Contacts of the strand formed by residues 877 - 884 (chain B) in PDB entry 2B7A
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 GLU 877 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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844B PHE* 5.7 1.9 - - - -
867B ARG* 4.3 0.4 - - - -
868B TYR* 2.9 35.2 + - + +
875B THR 3.9 0.6 + - - -
876B GLY* 1.3 71.4 - - - -
878B VAL* 1.3 72.8 + - - +
879B VAL* 3.7 8.0 + - + +
914B LYS* 3.4 41.5 + - - +
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Residues in contact with VAL 878 (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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852B LEU* 4.5 4.9 - - + -
865B MET* 3.7 31.6 - - + -
866B CYS 3.4 7.4 - - - +
867B ARG* 3.9 34.8 - - + +
876B GLY 4.7 1.3 - - - +
877B GLU* 1.3 82.4 - - - +
879B VAL* 1.3 65.5 + - - +
914B LYS* 5.4 1.0 - - - -
931B TYR* 3.6 39.7 + - + +
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Residues in contact with VAL 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844B PHE* 4.5 9.6 - - + -
849B LEU* 4.0 22.7 - - + -
865B MET* 3.7 3.5 - - - -
866B CYS 2.7 44.2 + - - +
868B TYR* 4.7 3.4 - - + +
877B GLU* 4.0 18.6 - - + +
878B VAL* 1.3 81.5 - - - +
880B ALA* 1.3 58.9 + - - +
881B VAL* 4.0 6.7 - - + -
914B LYS* 3.7 26.5 - - + -
928B ILE* 3.8 21.5 - - + -
929B MET 3.6 8.3 - - - +
931B TYR* 4.0 8.1 - - - +
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Residues in contact with ALA 880 (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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855B LEU* 4.2 5.8 - - + -
863B VAL* 4.0 10.8 - - + -
864B GLU 3.4 4.5 - - - -
879B VAL* 1.3 72.1 - - - +
881B VAL* 1.3 60.4 + - - +
882B LYS 4.1 0.4 + - - -
927B LEU 3.6 0.9 - - - +
928B ILE* 3.5 3.1 - - - +
929B MET* 2.7 39.5 + - + +
930B GLU 3.6 6.1 - - - +
931B TYR* 4.1 3.1 - - - +
2002B IZA 3.2 44.6 - - + +
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Residues in contact with VAL 881 (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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849B LEU* 3.9 13.0 - - + -
862B SER 3.7 0.7 - - - +
863B VAL* 3.3 3.8 - - - -
864B GLU* 2.7 48.3 + - + +
866B CYS* 3.8 31.6 - - + -
879B VAL* 4.0 8.1 - - + -
880B ALA* 1.3 77.4 - - - +
882B LYS* 1.3 61.3 + - - +
883B LYS* 4.0 1.1 + - + +
926B LYS* 3.7 39.9 - - + +
927B LEU 3.4 2.2 - - - -
928B ILE* 3.8 23.6 - - + -
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Residues in contact with LYS 882 (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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860B PHE* 4.9 19.3 - - - -
861B GLY 5.7 3.8 - - - +
862B SER 3.4 10.8 - - - +
863B VAL* 3.9 12.1 - - + -
880B ALA 4.1 1.0 + - - -
881B VAL* 1.3 73.6 - - - +
883B LYS* 1.3 66.6 + - - +
884B LEU* 5.9 1.3 - - - -
895B PHE* 3.4 16.0 - - + -
898B GLU* 2.7 38.4 + - - +
926B LYS* 3.4 6.4 - - - -
927B LEU* 2.8 47.4 + - + +
929B MET* 3.8 21.1 - - + -
994B ASP* 2.7 32.8 + - - +
996B GLY* 4.0 4.4 - - - -
2002B IZA 5.0 3.6 - - - -
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Residues in contact with LYS 883 (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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861B GLY* 3.3 3.3 - - - -
862B SER* 3.0 41.5 + - - +
864B GLU* 2.7 36.9 + - + +
881B VAL* 4.0 1.7 + - + +
882B LYS* 1.3 80.7 - - - +
884B LEU* 1.3 70.7 + - - +
885B GLN* 3.5 28.1 - - - +
895B PHE* 4.6 1.8 - - - -
925B LEU 4.6 2.7 - - - +
926B LYS* 3.8 28.5 - - + +
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Residues in contact with LEU 884 (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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860B PHE* 4.0 32.3 - - + +
882B LYS* 5.9 2.0 - - - -
883B LYS* 1.3 84.9 - - - +
885B GLN* 1.3 62.3 + - - +
886B HIS 4.3 7.2 - - - +
887B SER* 4.0 18.1 + - - +
891B HIS* 3.6 39.9 - - + +
892B LEU* 4.1 17.9 - - + +
895B PHE* 3.9 39.7 - - + -
898B GLU* 5.8 0.2 - - - +
925B LEU 4.8 4.7 + - - +
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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