Contacts of the helix formed by residues 626 - 636 (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 TRP 626 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B GLU* 2.8 56.7 + - + +
575B TYR* 4.4 3.5 - - - +
578B HIS* 3.1 33.8 - + - +
579B GLY* 3.8 15.3 - - - +
580B THR* 3.7 15.0 - - - +
624B PRO* 3.5 24.5 - - + +
625B CYS* 1.4 71.8 - - - +
627B ASP* 1.4 89.8 + - + +
629B HIS* 3.1 9.7 + - - +
630B ARG* 3.0 49.3 + - - +
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Residues in contact with ASP 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B PRO* 4.5 10.1 - - - +
590B TRP* 2.8 25.2 + - - -
623B ARG* 2.8 37.4 + - + +
624B PRO* 3.3 27.2 + - + +
626B TRP* 1.4 99.4 - - + +
628B VAL* 1.4 56.7 + - - +
630B ARG* 3.3 9.8 - - - +
631B LYS* 3.1 25.5 + - - +
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Residues in contact with VAL 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B TRP* 3.6 22.2 - - + -
598B LEU* 3.5 32.1 - - + -
614B GLU* 3.4 33.4 - - + +
617B VAL* 3.8 13.2 - - + +
618B GLY* 4.0 13.0 - - - +
623B ARG* 4.9 2.2 - - + +
624B PRO 3.4 11.7 - - - +
625B CYS* 3.3 17.5 - - - +
627B ASP* 1.4 73.3 - - - +
629B HIS* 1.3 63.4 - - - +
631B LYS* 4.0 4.7 - - - -
632B LEU* 4.0 8.5 - - - -
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Residues in contact with HIS 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B TYR* 3.5 41.0 - + + +
579B GLY* 5.1 0.7 - - - -
580B THR* 3.6 21.9 + - - -
612B ARG* 4.3 6.0 + - - -
614B GLU* 3.0 32.7 + - + -
625B CYS 3.1 14.6 + - - +
626B TRP 3.1 9.9 + - - +
628B VAL* 1.3 75.6 - - - +
630B ARG* 1.4 57.3 + - - +
632B LEU* 3.4 11.7 - - + +
633B GLN* 3.1 59.5 + - - +
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Residues in contact with ARG 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B THR* 3.3 42.9 + - + +
626B TRP* 3.0 33.4 + - - +
627B ASP* 3.3 17.5 + - - +
629B HIS* 1.4 73.0 + - - +
631B LYS* 1.4 55.3 + - - +
633B GLN* 3.2 11.0 + - - +
634B GLU* 2.8 55.6 + - + +
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Residues in contact with LYS 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B TRP* 3.5 59.3 + - + +
595B VAL* 3.6 25.7 - - - +
598B LEU* 4.4 1.8 - - + -
627B ASP 3.1 18.5 + - - +
628B VAL* 4.4 0.7 - - - -
630B ARG* 1.4 75.3 - - - +
632B LEU* 1.4 53.5 + - - +
634B GLU* 3.1 31.1 + - - +
635B LEU* 2.8 66.2 + - + +
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Residues in contact with LEU 632 (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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598B LEU* 3.8 34.7 - - + +
602B PHE* 3.7 30.5 - - + -
612B ARG* 3.5 21.5 - - - +
613B PRO* 4.8 0.9 - - + -
614B GLU* 3.3 31.2 - - - +
628B VAL 4.0 5.3 - - - -
629B HIS* 3.4 17.6 + - + +
631B LYS* 1.4 78.0 - - - +
633B GLN* 1.3 62.5 + - + +
635B LEU* 3.7 1.7 + - - +
636B ASP* 3.3 16.1 + - - -
637B LEU* 3.8 22.6 + - + +
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Residues in contact with GLN 633 (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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580B THR* 3.2 24.6 + - + +
629B HIS* 3.1 45.2 + - + +
630B ARG* 3.2 6.8 + - - +
632B LEU* 1.3 80.0 - - + +
634B GLU* 1.4 62.0 + - - +
636B ASP* 3.5 16.1 + - - +
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Residues in contact with GLU 634 (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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630B ARG* 2.8 51.8 + - - +
631B LYS* 3.1 37.0 + - - +
633B GLN* 1.4 73.0 - - - +
635B LEU* 1.4 61.9 + - + +
636B ASP* 3.5 3.8 + - - +
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Residues in contact with LEU 635 (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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595B VAL* 3.8 32.1 - - + +
598B LEU* 4.3 15.7 - - + -
599B GLU* 5.2 1.6 - - + +
631B LYS* 2.8 54.3 + - + +
632B LEU 4.1 1.1 - - - +
634B GLU* 1.4 73.3 - - - +
636B ASP* 1.4 67.8 + - - +
637B LEU* 3.5 29.7 + - + +
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Residues in contact with ASP 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B LEU 3.3 8.4 + - - -
633B GLN* 3.5 12.9 + - - +
634B GLU 3.3 4.4 - - - +
635B LEU* 1.4 78.0 - - - +
637B LEU* 1.3 65.3 + - - +
638B ARG* 3.4 39.1 + - - +
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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