Contacts of the strand formed by residues 92 - 99 (chain B) in PDB entry 6Z1V
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 ALA 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ARG* 4.0 18.6 - - + +
39B GLN 3.6 20.4 - - - +
40B ALA* 4.0 7.0 - - + +
41B PRO* 5.4 2.5 - - - -
89B GLU 5.8 0.2 - - - +
90B ASP 3.2 9.6 + - - +
91B THR* 1.3 79.0 - - - +
93B VAL* 1.3 60.6 + - - +
94B TYR* 3.4 15.7 - - + -
118B GLN* 3.7 9.9 - - - +
119B VAL 2.9 29.9 + - - +
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Residues in contact with VAL 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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38B ARG* 3.1 4.3 - - - -
39B GLN* 2.8 43.1 + - + +
92B ALA* 1.3 71.9 - - - +
94B TYR* 1.3 61.6 + - - +
95B TYR* 3.5 35.8 - - + +
115B GLN 4.7 1.3 - - - +
116B GLY* 3.7 20.2 - - - -
117B THR 3.6 8.7 - - - +
118B GLN* 3.3 24.9 - - + +
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Residues in contact with TYR 94 (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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6B GLU* 4.0 2.4 - - - +
20B LEU* 3.5 21.8 - - + -
36B TRP* 4.4 5.6 - + + -
37B PHE 3.3 8.3 - - - +
38B ARG* 2.9 43.8 + - + -
48B VAL* 4.5 7.0 - - + -
68B PHE* 3.9 8.8 - + - -
81B LEU* 4.2 14.1 - - + -
83B MET* 3.4 24.8 - - + +
90B ASP* 2.7 32.0 + - - +
92B ALA* 3.4 21.5 - - + -
93B VAL* 1.3 72.3 - - - +
95B TYR* 1.3 61.1 + - - +
116B GLY* 3.3 1.6 - - - -
117B THR* 2.9 36.7 + - - +
119B VAL* 3.6 22.0 - - + -
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Residues in contact with TYR 95 (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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6B GLU* 3.3 5.2 - - - +
35B GLY 3.8 0.2 - - - +
36B TRP* 3.2 10.1 - - - -
37B PHE* 2.8 38.3 + - - +
39B GLN* 3.5 18.4 + - + -
45B ARG* 3.2 63.0 + - + -
93B VAL* 3.5 31.5 - - + +
94B TYR* 1.3 73.6 - - - +
96B CYS* 1.3 59.5 + - - +
113B TRP* 3.8 19.7 - + + -
114B GLY 3.6 12.8 - - - -
115B GLN* 3.6 20.8 + - - -
116B GLY* 3.6 11.9 - - - -
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Residues in contact with CYS 96 (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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4B LEU* 3.6 12.6 - - + +
6B GLU* 2.8 25.9 + - - +
22B CYS* 2.0 53.4 - - + -
34B MET* 5.0 0.7 - - + -
35B GLY 3.3 8.7 - - - +
36B TRP* 3.8 13.9 - - + -
79B VAL* 4.4 5.2 - - + -
95B TYR* 1.3 74.4 - - - +
97B ALA* 1.3 60.1 + - - +
113B TRP* 3.5 3.1 - - - -
114B GLY 2.9 26.7 + - - -
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Residues in contact with ALA 97 (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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4B LEU* 3.7 4.9 - - - -
34B MET* 3.4 7.6 - - - +
35B GLY 2.9 29.4 + - - -
37B PHE* 4.0 9.6 - - + -
96B CYS* 1.3 74.9 - - - +
98B ALA* 1.3 61.1 + - - +
110B TRP* 3.5 18.3 - - + -
112B SER 3.1 14.8 - - - +
113B TRP* 3.8 28.7 - - + -
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Residues in contact with ALA 98 (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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2B VAL* 3.9 28.5 - - + -
4B LEU* 3.9 2.7 - - + +
32B TYR* 4.0 11.6 - - + -
33B VAL 3.4 4.7 - - - -
34B MET* 3.6 22.4 - - + -
97B ALA* 1.3 75.0 - - - +
99B THR* 1.3 63.0 + - - +
110B TRP* 3.5 4.3 - - - -
111B GLY 3.6 6.1 + - - -
112B SER* 3.0 28.1 + - - +
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Residues in contact with THR 99 (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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32B TYR* 3.4 9.0 - - - -
33B VAL* 2.7 33.6 + - + +
98B ALA* 1.3 76.2 - - - +
100B GLU* 1.3 60.6 + - - +
101B ARG 3.3 24.1 + - - +
104B LEU* 4.4 7.5 - - + +
109B ASP 3.0 22.3 + - - +
110B TRP* 3.6 41.6 - - + +
111B GLY 4.8 2.0 + - - +
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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