Contacts of the strand formed by residues 236 - 239 (chain C) in PDB entry 3P71
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 LEU 236 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C GLN 3.9 1.3 + - - +
163C ILE* 3.6 30.0 - - + +
164C PHE* 2.9 27.7 + - - +
229C ASN* 4.3 3.7 - - - +
234C LEU* 3.6 2.6 - - - +
235C THR* 1.3 88.1 + - - +
237C VAL* 1.3 68.1 + - - +
250C TRP* 3.6 25.4 - - + -
254C ARG 3.6 21.5 - - - +
255C ASN 3.6 12.6 - - - +
257C VAL* 3.8 27.8 - - + +
276C MET* 4.5 13.7 - - + -
278C LEU* 5.6 1.1 - - + -
284C TYR* 5.9 2.9 - - + -
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Residues in contact with VAL 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C PHE* 3.4 24.9 - - + +
166C LEU* 3.9 24.2 - - + -
169C GLY* 5.8 0.7 - - - -
170C LEU* 4.5 16.2 - - + -
220C PHE* 5.7 2.7 - - + -
225C SER* 5.6 1.6 - - - +
228C PHE* 4.4 10.1 - - + -
229C ASN* 3.4 22.6 + - - +
236C LEU* 1.3 73.4 - - - +
238C SER* 1.3 61.8 + - - +
239C ARG* 5.0 3.6 - - + -
255C ASN 2.9 14.7 + - - +
256C VAL* 3.3 22.1 - - + +
257C VAL 3.0 26.3 + - - +
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Residues in contact with SER 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.9 2.4 - - - +
83C MET* 3.7 11.4 - - - +
163C ILE* 4.4 7.0 - - - -
164C PHE 2.7 11.3 + - - +
165C CYS* 3.8 19.5 - - - -
166C LEU* 3.2 27.7 + - - +
236C LEU* 3.9 1.2 - - - -
237C VAL* 1.3 73.8 - - - +
239C ARG* 1.3 64.9 + - - +
257C VAL* 3.6 15.0 - - - -
259C ILE* 3.4 19.2 - - - +
276C MET* 3.8 13.7 - - - +
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Residues in contact with ARG 239 (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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83C MET* 3.4 10.3 - - - +
166C LEU* 3.1 20.6 - - + +
167C HIS 3.7 2.5 - - - +
168C GLY 2.4 31.2 + - - +
169C GLY* 5.1 0.7 - - - -
201C SER 3.4 1.4 + - - -
202C ASP* 3.1 25.5 + - - -
203C PRO* 3.4 17.6 - - - +
220C PHE* 5.0 3.8 - - - -
237C VAL* 5.0 2.9 - - + -
238C SER* 1.3 79.5 + - - +
240C ALA* 1.3 76.1 + - - +
241C HIS* 3.3 9.9 - - - +
242C GLN* 3.1 21.2 - - - +
256C VAL* 3.8 19.3 - - + -
257C VAL 3.0 15.8 + - - +
258C THR* 2.7 39.1 + - - +
259C ILE* 2.7 32.2 + - - +
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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