Contacts of the strand formed by residues 771 - 779 (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 GLY 771 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717B LEU* 2.7 39.6 + - - +
755B THR* 5.2 0.9 - - - -
756B TYR 3.0 14.1 - - - -
757B ILE* 4.2 0.9 - - - -
758B MET* 3.8 8.2 - - - +
769B VAL* 3.1 11.1 - - - +
770B LYS* 1.3 80.5 - - - +
772B VAL* 1.3 60.5 + - - -
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Residues in contact with VAL 772 (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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553B VAL* 4.1 8.7 - - + -
556B TRP* 3.5 25.3 - - + -
557B ALA* 6.1 0.7 - - + -
682B PHE* 3.8 24.9 - - + -
714B ILE* 4.0 6.1 - - + -
715B GLY 3.3 13.2 - - - +
717B LEU* 3.7 2.8 - - - +
755B THR* 3.5 2.6 - - - -
756B TYR* 2.8 37.4 + - + -
758B MET* 3.9 24.7 - - + -
769B VAL* 4.9 2.2 - - + -
771B GLY* 1.3 78.4 - - - +
773B PHE* 1.3 68.1 + - - +
2002B F83 4.0 13.7 - - + +
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Residues in contact with PHE 773 (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* 3.8 3.1 - - - -
685B GLU* 4.6 7.9 - - - -
694B PHE* 5.1 4.3 - + - -
713B LEU* 3.7 33.9 - - + -
714B ILE* 3.2 11.7 - - - +
715B GLY* 2.9 65.4 + - - -
716B ALA 4.0 6.7 - - - -
717B LEU* 3.7 30.1 - - + -
734B VAL* 4.5 4.0 - - + -
736B GLU* 5.6 1.6 - - - -
739B VAL* 3.9 34.8 - - + -
753B LEU* 4.2 18.8 - - + -
754B ARG 3.2 10.1 - - - +
755B THR* 4.7 2.0 - - - +
772B VAL* 1.3 74.1 - - - +
774B PHE* 1.3 62.6 + - - +
775B ALA* 4.3 1.1 - - + -
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Residues in contact with PHE 774 (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* 3.7 19.7 - + + -
557B ALA* 6.2 0.2 - - - -
560B CYS* 3.6 35.0 - - + -
561B LEU* 3.9 22.9 - - + -
564B THR* 3.3 31.0 - - - -
712B LEU* 4.3 16.4 - - + -
713B LEU 3.4 1.6 - - - -
714B ILE* 3.7 22.0 - - + -
752B ASP* 3.9 20.2 - - - -
753B LEU* 3.1 6.3 - - - +
754B ARG* 2.9 32.9 + - - +
773B PHE* 1.3 76.1 - - - +
775B ALA* 1.3 72.9 + - - +
776B TRP* 4.2 12.1 - - + -
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Residues in contact with ALA 775 (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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711B LEU 3.5 0.7 - - - +
712B LEU* 3.3 6.1 - - - +
713B LEU* 2.6 52.4 + - + +
739B VAL* 4.9 0.2 - - + -
743B LEU* 3.9 24.2 - - + -
752B ASP 3.3 5.2 - - - +
753B LEU* 3.7 18.2 - - + -
773B PHE* 4.4 5.2 - - + -
774B PHE* 1.3 81.0 - - - +
776B TRP* 1.3 60.8 + - - +
777B ALA* 3.9 0.9 - - + +
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Residues in contact with TRP 776 (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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564B THR* 3.7 17.3 - - + -
567B THR* 3.8 27.6 - - + -
569B GLU* 4.1 12.8 - - + -
570B VAL* 3.9 19.4 - - + +
710B HIS* 3.0 24.5 + + + -
711B LEU 3.6 2.2 - - - -
712B LEU* 3.6 23.6 - - + -
750B VAL* 3.8 1.1 - - - -
751B ARG* 2.8 78.9 + - + +
752B ASP* 2.8 32.2 + - + +
774B PHE* 4.2 8.9 - - + -
775B ALA* 1.3 72.5 - - - +
777B ALA* 1.3 70.5 + - - +
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Residues in contact with ALA 777 (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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710B HIS* 3.5 2.3 - - - -
711B LEU* 2.7 42.4 + - + +
743B LEU* 4.0 25.1 - - + -
748B TYR* 3.6 30.7 - - + -
749B LYS 3.4 7.9 - - - +
750B VAL* 4.6 2.2 - - - -
775B ALA* 3.9 1.3 - - + -
776B TRP* 1.3 79.8 - - - +
778B GLN* 1.3 60.1 - - - +
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Residues in contact with GLN 778 (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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708B GLY* 3.1 28.5 + - - +
709B GLY 3.3 13.2 - - - +
710B HIS* 3.2 25.1 + - + +
748B TYR* 3.6 2.7 - - - -
749B LYS* 2.8 42.3 + - + +
751B ARG* 3.2 31.3 + - + -
777B ALA* 1.3 74.3 - - - +
779B LYS* 1.3 54.5 + - - +
780B VAL* 2.6 21.9 + - - -
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Residues in contact with LYS 779 (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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702B THR* 3.1 34.1 + - + +
703B THR* 4.5 6.5 + - - +
705B LEU* 2.6 43.6 + - + +
706B ARG 3.4 16.9 - - - +
707B PRO* 3.9 15.7 - - + +
708B GLY* 2.8 25.6 + - - -
709B GLY 2.9 14.7 + - - +
746B SER 5.8 0.7 - - - +
747B GLY 3.6 7.9 - - - +
748B TYR* 3.3 16.6 - - + -
778B GLN* 1.3 65.8 - - - +
780B VAL* 1.3 67.7 + - - +
781B GLY* 3.0 1.1 + - - -
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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