Contacts of the helix formed by residues 787 - 792 (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 VAL 787 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754B GLU* 3.4 9.2 - - - -
755B CYS* 3.9 20.2 - - + +
765B ALA* 3.9 5.6 - - + -
768B ARG* 3.5 39.7 - - + +
769B ALA* 3.9 22.7 - - + -
780B HIS* 5.2 2.2 - - + +
784B CYS* 3.7 23.6 - - - +
785B GLN 3.7 1.0 - - - -
786B ASN* 1.3 83.2 - - - +
788B ALA* 1.3 55.2 + - - +
789B LEU 3.4 2.0 - - - -
790B GLN* 3.1 4.9 + - - +
791B ARG* 2.7 35.2 + - + +
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Residues in contact with ALA 788 (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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754B GLU* 3.1 6.5 + - - +
785B GLN 5.0 5.5 + - - +
786B ASN* 3.8 0.6 - - - -
787B VAL* 1.3 76.7 - - - +
789B LEU* 1.3 58.3 + - - +
791B ARG* 3.4 10.7 + - - +
792B GLY* 3.0 26.0 + - - -
793B ALA 4.4 0.5 + - - -
822B PHE* 3.5 47.3 - - + -
901B LYS* 5.3 7.0 - - + +
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Residues in contact with LEU 789 (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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754B GLU* 2.8 24.4 + - - +
788B ALA* 1.3 71.0 - - - +
790B GLN* 1.3 62.4 + - - +
792B GLY* 3.5 12.7 + - - -
822B PHE* 3.9 8.5 - - + -
825B GLU* 3.5 45.8 - - + +
892B MET* 4.0 15.7 - - + -
894B VAL* 3.7 21.1 - - + -
899B ARG* 3.5 38.2 + - + +
900B ILE 4.1 0.9 - - - +
901B LYS* 3.7 32.3 - - + +
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Residues in contact with GLN 790 (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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311B ARG* 5.3 1.4 + - - -
754B GLU* 3.0 29.0 + - - +
755B CYS 3.2 20.6 + - - -
757B PRO* 3.5 9.7 - - - +
769B ALA* 3.4 39.8 - - + +
771B PRO* 4.5 11.4 - - - +
787B VAL* 3.1 12.3 + - - +
789B LEU* 1.3 76.2 - - - +
791B ARG* 1.3 64.4 + - - +
792B GLY* 3.4 1.0 + - - -
894B VAL* 3.5 15.2 - - + +
895B ASN* 2.8 28.4 + - - +
899B ARG* 4.8 4.3 - - - +
2620B SER* 4.7 4.9 - - - +
2621B SER* 5.1 0.2 - - - -
2624B TYR* 5.5 0.5 - - - -
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Residues in contact with ARG 791 (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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311B ARG* 4.4 4.9 + - - -
768B ARG 3.7 14.3 + - - +
769B ALA 4.9 2.5 - - - -
771B PRO* 4.2 9.6 - - - +
774B ALA* 2.8 53.9 + - - +
775B TYR* 4.7 5.9 - - - +
777B GLU* 5.0 8.1 - - - +
780B HIS* 3.5 51.3 + - + +
787B VAL* 2.7 22.4 + - + +
788B ALA* 3.7 9.6 - - - +
790B GLN* 1.3 71.4 - - - +
792B GLY* 1.3 57.2 + - - +
793B ALA* 3.7 18.9 + - + +
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Residues in contact with GLY 792 (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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311B ARG* 3.5 35.5 + - - -
774B ALA* 5.3 0.7 - - - -
775B TYR* 4.3 4.5 + - - -
788B ALA 3.0 12.1 + - - -
789B LEU 3.7 11.4 - - - -
790B GLN 3.3 1.4 - - - -
791B ARG* 1.3 74.1 - - - +
793B ALA* 1.3 57.0 + - - +
794B ALA* 3.2 9.6 + - - +
822B PHE* 4.9 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