* 3.3 23.2 - + - -
147B GLU* 4.6 4.9 + - - -
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Residues in contact with SER 86 (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 VAL* 4.2 17.5 - - - -
85B TYR* 1.3 84.7 - - - +
87B VAL* 1.3 58.7 + - - +
88B THR* 2.9 32.8 + - - -
89B SER* 3.1 19.7 + - - +
92B SER* 3.0 17.1 + - - -
119B ASN 3.6 4.9 - - - -
120B LYS* 3.4 23.3 + - - +
129B ILE* 3.9 1.0 - - - +
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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