Contacts of the strand formed by residues 263 - 267 (chain A) in PDB entry 4QYJ
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 ALA 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A VAL* 4.7 9.9 - - + -
239A ALA 3.4 8.5 + - - +
240A LYS* 3.3 25.2 - - + -
241A VAL* 2.9 26.9 + - - +
262A LYS* 1.3 77.0 - - - +
264A VAL* 1.3 59.6 + - - +
485A HIS 5.7 1.1 - - - +
474B VAL* 5.4 2.8 - - - +
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Residues in contact with VAL 264 (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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240A LYS* 4.5 4.9 - - - +
241A VAL* 3.3 30.5 - - + -
253A ILE* 4.2 3.1 - - + +
254A GLY* 5.1 5.6 - - - +
257A CYS* 3.8 20.2 - - + -
262A LYS 4.8 2.7 - - - +
263A ALA* 1.3 77.4 - - - +
265A SER* 1.3 60.4 + - - +
266A LEU* 3.8 24.7 - - + -
474A VAL* 3.7 25.5 - - + +
475A GLY* 5.7 0.5 - - - -
485A HIS* 5.9 2.8 - - - -
258B GLY* 6.4 0.9 - - - -
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Residues in contact with SER 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LYS* 4.6 5.5 + - - -
240A LYS* 3.9 20.1 - - - +
241A VAL 2.6 10.2 + - - +
242A ALA* 3.7 21.9 - - - +
243A PHE 2.8 27.5 + - - -
264A VAL* 1.3 72.7 - - - +
266A LEU* 1.3 67.2 + - - +
267A GLU 5.1 0.2 + - - -
474A VAL 4.2 4.0 + - - -
475A GLY* 5.9 3.3 - - - -
476A ARG 5.5 2.4 + - - -
477A GLU* 4.0 15.8 + - - -
485A HIS* 6.5 0.9 - - - -
486A TYR* 5.4 1.4 + - - -
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Residues in contact with LEU 266 (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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243A PHE* 3.4 32.8 - - + -
250A GLY* 3.7 28.0 - - - +
253A ILE* 4.3 5.8 - - + -
254A GLY* 4.7 6.7 - - - +
264A VAL* 3.8 23.8 - - + -
265A SER* 1.3 83.2 + - - +
267A GLU* 1.3 60.3 + - - +
268A LEU* 3.8 9.0 - - + -
472A SER 4.0 0.2 - - - +
473A GLY* 3.3 4.9 - - - -
474A VAL* 3.2 47.0 + - + +
475A GLY 5.1 2.1 - - - +
258B GLY 5.0 0.9 - - - +
261B LEU* 3.9 23.3 - - + -
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Residues in contact with GLU 267 (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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174A MET* 6.1 0.4 - - + -
178A LYS* 5.1 4.7 - - - +
243A PHE 3.0 10.1 + - - -
244A THR* 3.2 45.2 - - + +
245A GLY 3.5 2.1 + - - +
265A SER* 5.1 0.8 + - - -
266A LEU* 1.3 70.3 - - - +
268A LEU* 1.3 66.6 + - - +
301A CYS* 5.9 3.7 - - - +
428A LEU* 6.2 4.0 - - + -
466A PHE* 5.4 13.5 - - + -
472A SER 3.8 3.1 - - - -
477A GLU* 6.2 0.9 - - + +
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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