Contacts of the helix formed by residues 172 - 181 (chain O) in PDB entry 5A0Q
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 GLN 172 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32O ILE* 6.1 1.2 - - - +
33O ASN* 3.5 29.8 + - - +
38O THR* 4.5 2.2 - - - +
167O ALA* 3.9 10.3 - - - +
168O ALA* 3.8 20.5 - - - +
169O GLY 3.3 28.9 + - - +
170O VAL 3.1 3.9 + - - +
171O LYS* 1.4 78.1 - - - +
173O THR* 1.3 60.5 + - + +
175O SER* 2.8 17.6 + - - -
176O THR* 2.7 27.9 + - - -
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Residues in contact with THR 173 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O VAL 5.4 1.6 - - - +
172O GLN* 1.3 82.8 - - + +
174O GLU* 1.3 87.8 + - + +
176O THR* 3.2 17.5 + - - -
177O SER* 3.4 15.9 + - - -
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Residues in contact with GLU 174 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O VAL 4.1 2.9 - - - +
171O LYS* 3.3 52.8 + - + +
173O THR* 1.3 96.2 - - + +
175O SER* 1.4 58.3 + - - +
177O SER* 3.9 14.6 + - - -
178O PHE* 4.0 3.3 + - - +
205O VAL* 3.7 23.8 - - + +
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Residues in contact with SER 175 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O THR* 4.9 2.7 - - - +
40O VAL* 4.4 6.4 - - - +
167O ALA* 3.2 21.8 - - - +
171O LYS 3.0 14.1 + - - -
172O GLN* 2.8 21.3 + - - -
174O GLU* 1.4 72.7 - - - +
176O THR* 1.4 61.8 + - - +
177O SER 3.2 2.2 - - - -
178O PHE* 3.0 6.6 + - - +
179O LEU* 3.0 23.7 + - - +
201O CYS* 3.4 21.4 - - - -
205O VAL* 3.3 17.4 - - - +
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Residues in contact with THR 176 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O PHE* 6.3 2.0 - - + -
167O ALA* 4.6 10.4 + - - +
172O GLN* 2.7 24.2 + - - +
173O THR* 3.2 10.4 + - - -
175O SER* 1.4 75.1 + - - +
177O SER* 1.3 57.1 + - - +
179O LEU* 3.4 13.6 + - + +
180O GLU* 3.0 27.7 + - + +
53P SER* 4.1 25.8 - - - +
55P LEU* 4.0 8.9 - - + +
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Residues in contact with SER 177 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173O THR 3.4 11.2 + - - -
174O GLU* 4.0 9.7 + - - -
175O SER 3.2 0.4 - - - -
176O THR* 1.3 79.7 - - - +
178O PHE* 1.3 57.3 + - - +
180O GLU* 3.2 13.9 + - - +
181O LYS* 3.0 40.7 + - - +
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Residues in contact with PHE 178 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174O GLU 4.0 2.6 + - - +
175O SER 3.0 9.4 + - - +
177O SER* 1.3 79.6 - - - +
179O LEU* 1.3 58.3 + - - +
181O LYS* 3.5 18.0 + - + +
182O LYS* 3.4 59.1 + - + +
197O THR* 4.7 3.8 - - + -
200O THR* 3.9 22.7 - - - -
201O CYS* 3.6 35.7 - - + -
204O THR* 4.5 18.8 - - + -
205O VAL* 4.3 16.8 - - + -
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Residues in contact with LEU 179 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O VAL* 4.0 20.6 - - + -
42O VAL* 4.6 9.0 - - + -
165O ALA* 2.6 40.8 - - + +
166O THR 3.6 16.6 - - - +
167O ALA* 3.9 13.7 - - + +
175O SER 3.0 14.1 + - - +
176O THR* 3.5 21.1 - - + +
178O PHE* 1.3 74.4 - - + +
180O GLU* 1.4 61.4 + - - +
182O LYS* 3.2 23.7 + - - +
197O THR* 5.0 7.9 - - + -
201O CYS* 4.2 11.7 - - + -
55P LEU* 3.5 22.1 - - + +
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Residues in contact with GLU 180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176O THR* 3.0 18.3 + - + +
177O SER* 3.2 10.8 + - - +
179O LEU* 1.4 72.7 - - - +
181O LYS* 1.4 65.0 + - + +
182O LYS 3.4 4.5 + - - -
52P LYS 5.3 0.7 - - - +
53P SER* 3.2 20.7 - - - +
54P ILE* 2.7 46.5 - - + +
55P LEU* 3.6 10.5 - - + -
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Residues in contact with LYS 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O SER* 3.0 25.0 + - - +
178O PHE* 3.6 23.3 - - + +
179O LEU 3.3 0.4 - - - -
180O GLU* 1.4 77.8 - - - +
182O LYS* 1.3 75.4 + - - +
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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