Contacts of the strand formed by residues 705 - 717 (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 LEU 705 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674B PRO* 3.9 3.3 - - - +
675B ALA 3.4 17.3 - - - +
676B ASP 3.5 18.8 - - - +
677B ALA* 3.6 20.9 - - - -
678B LEU* 4.0 14.8 - - + +
702B THR 3.1 10.7 + - - +
703B THR 4.3 1.6 - - - +
704B LEU* 1.3 79.0 - - - +
706B ARG* 1.3 65.8 + - - +
709B GLY* 3.8 9.6 - - - +
710B HIS 3.8 22.7 - - - +
711B LEU* 4.2 3.6 - - + +
748B TYR* 3.9 28.7 - - + +
779B LYS* 2.6 38.9 + - + -
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Residues in contact with ARG 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B SER 4.4 14.6 + - - -
674B PRO* 3.6 26.7 - - + +
675B ALA 3.0 17.5 + - - +
676B ASP* 3.1 32.3 + - - +
705B LEU* 1.3 77.5 - - - +
707B PRO* 1.3 90.1 + - + +
708B GLY* 3.1 26.5 + - - -
709B GLY* 2.9 28.6 + - - -
710B HIS* 5.3 4.9 - - - -
779B LYS* 3.4 6.8 - - - +
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Residues in contact with PRO 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B PRO* 5.2 2.5 - - + -
705B LEU 4.3 2.0 - - - +
706B ARG* 1.3 103.9 + - + +
708B GLY* 1.3 57.7 + - - +
779B LYS* 3.9 20.6 - - + +
781B GLY* 4.0 4.7 - - - -
782B LEU* 3.8 55.0 - - + +
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Residues in contact with GLY 708 (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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706B ARG* 3.1 17.4 + - - -
707B PRO* 1.3 70.0 - - - +
709B GLY* 1.3 61.7 + - - +
710B HIS* 4.0 4.9 + - - -
778B GLN* 3.1 28.5 + - - -
779B LYS 2.8 20.8 + - - -
781B GLY 4.2 8.9 + - - -
782B LEU 5.0 1.8 - - - -
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Residues in contact with GLY 709 (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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676B ASP 3.4 14.8 - - - -
705B LEU* 3.8 7.6 - - - -
706B ARG* 2.9 28.3 + - - +
707B PRO 3.1 0.8 - - - -
708B GLY* 1.3 83.0 - - - +
710B HIS* 1.3 59.9 + - - -
778B GLN* 3.3 4.0 - - - +
779B LYS 2.9 24.4 + - - -
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Residues in contact with HIS 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B GLU* 3.1 27.3 + - + -
570B VAL* 3.9 27.1 - - + -
571B SER 5.2 2.9 - - - -
676B ASP 3.3 9.3 + - - -
677B ALA* 3.1 7.2 - - + +
678B LEU 2.9 25.1 + - - +
705B LEU* 3.8 4.8 - - - +
706B ARG* 5.3 4.9 - - - -
708B GLY 4.0 4.6 + - - -
709B GLY* 1.3 77.7 - - - -
711B LEU* 1.3 60.9 + - - +
712B LEU* 5.3 1.3 - - + -
751B ARG* 4.0 8.7 - - - -
776B TRP* 3.0 31.5 + + + +
777B ALA 3.5 3.1 - - - +
778B GLN* 3.2 44.6 + - + +
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Residues in contact with LEU 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B LEU* 3.3 26.7 - - + +
679B VAL* 4.4 1.6 - - - +
680B SER* 4.7 4.3 - - - +
698B LEU* 4.2 12.6 - - + -
701B ILE* 4.9 5.6 - - + -
705B LEU* 4.2 3.8 - - + +
710B HIS* 1.3 75.8 - - - +
712B LEU* 1.3 85.2 + - - +
713B LEU* 4.4 18.4 - - + +
743B LEU* 4.2 17.3 - - + -
748B TYR* 3.6 45.5 - - + +
775B ALA 3.5 1.7 - - - +
777B ALA* 2.7 38.2 + - + +
