Contacts of the strand formed by residues 427 - 430 (chain A) in PDB entry 2OK5
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 427 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 3.8 24.4 - - + +
174A GLY* 5.2 1.3 - - - +
402A VAL* 3.5 4.7 - - + +
414A ILE* 3.6 50.3 - - + +
415A ASN* 3.4 26.9 - - + +
418A ALA* 3.7 13.2 - - + -
419A SER 5.1 2.7 - - - +
420A LYS* 6.1 0.2 - - - -
425A GLN* 2.9 27.6 + - + +
426A HIS* 1.3 84.5 - - + +
428A PHE* 1.3 63.4 + - - +
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Residues in contact with PHE 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 4.0 2.2 - - - -
200A ASP* 3.6 3.6 - - - -
205A VAL* 3.7 35.0 - - + -
208A ALA* 3.7 20.4 - - + -
209A PHE* 4.1 19.3 - + + -
401A TYR* 4.2 11.2 - + - -
402A VAL 2.9 16.6 + - - +
403A PHE* 3.6 38.1 - + + -
404A GLY* 2.7 32.0 + - - -
414A ILE* 4.0 5.7 - - - +
425A GLN* 3.3 50.0 - - + -
426A HIS 4.0 12.1 - - - -
427A VAL* 1.3 72.5 - - - +
429A LYS* 1.3 58.8 + - - +
430A VAL* 5.3 2.2 - - + -
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Residues in contact with LYS 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 3.7 13.9 - - - +
194A GLN* 6.1 0.2 - - - +
195A ASP 5.1 0.2 + - - -
196A SER* 3.9 20.6 + - - +
198A MET 3.8 18.0 + - - +
199A TYR* 3.5 24.1 - - + -
200A ASP* 2.7 41.0 + - - +
404A GLY 3.3 4.0 - - - +
406A GLY 3.6 21.1 - - - +
407A PRO* 4.4 12.6 + - - +
409A VAL* 4.1 22.3 + - + +
411A GLN* 3.6 36.5 - - - +
414A ILE* 4.9 4.0 - - + -
428A PHE* 1.3 74.3 - - - +
430A VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TYR* 3.3 11.0 - - - -
200A ASP 3.6 15.9 - - - +
202A PRO 4.9 1.6 - - - -
205A VAL* 4.0 20.2 - - + -
403A PHE* 6.0 0.4 - - + -
404A GLY 3.0 12.7 + - - +
405A VAL* 3.7 4.9 - - + -
406A GLY 2.9 25.1 + - - +
428A PHE* 5.3 2.5 - - + -
429A LYS* 1.3 73.8 - - - +
431A LYS* 1.3 59.4 + - - +
432A ASP 3.6 19.1 - - - +
435A ASN* 4.1 7.6 - - + +
436A LEU* 3.8 25.4 - - + +
439A VAL* 4.2 16.2 - - + -
1354A GOL 3.5 9.4 - - - +
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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