Contacts of the strand formed by residues 83 - 89 (chain B) in PDB entry 4LHZ
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 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B LYS 3.3 3.8 + - - -
11B LEU* 3.3 13.9 - - - +
12B LEU 3.2 17.5 + - - +
81B ALA* 3.4 0.6 - - - -
82B MET* 1.3 83.0 - - - +
84B ILE* 1.3 60.9 + - - -
85B MET* 5.0 0.2 - - - +
115B GLU* 2.9 15.7 - - - -
165B LEU* 3.6 10.1 - - - +
169B ILE* 3.9 14.5 - - - +
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Residues in contact with ILE 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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12B LEU* 3.1 21.8 - - + +
14B ILE* 2.6 42.0 - - + -
78B TYR* 5.3 2.5 - - + -
81B ALA* 4.0 16.6 - - + -
83B GLY* 1.3 75.5 - - - -
85B MET* 1.3 69.1 + - - +
86B LEU* 3.5 1.9 - - + +
106B ILE* 3.2 37.0 - - + -
110B ALA* 5.0 8.1 - - + -
114B VAL* 3.7 20.6 - - + -
115B GLU 3.0 4.0 + - - -
116B LYS* 3.5 6.1 - - + -
117B MET* 3.2 20.4 + - - +
165B LEU* 5.0 0.7 - - - -
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Residues in contact with MET 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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11B LEU* 6.1 1.3 - - + -
12B LEU 2.7 9.5 + - - +
13B LEU* 3.7 21.4 - - + -
14B ILE* 3.1 25.6 + - - +
83B GLY 5.0 0.7 - - - +
84B ILE* 1.3 76.5 - - - +
86B LEU* 1.3 60.0 + - - +
87B VAL* 3.7 12.4 + - + +
117B MET* 3.4 39.5 - - - +
119B LEU* 3.8 16.2 - - + -
161B ALA 3.8 15.5 - - - +
162B PHE* 3.4 51.1 - - + -
165B LEU* 3.9 19.3 - - + -
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Residues in contact with LEU 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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14B ILE* 3.4 8.7 - - + +
84B ILE* 3.5 11.0 - - + +
85B MET* 1.3 69.5 - - - +
87B VAL* 1.3 60.2 + - - +
88B TYR 4.1 0.2 + - - -
99B ILE* 4.2 15.9 - - + +
102B TRP* 3.5 12.3 - - + -
103B ILE* 3.4 37.5 - - + +
106B ILE* 3.0 39.0 - - + -
116B LYS* 4.3 13.7 - - + -
117B MET 2.9 19.7 + - - +
118B ILE* 3.6 11.8 - - + +
119B LEU 2.9 23.7 + - - -
145B ILE* 4.6 7.4 - - + -
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Residues in contact with VAL 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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13B LEU* 5.1 7.9 - - + -
14B ILE 2.9 8.2 + - - +
15B GLY* 3.7 12.3 - - - -
16B ASP 4.1 1.2 + - - -
19B VAL* 2.9 45.8 - - + +
20B GLY 4.7 0.7 - - - +
21B LYS* 4.1 27.6 - - + +
24B VAL* 5.5 3.6 - - + -
85B MET* 3.9 14.4 - - + +
86B LEU* 1.3 76.3 - - - +
88B TYR* 1.3 63.7 + - - +
95B SER 5.2 0.5 - - - +
99B ILE* 3.8 6.9 - - - +
102B TRP* 5.8 0.2 - - - -
119B LEU* 3.6 33.7 - - + +
121B ASN* 4.2 9.9 - - + -
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Residues in contact with TYR 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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19B VAL* 3.6 10.5 - - - -
87B VAL* 1.3 73.5 - - - +
89B ASP* 1.3 65.3 + - - +
90B ILE* 3.7 24.2 - - + +
95B SER* 3.6 16.6 - - - +
96B PHE* 3.3 44.5 - + + -
99B ILE* 3.6 24.0 - - + -
118B ILE* 3.9 17.3 - - + -
119B LEU 2.9 11.7 + - - +
120B GLY* 3.5 19.6 - - - -
121B ASN* 2.7 37.1 + - - +
131B VAL* 4.0 12.3 - - + +
132B SER 5.3 1.0 + - - -
136B GLY* 3.8 4.7 - - - -
147B PHE* 3.5 21.7 - + - -
149B GLU* 4.4 2.4 + - - -
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Residues in contact with ASP 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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18B GLY 4.4 2.9 - - - +
19B VAL* 3.8 18.0 - - - +
88B TYR* 1.3 79.8 - - - +
90B ILE* 1.3 63.0 + - - +
91B THR* 3.0 29.1 + - - +
92B ASN* 2.9 23.2 + - + +
95B SER* 2.9 21.5 + - - +
121B ASN 3.7 3.1 - - - -
122B LYS* 3.0 48.3 + - - +
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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