Contacts of the helix formed by residues 176 - 180 (chain K) in PDB entry 4HOK
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 THR 176 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127K ARG 4.7 0.8 + - - -
128K ASP* 2.9 22.4 + - - +
129K VAL 5.9 0.7 - - - -
130K LYS* 3.5 23.0 + - + +
175K GLY* 1.3 68.6 - - - -
177K ALA* 1.3 69.3 + - + +
178K ARG* 4.0 13.9 - - + +
179K TYR* 3.4 27.5 + - + +
180K ALA* 3.1 20.9 + - - +
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Residues in contact with ALA 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K LEU* 4.2 11.6 - - + +
175K GLY 3.4 4.6 + - - -
176K THR* 1.3 71.5 - - - +
178K ARG* 1.3 65.5 + - - +
180K ALA* 2.9 19.5 + - - +
185K HIS* 3.6 9.9 + - + -
224K LYS* 5.7 0.2 - - + -
225K TYR* 3.5 41.5 + - + +
228K ILE* 3.9 16.2 - - + -
232K LYS* 3.1 10.8 + - - -
301K SO4 5.8 1.8 - - - +
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Residues in contact with ARG 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K GLU* 6.0 0.2 - - - -
98K ARG* 4.8 2.0 - - - +
176K THR* 3.5 11.9 - - + +
177K ALA* 1.3 78.4 - - - +
179K TYR* 1.3 99.5 + - + +
205K TYR* 3.4 15.4 + - - -
211K LEU* 3.9 8.9 - - + +
213K TRP* 2.7 38.9 + - - +
214K GLN* 2.8 49.0 - - + +
228K ILE* 4.7 1.5 - - - +
232K LYS* 3.2 4.3 + - - -
301K SO4 2.6 41.2 + - - +
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Residues in contact with TYR 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K GLU* 4.7 0.9 + - - -
129K VAL 3.7 16.2 - - - +
130K LYS* 3.3 35.9 - - + -
131K PRO* 3.6 15.2 - - + +
132K ASP* 5.6 1.0 + - - -
176K THR* 3.4 20.7 + - + +
177K ALA 3.2 0.6 - - - -
178K ARG* 1.3 121.2 + - + +
180K ALA* 1.3 65.5 + - - +
198K SER* 2.9 33.0 + - - +
201K TYR* 3.7 7.3 - - + -
202K VAL* 3.9 20.2 - - + -
205K TYR* 3.6 23.7 + + + -
211K LEU* 3.9 15.9 - - + -
232K LYS* 4.0 0.7 - - - +
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Residues in contact with ALA 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173K LEU* 3.8 25.4 - - + -
175K GLY* 5.5 0.9 - - - -
176K THR 3.1 13.6 + - - +
177K ALA 2.9 15.6 + - - +
179K TYR* 1.3 77.4 - - - +
181K SER* 1.3 62.8 + - - +
184K THR* 4.1 10.1 - - + -
185K HIS* 3.7 8.7 - - + +
190K GLN* 5.7 0.4 - - - +
198K SER* 4.2 2.7 - - - -
201K TYR* 3.9 1.8 - - - -
232K LYS* 2.7 28.9 + - - +
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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