Contacts of the helix formed by residues 169 - 174 (chain A) in PDB entry 1OVM
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 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 4.1 16.4 - - + +
33A GLN* 5.9 7.5 - - + +
102A ALA 2.9 18.7 + - - +
103A PRO* 4.2 1.4 + - + -
104A GLY* 4.9 6.1 - - - +
167A LEU 3.4 2.8 + - - -
168A PRO* 1.3 71.5 - - - +
170A ASP* 1.3 63.2 + - - +
172A ALA* 3.3 20.7 + - - +
173A LYS* 3.6 12.7 + - - +
549B CYS 5.8 0.9 - - - +
550B ASN* 4.2 26.9 - - + +
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Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLY* 3.2 9.2 - - - -
105A THR* 3.0 46.4 + - - +
106A ALA 5.0 0.6 + - - -
168A PRO* 3.5 7.4 - - - +
169A ALA* 1.3 73.0 - - - +
171A VAL* 1.3 71.6 + - - +
173A LYS* 3.1 21.4 + - - +
174A LYS* 3.5 29.3 + - - +
550B ASN 5.7 2.0 - - - -
551B ASN 6.1 0.9 - - - +
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.4 14.8 - - + +
105A THR* 3.9 16.2 - - + -
140A LEU* 3.7 25.8 - - + +
141A THR* 4.0 26.5 - - - +
142A GLU* 4.0 9.4 - - + +
145A ALA* 4.7 3.4 - - + -
167A LEU* 4.0 13.5 - - + -
168A PRO* 3.0 24.3 + - + +
170A ASP* 1.3 78.9 - - - +
172A ALA* 1.3 63.9 + - - +
174A LYS* 3.0 25.1 + - + +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A CYS* 3.3 13.0 - - - +
7A VAL* 3.6 4.9 + - - -
8A ALA* 3.1 31.9 + - + +
33A GLN* 6.5 0.9 - - + -
34A PHE* 4.8 12.6 - - + +
37A HIS* 6.1 0.4 - - + -
167A LEU* 4.0 31.3 - - + +
168A PRO 3.1 6.5 + - - +
169A ALA* 3.4 14.1 - - - +
170A ASP 3.2 0.4 - - - -
171A VAL* 1.3 77.8 - - - +
173A LYS* 1.3 59.9 + - + +
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A CYS* 3.6 13.4 - - - +
33A GLN* 2.9 33.5 - - + +
37A HIS* 6.0 3.1 - - - +
169A ALA* 3.9 13.5 - - - +
170A ASP* 3.1 12.1 + - - +
172A ALA* 1.3 76.1 - - + +
174A LYS* 1.3 66.6 + - + +
175A ALA* 3.6 1.6 + - - -
550B ASN 2.8 20.7 + - - +
551B ASN* 2.7 35.5 + - - +
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A CYS* 3.0 3.5 - - - +
7A VAL* 2.9 37.4 + - + +
142A GLU* 2.9 53.8 + - + +
170A ASP* 3.5 32.3 + - - +
171A VAL* 3.0 19.4 + - + +
173A LYS* 1.3 78.0 - - + +
175A ALA* 1.3 66.1 + - - +
316C ASP 5.6 0.2 - - - -
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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
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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