Contacts of the strand formed by residues 417 - 422 (chain A) in PDB entry 2OCA
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 LEU 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A ASN* 4.1 9.0 - - + +
350A ALA 4.3 1.6 - - - -
351A PHE* 3.4 46.2 - - + +
392A LEU* 4.1 9.3 - - + +
408A PHE* 5.2 4.7 - - + -
414A VAL* 3.3 29.8 - - + -
415A LYS 2.6 11.7 + - - +
416A ASN* 1.3 71.0 - - - +
418A HIS* 1.3 60.7 + - - +
419A HIS 3.8 16.4 - - - +
420A VAL* 3.8 19.1 - - + -
440A LEU* 3.9 22.9 - - + +
446A LYS* 4.7 8.4 - - - +
447A THR 5.8 0.2 + - - -
449A ALA* 3.2 19.1 - - - +
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Residues in contact with HIS 418 (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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348A GLU* 3.3 24.2 + - + +
349A ASN* 2.7 44.2 + - - +
397A LYS* 3.6 22.6 - - - -
416A ASN* 3.1 29.5 + - + -
417A LEU* 1.3 75.3 - - - +
419A HIS* 1.3 81.0 + - + +
446A LYS* 3.8 34.2 - - + +
448A ILE 4.7 1.0 - - - +
449A ALA* 3.3 6.9 - - - +
450A THR* 3.0 27.2 + - - +
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Residues in contact with HIS 419 (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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343A LEU* 3.7 40.9 - - + +
346A LYS* 4.8 5.4 - - - -
348A GLU* 3.4 36.1 + - + -
349A ASN 3.0 11.8 + - - +
350A ALA* 3.4 7.0 - - + -
351A PHE* 2.8 29.4 + - - +
417A LEU* 3.7 4.2 - - - +
418A HIS* 1.3 90.1 - - + +
420A VAL* 1.3 64.7 + - - +
421A VAL* 4.2 0.4 - - + -
450A THR* 3.3 30.6 - - + +
452A TRP* 3.1 27.0 + + + +
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Residues in contact with VAL 420 (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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351A PHE* 3.4 9.0 - - + +
353A MET* 3.8 25.6 - - + -
408A PHE* 4.8 2.5 - - + -
417A LEU* 3.8 24.7 - - + -
419A HIS* 1.3 80.2 - - - +
421A VAL* 1.3 62.4 + - - +
422A LEU* 4.1 4.3 - - + -
436A ILE* 3.6 44.9 - - + -
440A LEU* 5.2 2.9 - - + -
449A ALA* 5.3 3.8 - - + -
450A THR 3.2 6.2 + - - +
451A VAL* 3.4 10.9 - - + +
452A TRP* 2.8 26.7 + - - -
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Residues in contact with VAL 421 (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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336A ILE* 4.3 16.2 - - + -
339A LEU* 3.7 33.9 - - + -
340A ALA* 5.5 2.9 - - + -
343A LEU* 4.4 11.7 - - + -
350A ALA* 5.0 5.4 - - + -
351A PHE 2.6 16.9 + - - +
352A VAL* 3.6 14.6 - - + +
353A MET* 2.8 28.0 + - - -
420A VAL* 1.3 74.8 - - - +
422A LEU* 1.3 63.3 + - - +
423A ALA 3.0 4.2 + - - -
452A TRP* 3.9 17.5 - - + -
454A LEU* 4.1 18.8 - - + -
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Residues in contact with LEU 422 (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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353A MET* 4.1 12.8 - - + -
405A TYR* 3.9 31.4 - - + +
420A VAL* 4.1 12.3 - - + -
421A VAL* 1.3 70.3 - - - +
423A ALA* 1.3 62.4 + - - +
424A HIS 3.2 4.9 + - - +
425A GLY* 4.3 5.5 + - - +
426A VAL* 4.1 24.9 - - + -
432A VAL* 4.3 9.2 - - + -
433A LEU* 5.5 4.7 - - + -
436A ILE* 4.3 10.8 - - + -
451A VAL* 4.1 17.0 - - + -
452A TRP 3.1 15.1 + - - +
453A ASP* 4.4 19.1 - - + +
454A LEU* 3.6 23.7 + - - +
488A TYR* 5.7 1.3 - - - +
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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