Contacts of the strand formed by residues 675 - 681 (chain B) in PDB entry 2OBF
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 675 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574B THR* 3.2 14.4 - - - +
576B ILE* 3.6 33.0 - - + +
672B PRO 3.9 3.8 + - - +
673B LEU* 4.0 0.4 - - - +
674B PRO* 1.3 74.1 - - - +
676B ASP* 1.3 63.4 + - - +
677B ALA 3.5 19.1 - - - +
678B LEU* 4.2 4.0 - - + -
704B LEU 2.8 11.6 + - - +
705B LEU* 3.4 2.7 - - + +
706B ARG* 3.0 26.2 + - - +
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Residues in contact with ASP 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571B SER 4.0 17.1 - - - +
572B GLY* 4.0 4.3 - - - -
573B ARG* 2.6 33.2 + - - +
574B THR* 2.9 23.6 + - - +
594B PHE* 4.0 4.3 - - + -
674B PRO 4.9 2.5 - - - +
675B ALA* 1.3 74.2 - - - +
677B ALA* 1.3 60.4 + - - +
705B LEU* 3.6 1.3 - - - -
706B ARG* 3.1 32.2 + - - +
709B GLY* 3.4 9.9 - - - -
710B HIS* 3.3 20.6 + - - +
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Residues in contact with ALA 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570B VAL* 4.3 11.9 - - + -
571B SER 5.6 0.2 - - - +
574B THR 3.4 2.0 + - - -
575B LEU* 3.4 12.7 - - + -
576B ILE 3.0 22.8 + - - -
594B PHE* 3.6 28.9 - - + -
675B ALA* 3.3 3.2 - - - +
676B ASP* 1.3 83.6 - - - +
678B LEU* 1.3 70.7 + - - +
679B VAL* 5.8 0.2 - - + -
705B LEU* 3.6 1.6 - - - -
710B HIS 3.1 13.7 - - - +
712B LEU* 6.5 0.7 - - + -
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Residues in contact with LEU 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B ILE* 3.2 34.5 - - + +
578B ILE* 4.3 11.2 - - + -
675B ALA* 4.2 9.4 - - + -
677B ALA* 1.3 83.8 - - - +
679B VAL* 1.3 67.2 + - - +
701B ILE* 3.2 46.0 - - + +
702B THR* 4.6 1.6 - - - +
704B LEU* 4.5 6.1 - - + +
705B LEU* 4.0 23.1 - - + -
710B HIS 2.9 8.0 + - - +
711B LEU* 3.3 17.8 - - + -
712B LEU* 2.9 25.3 + - - +
748B TYR* 4.8 1.3 - - - +
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Residues in contact with VAL 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561B LEU* 5.2 5.2 - - + -
565B PHE* 5.0 4.5 - - + -
575B LEU* 3.8 28.5 - - + -
576B ILE 2.9 7.2 + - - +
577B ASP* 3.0 19.8 - - + +
578B ILE* 2.6 34.4 + - - +
586B GLN* 3.9 31.4 - - + +
587B LEU* 4.5 4.9 - - + -
590B ALA* 5.1 0.4 - - + -
677B ALA* 5.8 0.2 - - + -
678B LEU* 1.3 79.2 - - - +
680B SER* 1.3 63.6 + - - +
681B ALA* 5.6 0.2 - - + -
711B LEU* 4.8 0.7 - - - -
712B LEU* 3.3 26.7 - - + +
714B ILE* 6.1 2.0 - - + -
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Residues in contact with SER 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B ASP* 4.1 1.6 - - - -
578B ILE* 2.8 36.2 + - - +
679B VAL* 1.3 79.6 - - - +
681B ALA* 1.3 61.6 + - - +
683B CYS* 3.7 14.8 + - - +
684B LEU* 4.8 4.2 + - - +
701B ILE* 5.1 3.4 - - - -
711B LEU* 4.9 3.8 - - - -
712B LEU 3.0 7.5 + - - +
713B LEU* 3.4 24.0 - - - +
714B ILE* 2.9 25.9 + - - +
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Residues in contact with ALA 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B ASP* 4.7 2.8 + - - -
578B ILE 4.2 3.0 + - - -
579B GLY 4.1 0.9 - - - +
585B TYR* 3.3 28.9 - - + +
586B GLN* 4.5 11.0 - - + -
679B VAL* 5.6 0.2 - - + -
680B SER* 1.3 76.8 + - - +
682B PHE* 1.3 70.3 + - + +
683B CYS* 3.1 4.2 + - - -
714B ILE* 3.2 23.3 - - + -
3002B SAH 2.9 33.3 + - - +
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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