Contacts of the strand formed by residues 857 - 862 (chain B) in PDB entry 2WAC
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 ASN 857 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813B GLU 4.5 3.8 + - - -
814B TYR* 3.6 20.0 - - + +
815B ALA 2.8 22.4 + - - -
848B VAL* 3.9 20.0 - - + +
850B LEU 3.5 9.2 - - - +
851B LYS* 3.6 26.3 - - - +
852B VAL* 3.0 28.3 + - - +
855B SER 3.9 0.7 - - - +
856B PRO* 1.3 72.3 - - - +
858B LEU* 1.3 62.7 + - - +
859B ALA 3.6 0.7 + - - -
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Residues in contact with LEU 858 (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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815B ALA* 3.5 18.2 - - + -
816B LEU 5.4 0.4 - - - +
817B ALA* 4.2 18.6 - - + -
818B LEU* 4.6 13.0 - - + +
848B VAL* 3.4 6.2 - - - +
849B GLU* 2.7 30.3 + - + -
850B LEU* 2.9 27.4 + - + +
852B VAL* 3.8 21.1 - - + -
856B PRO 4.4 1.3 - - - +
857B ASN* 1.3 73.0 - - - +
859B ALA* 1.3 54.4 + - - +
883B GLU* 5.1 0.7 - - - +
885B ARG* 4.1 27.1 - - - +
890B LEU* 4.1 26.7 - - + -
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Residues in contact with ALA 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B PHE* 4.5 4.8 - - + -
814B TYR* 3.9 32.3 - - + -
815B ALA 2.8 11.9 + - - +
816B LEU* 3.7 8.8 - - - +
817B ALA* 3.1 23.4 + - - +
846B LEU* 4.0 20.0 - - + -
847B ASN 3.1 12.3 - - - +
848B VAL* 4.2 1.1 - - - -
849B GLU 4.2 0.7 - - - +
858B LEU* 1.3 75.1 - - - +
860B THR* 1.3 61.4 + - - +
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Residues in contact with THR 860 (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 TYR* 5.3 3.3 - - - -
816B LEU* 5.3 2.2 - - - -
817B ALA* 3.9 10.1 - - + -
845B GLN 3.6 0.7 - - - +
846B LEU* 3.4 5.2 - - - +
847B ASN* 2.9 37.4 + - - +
849B GLU* 2.6 38.3 + - + +
859B ALA* 1.3 74.1 - - - +
861B LEU* 1.3 64.6 + - - +
862B ARG* 5.5 6.1 + - - +
869B ASP* 3.9 13.0 - - - +
893B LEU* 4.0 10.1 - - + -
897B TYR* 3.8 22.4 - - - +
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Residues in contact with LEU 861 (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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705B VAL* 4.6 0.7 - - + -
707B VAL* 3.9 18.4 - - + -
716B PHE* 3.6 36.6 - - + -
816B LEU* 4.5 7.2 - - + +
835B PHE* 3.7 31.9 - - + -
839B VAL* 4.2 6.1 - - + -
844B VAL* 3.8 20.4 - - + -
845B GLN 3.5 1.6 - - - -
846B LEU* 4.0 17.7 - - + -
859B ALA 4.2 0.4 + - - -
860B THR* 1.3 81.1 - - - +
862B ARG* 1.3 62.6 + - - +
869B ASP* 3.4 8.7 + - - +
870B PHE* 2.9 40.9 + - + +
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Residues in contact with ARG 862 (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 TYR* 4.5 27.2 + - + -
844B VAL* 3.6 4.0 - - - -
845B GLN* 2.8 50.2 + - + +
860B THR* 5.5 6.4 + - - +
861B LEU* 1.3 79.6 - - - +
863B ASP* 1.3 65.6 + - - +
864B PRO 3.5 0.3 - - - -
867B LYS* 2.6 50.2 + - - +
868B VAL 3.3 4.3 - - - +
869B ASP* 3.9 27.6 + - + +
870B PHE* 3.6 5.4 - - - -
893B LEU* 5.9 4.2 - - - +
896B GLN* 5.8 2.2 + - - -
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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