Contacts of the helix formed by residues 675 - 679 (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 GLU 675 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668B ALA 5.5 1.8 - - - +
671B THR 5.1 0.2 - - - +
672B ILE* 3.1 18.3 + - + +
673B THR 3.5 0.2 - - - -
674B HIS* 1.3 107.7 + - + +
676B HIS* 1.3 64.6 + - - +
677B ALA* 3.2 7.6 + - - +
678B VAL* 3.1 37.2 + - + +
679B ARG* 3.5 7.8 + - - +
752B ASN* 6.1 0.2 - - - -
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Residues in contact with HIS 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B THR 3.6 22.2 + - - -
674B HIS 3.4 8.8 + - - -
675B GLU* 1.3 70.8 - - - +
677B ALA* 1.3 61.4 + - - +
679B ARG* 3.2 23.9 + - - +
751B LEU 3.9 6.1 - - - -
752B ASN* 2.8 35.7 + - + +
753B ARG* 6.4 0.2 - - - -
859B LEU 5.2 0.9 - - - +
860B LEU* 3.5 23.4 - - + +
891B ILE* 3.3 37.9 + - + -
893B TYR* 3.7 14.3 + - + -
898B TRP* 3.1 35.2 + + + +
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Residues in contact with ALA 677 (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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675B GLU* 3.2 6.8 + - - +
676B HIS* 1.3 77.2 - - - +
678B VAL* 1.3 63.8 + - + +
859B LEU 5.6 0.9 - - - -
860B LEU* 5.3 0.7 - - - +
861B GLU* 3.5 30.4 - - + +
862B GLN* 3.0 26.9 + - - +
891B ILE* 6.1 5.7 - - + +
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Residues in contact with VAL 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B ILE* 3.8 36.4 - - + +
675B GLU* 3.1 27.6 + - + +
677B ALA* 1.3 83.5 - - + +
679B ARG* 1.3 62.1 + - - +
680B GLU* 3.7 1.6 + - - +
704B THR* 5.3 3.5 + - - +
862B GLN* 3.4 20.5 - - + +
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Residues in contact with ARG 679 (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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672B ILE* 3.4 37.2 - - + +
673B THR* 3.0 34.0 + - - +
675B GLU 3.5 8.1 - - - +
676B HIS* 3.2 26.4 + - - +
678B VAL* 1.3 79.9 - - - +
680B GLU* 1.3 67.4 + - - +
681B LEU* 4.2 8.7 + - + +
707B VAL* 3.9 30.9 - - - +
708B LEU 5.1 1.2 + - - -
710B GLU* 4.8 14.8 + - - +
753B ARG* 5.4 1.2 - - - +
860B LEU* 5.1 4.5 - - + +
862B GLN* 3.9 0.5 - - - +
863B GLU* 3.6 24.6 + - - +
893B TYR* 5.0 5.3 - - - -
896B HIS* 5.8 2.8 - - - -
898B TRP* 4.1 27.6 - - + -
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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