Contacts of the strand formed by residues 797 - 801 (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 797 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795B LYS* 3.4 15.9 + - + +
796B ALA* 1.3 78.9 - - - +
798B VAL* 1.3 63.0 + - - +
811B LEU* 3.9 25.6 - - + -
812B PHE 3.3 8.3 - - - +
813B ALA* 4.6 2.2 - - - -
814B ALA* 4.0 3.4 - - - +
817B ILE* 5.4 1.1 - - + -
823B VAL* 4.7 10.5 - - + -
824B ILE* 4.3 14.8 - - + -
875B LEU* 4.1 18.1 - - + +
914B LEU* 3.9 26.0 - - + -
2575B LEU* 3.8 13.9 - - - +
2576B PRO 5.3 1.9 - - - +
2577B GLN* 5.1 1.9 + - - +
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Residues in contact with VAL 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B VAL* 1.3 77.1 - - - +
799B LEU* 1.3 75.4 + - - +
811B LEU* 3.6 5.0 - - - +
812B PHE* 2.7 56.8 + - + +
814B ALA* 4.3 1.8 - - + -
875B LEU* 5.1 1.3 - - - -
2553B VAL* 5.0 0.4 - - + -
2554B PRO* 3.8 27.1 - - + -
2560B LEU* 3.9 14.4 - - + -
2561B PHE 4.5 0.9 - - - +
2569B LEU* 3.7 28.3 - - + -
2575B LEU* 3.8 16.6 - - + -
2576B PRO* 5.4 0.4 - - + -
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Residues in contact with LEU 799 (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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798B VAL* 1.3 80.0 - - - +
800B GLY* 1.3 59.4 + - - +
809B TYR* 3.8 34.3 - - + -
810B GLY 3.7 14.6 - - - +
811B LEU* 4.1 5.6 - - + +
875B LEU* 4.6 13.4 - - + +
878B TYR* 3.5 45.3 - - + -
2560B LEU* 3.4 5.8 - - - +
2561B PHE* 2.9 42.7 + - + +
2563B PRO* 4.0 29.1 - - + +
2566B LYS* 4.3 9.4 - - - -
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Residues in contact with GLY 800 (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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798B VAL 3.7 0.6 + - - -
799B LEU* 1.3 75.7 - - - +
801B LYS* 1.3 60.4 + - - -
809B TYR* 3.4 10.6 - - - -
810B GLY 3.0 28.7 + - - +
812B PHE* 3.7 13.0 - - - -
2559B PRO 3.1 13.7 - - - -
2560B LEU* 3.8 5.2 - - - -
2561B PHE* 3.8 10.1 - - - -
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Residues in contact with LYS 801 (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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298B GLU* 5.8 5.2 - - - +
301B PRO* 3.9 14.6 - - + -
800B GLY* 1.3 72.0 - - - -
802B SER* 1.3 69.9 + - - +
804B LEU 4.9 0.8 + - - -
806B ALA* 4.7 9.5 - - - +
807B CYS 4.6 6.9 - - - +
808B GLY* 3.6 24.8 + - - +
809B TYR* 4.5 0.7 - - - +
812B PHE* 3.3 12.9 - - - -
2558B GLN* 2.8 27.7 + - - +
2559B PRO* 2.8 38.7 + - + +
2561B PHE* 3.7 11.3 - - + -
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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