Contacts of the strand formed by residues 78 - 85 (chain B) in PDB entry 2WZJ
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 GLU 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 4.4 9.6 - - + +
69B LEU* 4.0 29.1 - - + +
70B ALA 3.4 10.3 - - - +
71B ARG* 4.9 13.4 + - + +
76B GLY 4.0 2.0 + - - +
77B LYS* 1.3 77.3 - - - +
79B VAL* 1.3 65.8 + - - +
116B PHE* 5.3 1.4 - - - -
131B TYR* 3.8 35.9 + - + +
133B SER* 5.5 1.0 - - - -
360B LEU* 5.5 0.5 - - - +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.7 30.5 - - + -
69B LEU* 3.6 7.3 - - - +
70B ALA* 2.9 41.5 + - + +
72B HIS 4.7 2.7 - - - +
77B LYS 4.7 2.2 - - - +
78B GLU* 1.3 81.0 - - - +
80B ALA* 1.3 60.3 + - - +
81B VAL* 4.4 2.5 - - + -
116B PHE* 3.7 27.8 - - + -
128B VAL* 3.8 11.9 - - + -
129B MET 3.5 8.3 - - - +
131B TYR* 3.8 7.0 - - - +
360B LEU* 3.8 22.2 - - + -
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Residues in contact with ALA 80 (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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59B ILE* 4.5 4.9 - - + -
67B VAL* 4.0 17.0 - - + -
68B LYS 3.5 4.0 - - - +
69B LEU* 4.7 0.4 - - - +
79B VAL* 1.3 72.8 - - - +
81B VAL* 1.3 61.9 + - - +
82B ARG 4.0 0.4 - - - -
129B MET* 2.8 52.8 + - + +
130B GLU 4.1 12.1 - - - +
131B TYR* 3.9 18.0 - - + +
198B ASN* 6.0 0.2 - - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 5.4 3.4 - - + -
53B TYR* 4.8 5.6 - - + -
55B LEU* 4.4 13.7 - - + -
67B VAL* 3.3 4.6 - - - -
68B LYS* 2.8 41.5 + - + +
70B ALA* 3.8 26.2 - - + -
79B VAL* 4.4 5.6 - - + -
80B ALA* 1.3 72.3 - - - +
82B ARG* 1.3 64.0 + - - +
83B ILE* 3.7 19.7 + - + +
126B TYR* 4.2 22.2 - - + -
127B LEU 3.4 7.2 - - - +
128B VAL* 3.9 21.1 - - + -
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 4.2 13.6 - - - +
66B LYS 3.5 23.6 - - - +
67B VAL* 3.8 7.8 - - - +
80B ALA 3.9 1.2 + - - -
81B VAL* 1.3 71.5 - - - +
83B ILE* 1.3 80.2 + - - +
84B ILE* 3.6 13.5 + - + +
125B LEU 3.6 1.7 - - - +
126B TYR* 3.5 3.8 - - - -
127B LEU* 2.8 47.0 + - + +
129B MET* 4.8 1.8 - - - -
196B PHE* 2.9 49.7 - - + -
197B SER 3.5 5.1 + - - -
198B ASN* 3.6 30.1 - - - +
200B PHE 3.7 19.8 + - - -
201B THR* 4.6 4.8 - - - +
202B PHE* 4.2 11.9 - - - -
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Residues in contact with ILE 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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55B LEU* 4.6 12.8 - - + -
66B LYS* 3.0 44.3 + - + +
68B LYS* 4.0 25.1 - - + -
81B VAL* 4.1 12.8 - - + +
82B ARG* 1.3 88.4 + - - +
84B ILE* 1.3 65.7 + - - +
85B ASP 4.4 0.3 + - - -
124B THR* 4.0 21.1 - - + -
125B LEU 3.7 2.2 - - - -
126B TYR* 3.8 26.0 - - + -
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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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82B ARG* 3.6 24.2 - - + +
83B ILE* 1.3 79.8 - - - +
85B ASP* 1.3 70.8 + - - +
86B LYS* 3.6 1.9 + - - +
89B LEU* 4.6 11.0 - - + -
97B LEU* 3.8 35.0 - - + -
124B THR* 3.4 7.9 - - - +
125B LEU* 2.8 51.1 + - + +
127B LEU* 4.5 7.4 - - + -
196B PHE* 3.5 35.2 - - + -
202B PHE* 4.3 8.1 - - + -
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Residues in contact with ASP 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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83B ILE 4.4 0.2 + - - -
84B ILE* 1.3 74.8 - - - +
86B LYS* 1.3 65.0 + - - +
87B THR* 2.8 39.6 + - - +
88B GLN* 3.2 39.1 + - + +
89B LEU* 3.8 11.1 - - - +
123B LYS* 3.2 8.3 - - - +
124B THR* 4.8 3.6 - - - +
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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