Contacts of the helix formed by residues 252 - 257 (chain C) in PDB entry 5OA3
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 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C ARG* 3.6 22.9 - - - +
181C PRO* 5.3 8.1 - - + -
182C CYS* 5.8 1.1 - - - -
250C TYR* 3.4 21.1 + - + +
251C LEU* 1.3 90.5 - - - +
253C PRO* 1.3 74.6 - - - +
254C ASP* 2.8 31.7 + - - +
255C LEU* 3.3 13.4 + - + +
256C TRP* 3.3 4.0 - - - -
99W PHE* 4.6 16.8 - - + -
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Residues in contact with PRO 253 (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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252C THR* 1.3 90.5 - - - +
254C ASP* 1.3 62.5 + - - +
256C TRP* 3.2 50.8 - - + +
46W TYR* 3.7 21.5 - - + +
99W PHE* 3.8 30.7 - - + -
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Residues in contact with ASP 254 (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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166C ARG* 3.9 7.6 + - - +
173C LYS* 5.3 9.6 + - - -
252C THR* 2.8 15.5 + - - +
253C PRO* 1.3 81.2 - - - +
255C LEU* 1.3 65.4 + - + +
256C TRP 3.2 3.2 + - - -
257C LYS* 4.3 9.2 + - - +
1V MET* 3.3 49.4 + - + +
2V GLN* 4.9 5.2 + - - -
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Residues in contact with LEU 255 (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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166C ARG* 3.9 19.5 - - - +
250C TYR 4.2 7.2 - - - +
251C LEU* 4.6 4.0 - - + -
252C THR* 3.3 43.2 + - + +
253C PRO 3.2 0.8 - - - -
254C ASP* 1.3 83.9 - - + +
256C TRP* 1.3 60.0 + - - +
257C LYS* 3.0 22.3 + - - +
1V MET* 4.6 13.9 - - + -
10V ASP* 5.8 0.7 - - - +
13V VAL* 5.0 11.7 - - + -
14V PRO* 5.0 19.5 - - + -
16V LYS* 3.3 18.5 - - + +
23V ILE* 4.4 19.3 - - + -
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Residues in contact with TRP 256 (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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251C LEU* 3.2 32.4 - - + +
252C THR 3.3 7.9 + - - -
253C PRO* 3.2 36.3 - - + +
254C ASP 3.2 2.0 - - - -
255C LEU* 1.3 75.0 - - - +
257C LYS* 1.3 63.3 + - - +
258C GLU* 3.7 6.4 + - - +
16V LYS* 3.5 9.6 + - - +
21V ASN* 5.9 1.1 - - - -
44W HIS 3.3 23.1 - - - -
45W GLY 4.4 0.4 - - - -
46W TYR* 3.7 50.0 - + - -
68W ARG* 3.4 70.7 + - + +
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Residues in contact with LYS 257 (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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254C ASP 4.3 7.7 + - - +
255C LEU* 3.0 9.5 + - - +
256C TRP* 1.3 78.3 - - - +
258C GLU* 1.3 69.4 + - - +
259C THR* 3.6 3.1 + - - +
16V LYS* 2.7 22.5 + - - +
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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