Contacts of the helix formed by residues 612 - 621 (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 ARG 612 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B TYR* 3.4 44.0 + - + +
602B PHE* 5.2 8.9 - - - -
605B ILE* 4.6 1.8 - - - -
611B LEU* 1.3 90.0 - - - +
613B PRO* 1.4 74.3 - - - +
614B GLU* 2.8 42.3 + - - +
615B CYS* 3.8 16.9 + - - +
616B PHE* 4.1 5.5 + - - +
629B HIS* 4.3 7.1 + - - -
632B LEU* 3.5 24.0 - - - +
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Residues in contact with PRO 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B LEU* 4.6 8.3 - - + -
601B MET* 4.3 6.5 - - + -
602B PHE* 4.0 47.1 - - + +
605B ILE* 4.0 28.0 - - + -
606B GLY 6.1 0.2 - - - +
612B ARG* 1.4 98.5 - - + +
614B GLU* 1.3 64.2 + - - +
616B PHE* 3.4 4.4 + - + +
617B VAL* 2.8 38.4 + - + +
628B VAL* 5.1 0.4 - - - -
632B LEU* 4.8 2.2 - - + -
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Residues in contact with GLU 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B TYR* 3.8 10.8 - - + -
612B ARG* 2.8 42.9 + - + +
613B PRO* 1.3 82.9 - - - +
615B CYS* 1.4 57.1 + - - +
617B VAL* 3.4 0.3 + - - -
618B GLY* 2.9 26.5 + - - -
625B CYS* 3.5 20.5 - - - +
628B VAL* 3.4 21.2 - - + +
629B HIS* 3.0 44.9 - - + +
632B LEU* 3.3 24.4 - - + +
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Residues in contact with CYS 615 (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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568B PRO 5.7 1.8 - - - -
569B PRO* 5.7 0.9 - - - -
570B CYS* 3.8 24.5 - - + +
572B ASN* 4.8 2.8 + - - +
574B CYS* 3.9 17.9 - - - -
575B TYR* 4.4 10.1 - - - -
611B LEU* 6.3 1.6 - - + -
612B ARG* 3.8 14.1 + - - +
613B PRO 3.5 0.4 - - - -
614B GLU* 1.4 73.1 - - - +
616B PHE* 1.4 57.1 + - - +
618B GLY* 3.7 1.2 - - - -
619B ALA* 3.0 27.9 + - - +
625B CYS* 3.7 21.5 - - - -
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Residues in contact with PHE 616 (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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601B MET* 3.6 48.7 - - + -
605B ILE* 5.4 3.1 - - + -
611B LEU* 5.3 9.2 - - + +
612B ARG 4.1 7.0 + - - +
613B PRO* 3.4 9.4 + - + +
615B CYS* 1.4 76.3 - - - +
617B VAL* 1.4 59.7 + - - +
619B ALA* 3.1 10.1 + - + +
620B ILE* 2.9 58.8 + - + +
2629B PHE* 5.7 9.6 - + - -
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Residues in contact with VAL 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B TRP* 4.4 0.4 - - + -
597B THR* 4.1 6.5 - - + +
598B LEU* 3.8 31.2 - - + +
601B MET* 3.7 33.2 - - + -
613B PRO 2.8 24.2 + - - +
616B PHE* 1.4 70.0 - - - +
618B GLY* 1.3 53.1 + - - +
620B ILE* 3.2 6.5 + - - +
621B LEU* 2.8 56.9 + - + +
628B VAL* 3.8 23.8 - - + +
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Residues in contact with GLY 618 (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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572B ASN* 3.8 10.4 + - - -
614B GLU 2.9 16.5 + - - -
615B CYS 3.7 2.5 - - - -
617B VAL* 1.3 77.9 - - - +
619B ALA* 1.4 57.9 + - - +
620B ILE 3.5 0.5 + - - -
621B LEU 3.5 14.3 - - - -
623B ARG* 3.2 33.3 + - - +
624B PRO 4.8 0.7 - - - -
625B CYS 5.1 0.2 - - - -
628B VAL* 4.0 9.6 - - - +
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Residues in contact with ALA 619 (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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572B ASN* 4.3 5.1 - - + +
615B CYS 3.0 15.4 + - - +
616B PHE* 3.1 14.1 + - + +
618B GLY* 1.4 74.4 - - - +
620B ILE* 1.4 65.4 + - + +
621B LEU 4.9 0.6 - - - -
2641B VAL* 4.8 13.9 - - - +
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Residues in contact with ILE 620 (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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597B THR* 3.6 30.3 - - + -
616B PHE* 2.9 54.0 + - + +
617B VAL* 4.0 3.6 - - - +
619B ALA* 1.4 82.0 - - + +
621B LEU* 1.3 69.5 + - + +
2644B ARG* 5.1 5.7 - - - +
2647B GLY* 3.3 45.3 - - - +
2648B GLU* 4.6 1.6 - - - +
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Residues in contact with LEU 621 (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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590B TRP* 3.7 35.7 - - + -
594B GLU* 3.7 38.7 - - + +
597B THR* 3.8 21.1 - - + +
617B VAL* 2.8 25.0 + - + +
618B GLY 3.5 6.1 - - - -
619B ALA 4.9 0.9 - - - -
620B ILE* 1.3 93.4 - - + +
623B ARG* 3.2 45.2 + - + +
2648B GLU* 6.1 2.7 - - + -
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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