Contacts of the helix formed by residues 164 - 169 (chain W) in PDB entry 6VMK
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 ASP 164 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52M ASN* 2.8 29.2 + - - +
54M THR* 5.9 2.9 - - - -
132W PRO* 3.7 29.1 - - + +
162W VAL* 4.3 2.1 + - - -
163W LEU* 1.3 79.6 - - - +
165W ARG* 1.3 63.8 + - - +
166W ALA* 3.4 6.8 + - - +
167W THR* 2.8 35.2 + - - -
168W CYS* 3.0 19.4 + - - +
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Residues in contact with ARG 165 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M THR* 5.4 1.7 + - - +
31M SER* 3.8 23.8 + - - +
129W ASP* 2.8 42.8 + - - +
163W LEU 3.7 1.9 + - - -
164W ASP* 1.3 74.9 - - - +
166W ALA* 1.3 58.0 + - - +
168W CYS* 3.2 7.3 + - - +
169W ASN* 2.9 33.7 + - - +
176W ILE* 3.4 27.1 - - + +
177W THR 2.7 26.3 + - - -
178W GLU* 3.5 21.4 + - - +
180W LEU 2.8 22.6 + - - -
181W MET* 4.8 4.1 - - - +
182W CYS* 5.4 1.3 - - - +
230W ARG* 3.7 2.4 - - - +
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Residues in contact with ALA 166 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M THR 3.9 14.9 + - - +
31M SER 3.3 20.1 + - - +
32M TYR 4.0 7.2 - - - +
33M TYR* 3.5 27.4 + - + -
52M ASN* 3.8 14.4 - - - +
53M PRO* 4.4 0.9 - - + -
54M THR* 5.3 0.4 - - - +
99M GLU 5.4 0.2 - - - +
164W ASP* 3.3 9.7 + - - +
165W ARG* 1.3 78.3 - - - +
167W THR* 1.3 63.5 + - - +
169W ASN* 3.1 12.1 + - - +
170W ARG* 3.5 7.6 + - - +
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Residues in contact with THR 167 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M TYR* 3.2 29.5 + - - +
52M ASN* 3.8 0.2 + - - -
163W LEU* 4.2 20.6 - - + -
164W ASP* 2.8 31.1 + - - -
166W ALA* 1.3 75.0 - - - +
168W CYS* 1.3 62.5 + - - +
170W ARG* 3.1 19.8 + - - +
171W HIS* 3.0 35.0 - - + +
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Residues in contact with CYS 168 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163W LEU* 4.2 7.2 - - + -
164W ASP 3.0 17.2 + - - +
165W ARG* 3.2 6.9 + - - +
167W THR* 1.3 77.9 - - - +
169W ASN* 1.3 58.2 + - - +
171W HIS* 3.2 6.1 - - - +
172W HIS* 3.0 49.7 + - - +
176W ILE* 3.7 4.7 - - + -
182W CYS* 2.0 52.0 - - + -
225W PRO* 4.0 8.7 - - - -
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Residues in contact with ASN 169 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M SER* 2.9 30.8 + - - +
32M TYR* 4.4 9.8 - - + -
99M GLU 4.5 1.8 - - - +
100M GLY* 3.3 10.4 - - - -
165W ARG* 2.9 18.6 + - - +
166W ALA 3.1 4.9 + - - +
167W THR 3.1 0.6 - - - -
168W CYS* 1.3 74.0 - - - +
170W ARG* 1.3 66.6 + - - +
172W HIS 4.7 0.2 - - - +
173W ASP* 3.2 1.8 - - - +
174W GLY* 2.9 37.2 + - - +
175W ALA 3.2 1.0 + - - -
176W ILE* 2.9 52.8 + - - +
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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