Contacts of the helix formed by residues 176 - 181 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C THR 4.9 0.4 + - - +
145C PRO* 4.7 2.0 - - + -
173C ASN* 3.5 8.9 + - - +
174C THR 3.4 0.2 - - - -
175C PHE* 1.3 86.8 - - + +
177C SER* 1.3 76.1 + - - +
180C LEU* 3.4 32.2 - - + +
181C GLN* 3.7 34.1 - - + +
251C VAL* 4.9 1.2 - - - +
292C MSE 4.3 13.9 - - - -
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Residues in contact with SER 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ASN* 2.9 23.5 + - - -
174C THR 3.6 2.4 + - - -
175C PHE 3.5 1.8 - - - -
176C ALA* 1.3 89.9 + - - +
178C PRO* 1.4 69.6 - - - +
179C VAL* 3.1 29.0 + - - +
180C LEU 3.1 7.4 + - - -
181C GLN 3.2 8.3 + - - -
193C TYR* 4.2 1.8 - - - -
198C SER* 3.8 21.3 - - - -
199C ILE* 5.0 2.7 - - - -
247C LEU* 4.4 10.5 - - - -
251C VAL* 3.9 6.2 - - - +
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Residues in contact with PRO 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 3.3 17.0 - - + -
61C LEU* 5.9 1.3 - - + -
64C LEU* 4.0 24.9 - - + -
65C GLU* 4.1 10.3 - - + +
173C ASN* 3.8 0.2 - - - -
177C SER* 1.4 85.2 - - - +
179C VAL* 1.3 62.9 + - - +
180C LEU 3.3 0.7 - - - -
181C GLN 3.5 11.3 - - - +
182C GLN* 3.0 32.6 + - - +
193C TYR* 3.4 34.1 - - + +
199C ILE* 4.3 12.6 - - + -
247C LEU* 4.4 7.0 - - + -
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 3.8 19.2 - - + -
177C SER* 3.0 16.3 - - - +
178C PRO* 1.3 80.4 - - - +
180C LEU* 1.3 59.5 + - + +
182C GLN* 6.0 0.2 - - - +
247C LEU* 3.4 32.8 - - + +
248C SER* 4.0 12.8 - - - +
251C VAL* 3.8 19.3 - - + -
252C HIS* 3.6 34.7 + - + +
293C SER* 3.4 10.0 + - - -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C PHE 5.6 0.7 - - - +
176C ALA* 3.4 29.4 - - + +
177C SER 3.1 2.4 + - - -
179C VAL* 1.3 87.8 - - + +
181C GLN* 1.3 59.8 + - - +
182C GLN* 5.5 1.8 - - - -
251C VAL* 3.8 29.6 - - + -
252C HIS* 4.3 8.3 - - + +
255C VAL* 4.1 2.7 - - + -
291C GLN 4.1 0.3 - - - +
292C MSE 3.2 8.8 - - + -
293C SER* 3.0 36.1 + - - +
294C ALA* 3.7 32.1 - - + +
296C GLY* 3.8 34.1 - - - +
297C ALA 5.3 0.2 - - - +
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Residues in contact with GLN 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C THR* 3.1 31.9 + - - +
145C PRO* 4.8 0.2 - - - +
155C VAL* 5.2 0.9 - - - -
171C VAL* 4.3 6.1 - - - +
173C ASN* 2.7 47.5 + - - +
176C ALA* 3.7 12.8 - - + +
177C SER 3.2 6.1 + - - +
178C PRO* 3.5 9.0 - - - +
179C VAL 3.8 0.4 - - - -
180C LEU* 1.3 79.6 - - - +
182C GLN* 1.3 65.6 + - - +
183C PRO* 3.3 5.0 - - + +
186C LEU* 4.0 17.7 - - + -
291C GLN* 3.2 40.7 + - - +
292C MSE 3.9 14.2 - - + +
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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
------------------------------------------------------------
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