Contacts of the helix formed by residues 164 - 173 (chain B) in PDB entry 4J6V
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 THR 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B GLU* 3.8 7.4 - - - -
98B ALA* 4.4 7.9 - - + +
162B LEU 4.2 8.1 - - - +
163B PRO* 1.3 77.2 - - - +
165B ARG* 1.3 64.2 + - - +
166B ASP* 3.4 9.7 + - - +
167B ASP* 3.0 42.9 + - - +
168B VAL* 3.3 14.2 + - - +
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Residues in contact with ARG 165 (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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95B GLU* 3.8 28.5 + - + +
96B THR* 3.3 27.7 - - - +
99B GLN* 2.3 60.0 + - - +
164B THR* 1.3 74.5 - - - +
166B ASP* 1.3 61.4 + - - +
168B VAL* 3.2 5.6 + - - +
169B LEU* 3.0 38.4 + - + +
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Residues in contact with ASP 166 (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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164B THR* 3.2 8.8 + - - +
165B ARG* 1.3 79.5 - - - +
167B ASP* 1.3 65.3 + - - +
169B LEU* 3.8 14.6 - - - +
170B ASN* 2.9 39.2 + - - +
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Residues in contact with ASP 167 (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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163B PRO* 3.5 8.8 - - - +
164B THR* 3.0 40.9 + - - +
166B ASP* 1.3 75.8 - - - +
168B VAL* 1.3 63.1 + - - +
170B ASN* 3.5 8.7 + - - +
171B ALA* 3.2 21.5 + - - +
193B GLN* 5.7 0.2 - - - +
202B GLN* 4.4 16.7 - - + +
203B LEU* 3.9 25.1 - - + +
206B ARG* 5.5 0.9 - - - -
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Residues in contact with VAL 168 (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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94B TRP* 4.0 9.2 - - + -
95B GLU* 3.9 25.6 - - + +
164B THR 3.3 9.8 + - - +
165B ARG* 3.2 9.1 + - - +
167B ASP* 1.3 75.5 - - - +
169B LEU* 1.3 70.1 + - + +
171B ALA* 3.1 8.5 + - - +
172B LEU* 3.0 36.9 + - + +
203B LEU* 3.7 22.9 - - + -
237B ILE* 3.9 31.2 - - + -
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Residues in contact with LEU 169 (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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165B ARG* 3.0 25.5 + - + +
166B ASP* 3.8 17.5 - - - +
168B VAL* 1.3 79.2 - - + +
170B ASN* 1.3 64.6 + - - +
172B LEU* 3.2 29.1 + - + +
173B LYS* 3.4 23.0 + - - +
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Residues in contact with ASN 170 (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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166B ASP* 2.9 30.4 + - - +
167B ASP* 3.8 10.1 + - - +
169B LEU* 1.3 72.9 - - - +
171B ALA* 1.3 67.7 + - - +
173B LYS* 3.1 43.5 + - + +
174B ILE* 3.9 10.0 - - - +
193B GLN* 5.5 2.4 + - - -
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Residues in contact with ALA 171 (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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167B ASP 3.2 13.6 + - - +
168B VAL* 3.1 10.8 + - - +
170B ASN* 1.3 75.5 - - - +
172B LEU* 1.3 63.1 + - + +
173B LYS 3.1 0.2 - - - -
174B ILE* 3.1 20.9 + - - +
190B PHE* 3.3 26.2 - - + -
193B GLN* 3.8 30.9 - - + +
194B LEU* 4.9 5.4 - - + +
203B LEU* 4.0 11.9 - - + -
237B ILE* 5.6 1.6 - - + -
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Residues in contact with LEU 172 (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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168B VAL* 3.0 30.3 + - + +
169B LEU* 3.2 22.8 + - + +
171B ALA* 1.3 76.5 - - - +
173B LYS* 1.3 57.5 + - - +
174B ILE 3.3 0.2 - - - -
190B PHE* 4.1 1.8 - - + -
237B ILE* 3.5 36.3 - - + +
240B VAL* 3.8 21.1 - - + -
241B TRP* 3.6 29.6 - - + +
244B ILE* 3.8 14.8 - - + +
245B HIS* 2.8 27.5 + - - -
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Residues in contact with LYS 173 (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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169B LEU* 3.4 19.4 - - - +
170B ASN* 3.1 34.8 + - - +
171B ALA 3.1 0.8 - - - -
172B LEU* 1.3 78.0 - - - +
174B ILE* 1.3 63.5 + - + +
175B THR* 3.5 12.8 + - - +
245B HIS* 4.2 5.7 - - - -
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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