Contacts of the strand formed by residues 856 - 861 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644A ASP 3.2 12.5 + - - -
645A SER* 2.8 39.6 + - - +
646A MET* 3.4 22.1 - - + +
647A ILE* 3.7 8.5 - - + -
853A SER 3.0 31.0 + - - +
854A MET* 3.1 16.5 + - + +
855A GLY* 1.3 73.0 - - - +
857A LEU* 1.3 65.8 + - - +
858A ARG* 3.3 11.5 - - - +
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Residues in contact with LEU 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A VAL* 3.7 40.6 - - + +
614A LYS 5.6 0.4 - - - +
638A PRO* 5.8 3.1 - - + -
646A MET* 2.7 44.8 + - + +
648A LEU* 4.7 14.1 - - + +
850A TYR* 3.7 35.2 - - + -
851A VAL 3.5 18.6 - - - +
852A THR* 3.7 11.2 - - + -
855A GLY 3.2 2.9 + - - +
856A LYS* 1.3 69.8 - - - +
858A ARG* 1.3 63.0 + - - +
859A GLY 3.4 24.2 - - - +
860A VAL* 5.0 2.2 - - + -
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Residues in contact with ARG 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A MET* 4.6 3.4 - - - -
611A ARG* 3.3 62.9 + - - +
613A VAL* 5.3 4.1 - - - +
646A MET* 5.3 7.5 - - - +
830A GLU* 3.3 25.9 + - - +
851A VAL 2.8 14.1 + - - +
853A SER* 3.7 9.9 - - - +
856A LYS* 3.3 23.8 - - - +
857A LEU* 1.3 80.6 + - - +
859A GLY* 1.3 56.7 + - - +
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Residues in contact with GLY 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A MET* 3.9 20.6 - - - -
610A VAL 3.2 11.7 - - - -
611A ARG* 4.3 0.2 - - - -
613A VAL* 5.7 0.4 - - - -
851A VAL* 2.9 31.9 + - - +
857A LEU* 3.4 7.1 - - - +
858A ARG* 1.3 77.7 - - - +
860A VAL* 1.3 68.1 + - - +
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Residues in contact with VAL 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A ILE 4.3 0.3 - - - +
609A MET* 3.4 3.2 - - - -
610A VAL* 2.5 59.4 + - + +
612A ASP 4.0 14.8 - - - +
613A VAL* 5.1 2.0 - - + -
614A LYS* 5.4 7.6 - - - +
848A LEU* 5.5 8.7 - - + -
849A ALA 3.3 10.1 - - - +
850A TYR* 4.4 22.2 - - + -
857A LEU* 5.0 6.7 - - + -
859A GLY* 1.3 80.1 - - - +
861A LEU* 1.3 69.8 + - - +
862A ALA* 4.2 5.1 + - + +
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Residues in contact with LEU 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A VAL* 3.9 25.8 - - + -
608A ILE* 3.7 31.4 - - + -
609A MET* 4.8 5.8 - - + +
828A LEU* 4.8 6.7 - - + -
834A LEU* 6.4 0.2 - - + -
837A THR* 4.4 12.1 - - + -
841A PHE* 3.9 11.6 - - + -
848A LEU* 3.6 5.0 - - - +
849A ALA* 2.9 46.1 + - + +
851A VAL* 4.2 13.3 - - + +
860A VAL* 1.3 75.6 - - - +
862A ALA* 1.3 61.5 + - - +
865A GLU* 5.9 0.2 - - - -
866A LEU* 3.6 34.3 - - + +
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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