Contacts of the strand formed by residues 256 - 259 (chain A) in PDB entry 5A2E
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 GLY 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLY 3.4 12.8 - - - -
173A ARG* 4.2 0.2 - - - -
174A VAL* 4.0 4.5 - - - -
190A TRP* 3.0 24.4 + - - -
211A LEU* 3.1 23.9 + - - +
212A PRO 4.4 2.0 + - - -
216A PHE* 4.1 14.8 - - - -
254A ASP 3.9 0.4 + - - -
255A ALA* 1.3 73.6 - - - +
257A VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 3.5 39.7 - - + -
171A ALA* 3.5 2.4 - - - -
172A GLY 3.1 26.6 + - - -
174A VAL* 3.6 11.2 - - + -
190A TRP* 4.8 1.6 - - + -
195A ALA* 3.6 32.5 - - + +
198A VAL* 4.0 8.5 - - + -
199A CYS* 3.8 21.3 - - - -
209A GLN 3.6 8.5 - - - +
211A LEU 4.6 0.4 - - - +
216A PHE* 3.8 4.1 - - - -
256A GLY* 1.3 74.2 - - - +
258A VAL* 1.3 72.9 + - - +
259A CYS* 4.2 1.8 - - - -
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A CYS 4.3 2.2 - - - -
171A ALA* 4.4 2.0 - - + -
207A ALA* 3.9 2.1 - - - -
208A VAL* 2.9 32.5 + - + +
209A GLN* 3.1 27.2 + - + +
211A LEU* 3.3 34.1 - - + -
215A HIS* 5.7 0.9 - - + -
216A PHE* 4.4 5.2 - - + -
257A VAL* 1.3 75.5 - - - +
259A CYS* 1.3 68.2 + - - +
262A HIS* 4.2 24.0 - - + -
281A HIS* 4.8 14.8 - - + +
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Residues in contact with CYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 4.7 3.8 - - - -
170A CYS* 3.2 22.0 + - + +
198A VAL* 5.0 1.3 - - - -
199A CYS* 2.0 50.5 - - - -
202A LEU* 5.3 0.9 - - - -
204A CYS* 3.5 28.3 - - + +
206A TRP 3.5 5.2 - - - -
208A VAL* 3.8 8.0 - - - +
257A VAL* 4.2 11.9 - - - -
258A VAL* 1.3 78.6 - - - +
260A SER* 1.3 64.8 + - - +
261A GLU 3.4 0.4 - - - -
262A HIS* 3.4 15.9 + - - +
281A HIS* 6.0 1.0 - - - -
284A GLY 5.2 0.3 + - - -
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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