Contacts of the strand formed by residues 870 - 878 (chain B) in PDB entry 2XWB
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 SER 870 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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830B TYR* 5.0 0.6 - - - +
831B ASN* 3.0 32.0 + - - +
832B TYR* 6.6 0.2 - - - -
866B ILE* 3.7 1.1 - - - +
867B PRO* 2.7 45.7 + - - +
868B PRO 3.1 4.0 - - - -
869B LYS* 1.3 79.6 - - - +
871B SER* 1.3 64.7 + - - +
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Residues in contact with SER 871 (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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312A SER* 5.6 4.7 - - - -
828B VAL* 4.1 9.6 - - - +
829B LEU 3.5 9.6 - - - -
830B TYR* 3.7 33.7 - - - -
866B ILE* 4.3 3.8 - - - -
867B PRO* 5.6 2.1 - - - +
870B SER* 1.3 81.7 + - - +
872B LEU* 1.3 64.5 + - - +
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Residues in contact with LEU 872 (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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312A SER* 5.9 0.4 - - - -
827B ALA 3.6 1.0 - - - +
828B VAL* 3.3 4.6 - - - -
829B LEU* 2.8 41.6 + - + +
864B VAL* 3.6 43.3 - - + -
865B THR 4.7 7.4 - - - +
866B ILE* 4.4 17.7 - - + -
867B PRO* 5.9 1.6 - - + -
871B SER* 1.3 78.9 - - - +
873B SER* 1.3 78.9 + - - +
874B VAL* 4.7 5.2 - - + -
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Residues in contact with SER 873 (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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312A SER* 4.1 24.4 - - - -
314A SER* 3.9 4.0 + - - -
826B ARG* 3.2 42.4 + - - +
827B ALA 3.6 3.1 - - - -
828B VAL* 4.1 5.9 - - - +
872B LEU* 1.3 87.8 - - - +
874B VAL* 1.3 61.2 + - - +
875B PRO* 3.5 9.8 - - - +
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Residues in contact with VAL 874 (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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827B ALA* 2.8 46.2 + - + +
829B LEU* 3.9 18.6 - - + -
842B VAL* 4.0 18.2 - - + -
862B GLN* 4.3 13.7 - - + +
864B VAL* 4.9 9.9 - - + -
872B LEU* 4.7 11.7 - - + +
873B SER* 1.3 79.1 + - - +
875B PRO* 1.3 71.3 - - + +
876B TYR* 3.7 33.9 + - + +
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Residues in contact with PRO 875 (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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824B GLU* 3.1 25.8 - - - +
825B ILE 3.9 3.6 - - - +
826B ARG* 4.2 13.0 - - - +
860B HIS* 5.0 3.6 - - - -
862B GLN* 5.1 3.1 + - - -
873B SER 3.5 9.2 - - - +
874B VAL* 1.3 91.7 - - + +
876B TYR* 1.3 69.4 + - - +
877B VAL* 5.8 1.6 - - + -
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Residues in contact with TYR 876 (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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824B GLU* 3.3 3.8 - - - +
825B ILE* 2.8 61.3 + - + +
827B ALA* 4.2 13.0 - - + -
842B VAL* 3.6 21.8 + - + +
843B GLU* 3.7 1.2 - - - -
844B LEU* 3.4 47.9 + - + -
860B HIS* 3.2 38.5 + + - -
862B GLN* 3.5 13.4 + - - -
874B VAL* 3.7 33.4 - - + -
875B PRO* 1.3 74.1 - - - +
877B VAL* 1.3 65.8 + - - +
878B ILE* 3.9 1.0 + - + -
890B VAL* 4.2 19.7 - - + -
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Residues in contact with VAL 877 (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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822B GLN* 4.1 24.0 - - - +
823B VAL 3.5 6.7 - - - +
824B GLU* 4.3 21.5 - - + +
844B LEU* 5.5 0.2 - - - +
851B CYS 4.0 1.1 - - - +
852B SER* 3.8 15.6 - - - -
853B LEU* 5.0 15.0 + - + -
860B HIS* 6.1 0.6 - - - -
875B PRO* 5.8 1.3 - - + -
876B TYR* 1.3 73.8 - - - +
878B ILE* 1.3 69.2 + - - +
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Residues in contact with ILE 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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822B GLN* 3.7 1.1 - - - +
823B VAL* 3.0 43.9 + - + +
825B ILE* 4.1 31.0 - - + -
844B LEU* 4.1 16.6 - - + -
850B PHE* 3.7 39.7 - - + -
851B CYS 3.5 7.9 - - - +
852B SER* 3.8 18.2 - - - -
876B TYR 4.8 3.4 - - - +
877B VAL* 1.3 81.5 - - - +
879B VAL* 1.3 68.0 + - - +
880B PRO* 5.0 1.3 - - + -
888B VAL* 4.6 7.0 - - + -
907B LEU* 5.0 4.5 - - + -
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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