Contacts of the strand formed by residues 856 - 860 (chain B) in PDB entry 5KJH
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 LEU 856 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831B ILE* 3.8 16.6 - - + -
836B GLY* 4.5 3.6 - - - +
839B ARG* 6.0 0.4 - - + -
840B GLU* 3.5 26.0 - - - +
854B SER* 3.4 9.5 + - - +
855B TYR* 1.3 78.0 - - - +
857B PHE* 1.4 59.5 + - - +
866B TRP* 3.8 16.2 - - + -
867B VAL 3.4 3.8 - - - +
868B ASP* 3.7 35.7 - - + +
2533B LEU* 3.7 30.3 - - + -
2534B PRO 3.7 19.7 - - - +
2535B GLY* 3.6 1.0 - - - -
2536B ARG* 3.0 33.3 + - - -
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Residues in contact with PHE 857 (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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826B TYR* 3.7 31.9 - + + -
856B LEU* 1.4 72.9 - - - +
858B THR* 1.4 86.8 + - - +
859B LEU 3.2 0.7 + - - -
866B TRP* 3.4 4.3 - - - -
867B VAL* 2.8 38.5 + - + +
889B PRO* 3.7 28.3 - - + -
891B ILE* 5.2 0.2 - - + -
900B ILE* 3.8 30.7 - - + -
902B PHE* 4.1 7.4 - + - -
916B PHE* 3.8 17.0 - + - -
2536B ARG* 3.4 40.8 - - + -
2537B GLY* 3.9 14.4 - - - -
2538B VAL* 4.2 7.4 - - + -
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Residues in contact with THR 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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857B PHE* 1.4 86.7 - - - +
859B LEU* 1.3 61.2 + - - +
860B LEU 4.4 0.9 - - - -
861B GLU* 3.7 41.7 - - + +
865B ILE 4.1 0.4 - - - -
866B TRP* 3.1 48.4 - - + +
891B ILE* 4.2 8.3 - - - +
921B ASN* 4.6 4.2 + - - -
2536B ARG 2.9 15.7 + - - -
2537B GLY* 4.6 9.0 - - - -
2538B VAL 5.2 0.2 + - - -
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Residues in contact with LEU 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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313B ASN* 4.9 1.8 - - - +
676B HIS* 5.2 1.2 - - - +
677B ALA* 5.6 1.0 - - - -
830B LEU* 3.8 28.0 - - + -
857B PHE 3.2 2.0 + - - -
858B THR* 1.3 72.1 - - - +
860B LEU* 1.3 72.5 + - + +
861B GLU 4.0 1.2 + - - -
865B ILE* 2.9 23.6 + - + +
867B VAL* 4.0 15.7 - - + -
891B ILE* 3.7 27.7 - - + +
898B TRP* 3.4 47.6 - - + +
899B ARG* 4.0 4.3 - - - +
900B ILE* 3.7 29.4 - - + +
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Residues in contact with LEU 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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676B HIS* 3.5 26.5 - - + +
677B ALA* 4.9 0.9 - - - +
679B ARG* 5.1 5.6 - - + +
681B LEU* 3.9 32.5 - - + -
858B THR* 4.4 0.4 - - - -
859B LEU* 1.3 87.5 - - + +
861B GLU* 1.3 53.1 + - - +
862B GLN 3.5 2.7 - - - -
863B GLU* 3.4 13.0 + - + +
864B GLY* 2.8 31.4 + - - -
865B ILE* 3.0 30.7 + - + -
898B TRP* 3.6 52.7 - - + +
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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