Contacts of the strand formed by residues 856 - 861 (chain B) in PDB entry 6QVC
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 LYS 856 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644B ASP 3.2 12.3 + - - -
645B SER* 2.8 39.9 + - - +
646B MET* 3.4 22.6 - - + +
647B ILE* 3.7 8.7 - - + -
852B THR* 3.7 0.2 - - - -
853B SER 3.0 31.5 + - - +
854B MET* 3.1 15.7 - - + +
855B GLY* 1.3 72.8 - - - +
857B LEU* 1.3 65.2 + - - +
858B ARG* 3.3 12.0 - - - +
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Residues in contact with LEU 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B VAL* 3.7 39.6 - - + +
614B LYS 5.6 0.2 - - - +
638B PRO* 5.8 3.4 - - + -
646B MET* 2.7 45.5 + - + +
648B LEU* 4.7 14.6 - - + +
850B TYR* 3.7 33.9 - - + -
851B VAL 3.5 17.9 - - - +
852B THR* 3.7 12.3 - - + -
855B GLY 3.2 2.9 + - - +
856B LYS* 1.3 70.7 - - - +
858B ARG* 1.3 62.4 + - - +
859B GLY 3.4 24.5 - - - +
860B VAL* 5.0 2.7 - - + -
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Residues in contact with ARG 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B MET* 4.9 2.9 - - - -
611B ARG* 3.3 63.3 + - - +
613B VAL* 5.3 3.4 - - - +
646B MET* 5.3 7.2 - - - +
830B GLU* 3.3 26.7 + - - +
851B VAL 2.8 14.3 + - - +
853B SER* 3.7 10.8 - - - +
856B LYS* 3.3 23.2 - - - +
857B LEU* 1.3 81.1 + - - +
859B GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 859 (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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609B MET* 3.9 21.1 - - - -
610B VAL 3.2 13.2 - - - -
611B ARG* 4.3 0.2 - - - -
613B VAL* 5.7 0.9 - - - -
851B VAL* 2.9 33.4 + - - -
857B LEU* 3.4 6.9 - - - +
858B ARG* 1.3 77.9 - - - +
860B VAL* 1.3 66.5 + - - +
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Residues in contact with VAL 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B ILE 4.3 0.3 - - - +
609B MET* 3.4 3.6 - - - +
610B VAL* 2.5 59.3 + - + +
612B ASP 4.0 15.5 - - - +
613B VAL* 5.1 2.0 - - + -
614B LYS* 5.4 7.9 - - - +
848B LEU* 5.5 9.0 - - + -
849B ALA 3.3 11.9 - - - +
850B TYR* 4.4 23.1 - - + -
857B LEU* 5.0 6.1 - - + -
859B GLY* 1.3 79.1 - - - +
861B LEU* 1.3 67.6 + - - +
862B ALA* 4.2 5.2 + - + +
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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
----------------------------------------------------------
605B VAL* 3.9 26.0 - - + -
608B ILE* 3.7 31.9 - - + -
609B MET* 4.8 5.6 - - + +
828B LEU* 4.8 6.7 - - + -
834B LEU* 6.4 0.7 - - + -
837B THR* 4.4 11.4 - - + -
841B PHE* 3.9 12.2 - - + -
848B LEU* 3.6 5.0 - - - +
849B ALA* 2.9 46.9 + - + -
851B VAL* 4.2 14.1 - - + +
860B VAL* 1.3 76.1 - - - +
862B ALA* 1.3 62.0 + - - +
866B LEU* 3.6 34.1 - - + +
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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
------------------------------------------------------------
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