Contacts of the helix formed by residues 4214 - 4218 (chain C) in PDB entry 4O2W
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 GLY4214 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4213C ASP* 1.3 77.7 + - - +
4215C ASP* 1.3 68.9 + - - +
4217C GLY* 3.0 15.2 + - - -
4218C LYS 4.6 1.3 - - - -
4219C LEU* 4.0 11.0 - - - -
4223C ASN 3.8 0.8 - - - +
4224C SER* 3.0 33.3 + - - -
4225C THR 3.8 10.1 - - - -
4226C ALA* 3.7 6.9 - - - +
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Residues in contact with ASP4215 (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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4196C ASN* 5.6 0.3 + - - -
4213C ASP* 2.9 18.9 + - - +
4214C GLY* 1.3 79.7 - - - +
4216C TYR* 1.3 84.7 + - + +
4217C GLY 3.0 3.3 + - - -
4218C LYS* 3.3 18.7 + - - +
4224C SER* 4.3 6.0 - - - +
4249C GLN* 3.7 10.8 + - - +
4401C UNX 1.9 37.0 + - - -
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Residues in contact with TYR4216 (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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4214C GLY 3.4 0.4 + - - -
4215C ASP* 1.3 80.4 - - + +
4217C GLY* 1.3 54.8 + - - +
4218C LYS 3.3 0.2 - - - -
4224C SER* 4.0 7.1 + - - -
4249C GLN* 3.4 44.4 - - + +
4264C GLY* 3.1 11.1 - - - -
4265C GLN* 3.5 57.6 + - + +
4266C ASP* 5.4 2.5 - - - -
4279C HIS* 2.6 38.5 + + - -
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Residues in contact with GLY4217 (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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4214C GLY 3.0 6.3 + - - -
4215C ASP 3.0 1.0 + - - -
4216C TYR* 1.3 77.9 - - - +
4218C LYS* 1.3 56.9 + - - +
4219C LEU 3.2 3.4 - - - -
4220C GLY* 3.0 19.8 + - - -
4223C ASN 3.4 14.1 - - - -
4224C SER* 3.8 5.2 + - - -
4263C PHE* 3.9 0.7 - - - -
4264C GLY* 3.9 3.0 + - - -
4279C HIS 3.6 3.3 - - - +
4280C ASN* 3.3 37.1 - - - -
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Residues in contact with LYS4218 (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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4196C ASN* 2.6 29.4 + - - -
4197C HIS* 3.7 28.0 + - + +
4199C LEU* 4.8 0.3 - - - +
4213C ASP* 3.2 37.5 + - - +
4214C GLY 4.0 1.0 + - - -
4215C ASP 3.3 11.8 + - - +
4216C TYR 3.3 1.8 - - - -
4217C GLY* 1.3 76.0 - - - +
4219C LEU* 1.3 58.4 + - - +
4220C GLY 3.3 0.4 - - - -
4248C THR 3.4 8.5 + - - -
4249C GLN* 2.8 57.3 + - - +
4250C PHE* 3.9 7.4 - - - -
4251C SER* 2.7 25.1 + - - -
4263C PHE* 3.2 11.8 - - - -
4264C GLY* 3.8 7.6 - - - -
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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