Contacts of the helix formed by residues 176 - 181 (chain B) in PDB entry 4XQ2
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 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B PRO* 4.4 13.5 - - + -
173B ASN* 3.3 8.1 + - - +
175B PHE* 1.3 81.7 - - + +
177B SER* 1.3 75.7 + - - +
180B LEU* 3.3 32.7 - - + +
181B GLN* 3.8 32.3 - - + +
198B SER* 5.4 0.2 - - - -
251B VAL* 4.9 2.1 - - - +
292B MSE 5.2 6.1 - - + -
296B GLY* 5.8 0.7 - - - -
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASN* 3.0 20.9 + - - -
174B THR 3.7 3.0 + - - -
175B PHE 3.6 1.2 - - - -
176B ALA* 1.3 88.7 + - - +
178B PRO* 1.3 73.8 - - - +
179B VAL* 3.0 25.5 + - - +
180B LEU 3.1 5.9 + - - -
181B GLN 3.2 10.0 + - - +
193B TYR* 4.2 3.4 - - - -
198B SER* 4.0 26.7 - - - -
199B ILE* 4.9 2.2 - - - -
247B LEU* 4.5 3.8 - - - -
251B VAL* 3.8 8.2 - - - +
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Residues in contact with PRO 178 (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 PHE* 4.1 4.3 - - + -
61B LEU* 6.2 0.2 - - + -
64B LEU* 3.8 37.5 - - + -
65B GLU* 4.4 5.8 - - + +
173B ASN* 3.9 0.8 - - - -
177B SER* 1.3 89.0 - - - +
179B VAL* 1.3 63.8 + - - +
180B LEU 3.2 0.7 + - - -
181B GLN 3.4 15.3 + - - +
182B GLN* 2.6 35.1 + - - +
193B TYR* 3.9 25.4 - - + +
199B ILE* 4.1 10.5 - - + -
247B LEU* 3.9 13.7 - - + -
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.6 25.3 - - + -
177B SER* 3.0 14.5 + - - +
178B PRO* 1.3 79.8 - - - +
180B LEU* 1.3 57.3 + - - +
247B LEU* 3.6 29.6 - - + +
248B SER* 3.8 24.9 - - - -
251B VAL* 4.0 15.7 - - + -
252B HIS* 3.5 27.6 + - + +
293B SER* 3.2 12.0 + - - -
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Residues in contact with LEU 180 (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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176B ALA* 3.3 29.8 - - + +
177B SER 3.1 3.0 + - - -
179B VAL* 1.3 80.0 - - - +
181B GLN* 1.3 60.9 + - - +
182B GLN* 5.7 0.7 - - - -
251B VAL* 3.7 14.8 - - + -
252B HIS* 3.5 33.2 - - + -
255B VAL* 4.0 9.6 - - + -
291B GLN 4.1 0.9 - - - +
292B MSE 3.5 6.7 - - + -
293B SER* 2.8 34.9 + - - +
294B ALA* 3.3 35.7 - - + +
296B GLY* 3.7 25.8 - - - +
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Residues in contact with GLN 181 (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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144B THR* 2.9 37.5 + - - +
155B VAL* 5.1 0.7 - - - -
171B VAL* 4.2 5.1 - - - +
173B ASN* 2.5 48.4 + - - +
176B ALA* 3.8 12.7 - - + +
177B SER 3.2 6.8 + - - +
178B PRO* 3.4 9.2 + - - +
179B VAL 3.7 0.6 - - - -
180B LEU* 1.3 81.4 - - - +
182B GLN* 1.3 66.7 + - - +
183B PRO* 3.4 4.2 - - + +
186B LEU* 4.1 16.4 - - + -
193B TYR* 4.5 0.2 + - - -
291B GLN* 3.4 31.5 + - - +
292B MSE 3.7 18.0 - - + +
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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