Contacts of the strand formed by residues 859 - 864 (chain J) in PDB entry 6H25
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 ALA 859 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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856J ARG* 2.3 58.1 + - + +
858J ASN* 1.3 82.0 - - - +
860J ILE* 1.3 62.0 + - - +
872J THR* 4.6 0.9 - - - +
873J VAL 3.1 15.7 - - - +
874J PHE* 3.5 26.7 - - + -
875J PHE* 4.0 7.4 - - - +
894J LEU* 4.8 2.0 - - - +
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Residues in contact with ILE 860 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852J ILE* 3.6 35.4 - - + -
854J PHE 3.6 5.6 - - - +
855J VAL* 3.9 29.2 - - + -
856J ARG* 4.1 1.3 - - - +
859J ALA* 1.3 80.8 - - - +
861J VAL* 1.3 61.4 + - - +
862J VAL* 4.3 3.7 + - + +
872J THR* 3.6 2.4 - - - -
873J VAL* 2.9 48.6 + - + +
875J PHE* 5.4 12.1 - - + -
894J LEU* 5.2 13.7 - - + -
901J PHE* 5.2 18.4 - - + -
907J VAL* 5.6 0.4 - - + -
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Residues in contact with VAL 861 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852J ILE* 4.1 0.2 - - - +
853J LEU* 3.2 4.7 + - - +
854J PHE* 2.9 70.2 + - + +
856J ARG* 5.2 9.9 - - + +
860J ILE* 1.3 73.9 - - - +
862J VAL* 1.3 69.5 + - - +
870J GLU* 4.8 10.1 - - + +
871J GLY 3.4 24.7 - - - +
872J THR* 3.7 15.7 - - - +
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Residues in contact with VAL 862 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850J ALA* 4.0 17.9 - - + -
851J TYR 3.4 14.4 - - - +
852J ILE* 3.2 34.3 - - + +
853J LEU* 4.0 3.8 - - - +
860J ILE* 4.7 9.2 - - + +
861J VAL* 1.3 83.4 - - - +
863J LEU* 1.3 62.5 + - - +
864J ILE* 5.0 5.2 - - + -
870J GLU* 3.5 5.2 - - - +
871J GLY* 2.8 40.6 + - - +
873J VAL* 5.4 4.7 - - + -
907J VAL* 4.4 7.4 - - + -
909J VAL* 4.5 13.9 - - + -
925J MET* 5.6 6.1 - - + -
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Residues in contact with LEU 863 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635J PRO* 3.8 31.9 - - + -
735J TYR* 3.7 24.9 - - + +
739J LEU* 5.0 11.4 - - + -
742J ILE* 4.2 21.3 - - + -
850J ALA* 2.8 24.6 - - - +
851J TYR* 2.8 22.0 + - + +
853J LEU* 4.9 5.4 - - + +
862J VAL* 1.3 74.0 - - - +
864J ILE* 1.3 75.3 + - - +
865J PRO* 3.8 8.9 - - + +
868J GLY* 4.8 4.3 - - - -
869J LEU 3.4 13.7 - - - +
870J GLU* 4.7 13.0 - - + +
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Residues in contact with ILE 864 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840J PHE* 5.5 1.3 - - + -
848J GLU* 3.8 34.3 - - + +
849J GLU 5.4 0.2 - - - +
850J ALA* 3.2 21.8 - - + -
862J VAL* 5.0 4.3 - - + -
863J LEU* 1.3 73.5 - - - +
865J PRO* 1.3 57.0 - - + -
866J LYS 3.8 9.6 - - - +
867J TYR* 4.0 14.6 - - + +
868J GLY* 2.6 35.4 + - - +
869J LEU* 2.9 16.8 + - + +
909J VAL* 4.2 16.6 - - + -
911J ILE* 3.9 29.8 - - + -
925J MET* 5.1 7.4 - - + -
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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