Contacts of the helix formed by residues 85 - 93 (chain B) in PDB entry 6WCZ
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 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASP* 4.7 0.9 - - - -
82B CYS* 2.6 34.9 + - - -
83B GLY 3.4 0.6 - - - -
84B ARG* 1.3 72.1 - - - +
86B GLY* 1.3 58.1 + - - +
87B TRP* 3.1 6.2 - - - -
88B SER* 2.3 38.5 + - - -
89B TYR* 3.1 10.6 + - - -
126B LEU* 4.6 8.7 - - - -
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Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA* 3.7 18.8 - - - +
56B SER* 3.3 21.6 + - - -
59B SER* 2.6 22.3 + - - -
84B ARG 3.2 5.3 + - - -
85B GLY* 1.3 73.8 - - - +
87B TRP* 1.3 61.0 + - - +
89B TYR* 3.6 5.8 - - - +
90B TYR* 2.9 20.8 + - - +
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Residues in contact with TRP 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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56B SER* 5.1 8.5 - - - -
57B ARG 5.9 1.1 - - - -
58B GLY* 4.3 26.5 - - - -
59B SER* 3.8 4.2 + - - +
61B LYS* 5.6 1.6 - - - +
62B LEU* 3.4 36.4 - - + +
79B ASP* 4.0 13.0 - - - +
81B GLY 4.6 4.5 - - - -
82B CYS* 3.2 31.6 - - - -
83B GLY* 5.0 1.3 - - - -
84B ARG* 4.6 5.4 - - + -
85B GLY* 4.2 4.3 - - - -
86B GLY* 1.3 83.2 - - - +
88B SER* 1.3 58.0 + - - +
90B TYR* 3.3 6.1 + - - +
91B ALA* 2.9 27.1 + - - +
144B LEU* 4.6 13.5 - - + -
146B ASP* 2.8 41.5 + - + +
220B TYR* 5.6 3.8 + - - -
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 6.3 0.4 - - - -
79B ASP* 3.9 16.1 + - - -
85B GLY* 2.3 28.5 + - - -
87B TRP* 1.3 76.4 - - - +
89B TYR* 1.3 64.6 + - - +
91B ALA* 3.1 10.1 + - - +
92B ALA* 2.9 27.4 + - - +
100B VAL* 3.8 30.5 - - - +
124B VAL* 5.1 2.0 - - - +
126B LEU* 3.7 20.5 - - - +
144B LEU* 6.2 0.7 - - - -
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Residues in contact with TYR 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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54B ALA* 3.6 25.1 - - + +
84B ARG 4.3 4.7 - - - -
85B GLY 3.1 5.7 + - - -
86B GLY* 3.6 14.1 - - - +
87B TRP 3.3 0.2 - - - -
88B SER* 1.3 86.1 + - - +
90B TYR* 1.3 61.0 + - - +
92B ALA* 3.3 21.6 + - + +
93B THR* 3.8 9.4 - - - +
114B MET* 2.7 46.7 + - + -
115B LEU* 3.5 8.3 - - - +
116B VAL* 3.4 30.6 + - + -
118B SER* 5.2 17.2 - - - +
119B TYR 4.9 2.5 - - - +
120B GLY 5.9 2.9 - - - -
121B TRP* 4.3 10.8 - + - -
124B VAL* 4.5 22.9 - - + -
126B LEU* 5.3 7.4 - - + +
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Residues in contact with TYR 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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59B SER* 3.8 23.1 - - - +
62B LEU* 3.4 43.1 + - + -
63B ARG* 3.2 41.3 + - + -
66B VAL* 4.5 8.4 - - + +
67B GLU* 4.0 10.9 - - - +
86B GLY 2.9 16.6 + - - +
87B TRP* 3.7 3.8 - - - +
89B TYR* 1.3 74.7 - - - +
91B ALA* 1.3 64.0 + - - +
93B THR* 2.8 38.8 + - + -
94B ILE* 3.3 16.4 - - + +
257B VAL* 4.1 15.5 - - + -
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Residues in contact with ALA 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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62B LEU* 5.3 7.4 - - + -
73B PRO* 6.0 5.6 - - + -
77B VAL* 4.9 18.4 - - + -
87B TRP 2.9 14.3 + - - +
88B SER* 3.1 14.3 + - - +
90B TYR* 1.3 78.3 - - - +
92B ALA* 1.3 61.9 + - - +
93B THR 3.2 1.0 + - - -
94B ILE* 3.3 16.3 + - + +
97B VAL* 3.2 29.2 - - + +
100B VAL* 5.5 3.1 - - + -
144B LEU* 5.7 4.5 - - + -
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Residues in contact with ALA 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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88B SER 2.9 11.2 + - - +
89B TYR* 3.3 17.5 - - + +
90B TYR 3.1 0.4 - - - -
91B ALA* 1.3 78.3 - - - +
93B THR* 1.3 57.2 + - - +
94B ILE 3.2 0.2 - - - -
97B VAL* 4.7 8.6 - - - +
100B VAL* 5.3 5.4 - - + -
119B TYR* 4.0 19.8 - - - +
120B GLY* 4.1 13.7 - - - +
123B ILE* 4.6 13.0 - - + +
124B VAL* 6.4 1.1 - - + -
264B ARG* 2.8 27.7 + - - -
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Residues in contact with THR 93 (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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89B TYR 3.8 15.0 - - - +
90B TYR* 2.8 31.1 + - + +
92B ALA* 1.3 79.0 - - + +
94B ILE* 1.3 68.5 + - - +
95B ARG* 3.5 9.9 + - - +
119B TYR* 4.4 20.5 - - + +
259B LEU* 4.1 35.8 - - + +
264B ARG* 3.2 6.5 + - - +
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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