Contacts of the strand formed by residues 409 - 413 (chain A) in PDB entry 2OKC
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 TRP 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A THR* 4.0 16.6 - - + -
363A TRP* 3.4 53.6 - + + -
364A PHE 3.3 23.3 - - - -
365A TYR* 3.6 32.3 - + + -
388A PHE* 4.4 3.8 - + - -
391A CYS* 3.3 50.4 + - + +
392A TYR* 4.3 5.6 - - - -
394A ASN 3.7 3.8 + - - -
395A ARG* 3.8 24.0 - - - -
396A VAL 3.3 24.3 + - - -
397A GLU* 4.0 1.3 - - - -
398A ILE* 3.1 26.9 + - + +
399A TYR* 2.9 24.5 + - - -
407A GLY 3.3 0.8 - - - -
408A ARG* 1.3 77.4 - - - +
410A ARG* 1.3 59.3 + - - +
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Residues in contact with ARG 410 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A ILE 3.8 0.5 - - - +
363A TRP* 3.4 5.4 - - - -
364A PHE* 2.8 33.3 + - - +
397A GLU* 3.6 14.8 - - - +
399A TYR* 3.4 48.8 + - + -
409A TRP* 1.3 76.6 - - - +
411A LYS* 1.3 66.9 + - - +
412A TYR* 3.2 47.9 + - + -
416A GLU* 5.4 2.4 + - - -
429A TRP* 3.3 48.7 - - + +
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Residues in contact with LYS 411 (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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361A GLU* 2.9 38.7 + - + +
362A ILE 3.7 3.8 - - - +
363A TRP* 3.4 45.9 - - + +
397A GLU* 3.1 34.8 + - + +
410A ARG* 1.3 79.2 + - - +
412A TYR* 1.3 67.0 + - - +
413A PRO* 4.2 8.9 - - - +
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Residues in contact with TYR 412 (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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361A GLU* 3.3 2.2 - - - -
362A ILE* 2.8 40.9 + - - +
364A PHE* 3.6 25.4 - + - -
410A ARG* 3.2 58.0 + - + -
411A LYS* 1.3 78.9 - - - +
413A PRO* 1.3 67.3 - - + +
416A GLU* 3.7 25.4 - - + -
417A ILE* 3.8 22.0 - - + -
427A ILE* 3.2 39.8 - - + +
428A THR 4.9 0.5 + - - -
429A TRP* 3.6 12.0 - + - +
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Residues in contact with PRO 413 (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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360A LYS 3.7 8.7 - - - +
361A GLU* 4.3 6.7 - - + -
411A LYS* 4.2 9.8 - - - +
412A TYR* 1.3 89.2 - - + +
414A VAL* 1.3 66.7 + - - +
415A ASP* 3.2 20.9 + - - +
416A GLU* 3.3 42.0 + - + +
417A ILE* 3.7 5.9 + - - +
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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