Contacts of the strand formed by residues 257 - 260 (chain B) in PDB entry 2H1H
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 VAL 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B VAL* 3.2 15.9 - - + +
184B LEU* 4.0 25.8 - - + -
251B LEU* 3.9 15.7 - - + +
254B ALA* 4.1 13.2 - - + -
256B PHE* 1.3 83.1 - - - +
258B VAL* 1.3 72.6 + - - +
268B THR* 3.6 22.4 - - + +
273B ARG* 4.9 2.5 - - + -
274B PRO 2.9 9.3 + - - +
275B ASN* 3.4 17.6 - - - +
276B ILE* 2.7 36.6 + - - +
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL 3.1 3.9 + - - +
183B PHE* 3.3 33.8 - - + -
184B LEU 2.8 23.6 + - - -
194B TRP* 4.9 0.9 - - + -
199B TRP* 3.7 20.2 - - + -
202B LEU* 4.2 12.3 - - + -
256B PHE* 3.6 15.5 - - + -
257B VAL* 1.3 77.7 - - - +
259B SER* 1.3 65.3 + - - +
276B ILE* 3.1 14.4 - - + +
278B VAL* 4.6 9.6 - - + -
312B VAL* 4.4 12.1 - - + -
316B ILE* 4.0 16.4 - - + -
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Residues in contact with SER 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.3 36.1 - - - -
199B TRP* 4.2 2.2 - - - -
257B VAL* 4.2 0.2 - - - -
258B VAL* 1.3 78.6 - - - +
260B VAL* 1.3 62.4 + - - +
265B SER* 3.1 17.3 + - - -
275B ASN* 3.1 19.8 + - - -
276B ILE 2.7 11.3 + - - -
277B THR* 3.0 7.1 + - - -
278B VAL* 2.7 37.3 + - - +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU 3.0 18.3 + - - +
185B HIS 4.1 7.2 - - - +
186B ALA 3.5 25.8 - - - +
187B THR* 3.7 15.0 - - + -
192B LYS 3.6 22.2 - - - +
193B HIS* 4.4 1.3 - - - -
194B TRP 4.1 15.5 - - - +
199B TRP* 4.1 15.3 - - + -
259B SER* 1.3 81.9 + - - +
261B ASP* 1.3 59.2 + - - +
262B THR* 2.8 18.7 + - + +
265B SER* 3.7 5.5 - - - -
277B THR* 3.8 2.0 - - - +
278B VAL* 4.0 13.5 - - + -
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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