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Residues in contact with LEU 712 (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* 4.1 16.2 - - + -
564B THR* 3.8 24.9 - - + -
565B PHE* 3.4 40.4 - - + -
570B VAL* 5.0 8.5 - - + -
678B LEU 2.9 13.2 + - - +
679B VAL* 3.3 12.9 - - + +
680B SER 3.0 25.8 + - - +
710B HIS* 5.3 1.1 - - + -
711B LEU* 1.3 82.9 - - - +
713B LEU* 1.3 58.9 + - - +
714B ILE* 5.5 1.6 - - - -
774B PHE* 4.3 11.0 - - + -
775B ALA 3.3 3.8 - - - +
776B TRP* 3.6 30.3 - - + -
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Residues in contact with LEU 713 (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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680B SER* 3.4 32.1 - - - +
684B LEU* 4.6 26.0 - - + +
685B GLU* 6.1 0.4 - - - +
694B PHE* 5.0 7.4 - - + -
698B LEU* 5.0 4.5 - - + -
701B ILE* 5.4 1.1 - - + -
711B LEU* 3.9 19.5 - - + -
712B LEU* 1.3 73.5 - - - +
714B ILE* 1.3 65.4 + - - +
739B VAL* 4.7 7.9 - - + -
743B LEU* 4.4 20.4 - - + -
773B PHE* 3.7 24.4 - - + +
774B PHE* 3.4 2.8 - - - -
775B ALA* 2.6 50.7 + - + +
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Residues in contact with ILE 714 (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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556B TRP* 5.5 2.7 - - + -
557B ALA* 4.9 13.5 - - + -
561B LEU* 4.2 29.4 - - + -
585B TYR* 4.7 9.2 - - + -
586B GLN* 5.4 2.0 - - + -
679B VAL* 6.1 2.5 - - + -
680B SER 2.9 6.9 + - - +
681B ALA* 3.2 20.9 - - + -
682B PHE* 2.6 57.9 + - + -
683B CYS 4.7 0.2 + - - -
685B GLU* 4.7 1.4 - - - +
712B LEU 5.5 1.1 - - - -
713B LEU* 1.3 81.2 - - - +
715B GLY* 1.3 58.0 + - - +
772B VAL* 4.0 6.7 - - + -
773B PHE* 3.2 13.0 - - - +
774B PHE* 3.7 25.4 - - + -
2002B F83 6.4 0.2 - - + -
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Residues in contact with GLY 715 (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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682B PHE* 3.7 10.3 - - - -
685B GLU* 3.0 13.0 - - - -
714B ILE* 1.3 77.9 - - - +
716B ALA* 1.3 61.7 + - - -
772B VAL* 3.3 7.3 - - - +
773B PHE* 2.9 50.8 + - - -
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Residues in contact with ALA 716 (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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682B PHE* 3.6 13.4 - - + -
685B GLU* 2.7 26.1 + - + +
715B GLY* 1.3 73.8 - - - -
717B LEU* 1.3 60.9 + - - +
718B GLU 4.0 0.3 + - - -
719B GLU* 4.0 26.8 + - + +
732B VAL 5.5 0.2 - - - +
733B PRO* 5.9 0.2 - - - +
734B VAL* 3.6 21.0 + - - +
769B VAL* 3.7 17.7 - - + -
771B GLY 3.8 4.3 - - - -
773B PHE* 4.2 0.6 - - - -
2002B F83 4.3 3.8 - - - +
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Residues in contact with LEU 717 (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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716B ALA* 1.3 70.7 - - - +
718B GLU* 1.3 73.3 + - + +
719B GLU 3.3 2.4 + - - -
734B VAL* 3.6 5.8 - - + +
735B SER* 3.7 7.6 - - - +
736B GLU* 3.6 30.7 - - + +
755B THR* 3.5 39.0 - - + +
769B VAL* 3.7 0.7 - - - +
770B LYS* 2.9 24.1 + - + -
771B GLY* 2.7 21.8 + - - +
772B VAL 3.7 18.8 - - - +
773B PHE* 3.7 28.9 - - + -
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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