Contacts of the helix formed by residues 591 - 606 (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 SER 591 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589B PRO 3.6 3.4 + - - -
590B TRP* 1.3 75.9 - - - +
592B GLU* 1.4 64.3 + - - +
593B ASN* 3.8 7.5 + - - +
594B GLU* 2.8 35.7 + - - +
595B VAL* 3.1 21.1 + - - +
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Residues in contact with GLU 592 (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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591B SER* 1.4 72.0 - - - +
593B ASN* 1.3 64.7 + - - +
595B VAL* 3.1 10.9 + - - +
596B GLY* 2.9 25.3 + - - -
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Residues in contact with ASN 593 (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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591B SER* 3.4 7.3 + - - +
592B GLU* 1.3 82.6 - - - +
594B GLU* 1.3 52.6 + - + +
596B GLY* 3.7 2.7 + - - +
597B THR* 2.7 35.0 + - - -
600B TRP* 4.2 5.6 - - - -
2644B ARG* 3.5 27.3 - - - +
2648B GLU* 3.5 25.6 + - - +
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Residues in contact with GLU 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B PRO 3.8 1.9 - - - +
590B TRP* 3.4 25.4 - - + -
591B SER* 2.8 43.2 + - - +
593B ASN* 1.3 75.3 - - + +
595B VAL* 1.4 66.8 + - - +
597B THR* 3.4 6.1 + - - -
598B LEU 3.3 14.0 + - - -
621B LEU* 3.7 27.7 - - + +
623B ARG* 2.9 40.5 + - - +
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Residues in contact with VAL 595 (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* 4.1 17.0 - - + +
591B SER 3.1 15.6 + - - +
592B GLU* 3.4 9.9 - - - +
594B GLU* 1.4 73.4 - - - +
596B GLY* 1.3 61.5 - - - +
598B LEU* 3.1 9.2 + - - +
599B GLU* 3.0 43.1 + - - +
631B LYS* 3.6 27.4 - - - +
635B LEU* 3.8 25.0 - - + +
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Residues in contact with GLY 596 (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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592B GLU 2.9 13.9 + - - -
593B ASN* 3.9 3.4 - - - -
595B VAL* 1.3 76.6 - - - +
597B THR* 1.3 54.9 + - - +
599B GLU* 3.1 17.3 + - - +
600B TRP* 2.9 49.2 + - - -
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Residues in contact with THR 597 (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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593B ASN 2.7 21.6 + - - -
594B GLU 3.6 9.0 - - - -
595B VAL 3.3 0.6 - - - -
596B GLY* 1.3 73.8 - - - +
598B LEU* 1.4 63.0 + - - +
600B TRP* 3.3 30.5 - - + +
601B MET* 3.1 33.5 + - + +
617B VAL* 4.3 11.0 - - + -
620B ILE* 3.6 30.7 - - + -
621B LEU* 3.8 13.9 - - + +
2648B GLU* 3.8 11.3 - - - +
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Residues in contact with LEU 598 (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* 4.2 17.7 - - + -
594B GLU 3.3 8.3 + - - +
595B VAL 3.1 10.0 + - - +
597B THR* 1.4 77.4 - - - +
599B GLU* 1.3 52.7 + - - +
601B MET* 3.9 0.2 - - - -
602B PHE* 2.8 37.9 + - - +
613B PRO* 4.6 9.2 - - + -
614B GLU 5.3 0.2 - - - +
617B VAL* 3.8 17.6 - - + +
628B VAL* 3.5 29.8 - - + -
631B LYS* 4.4 0.9 - - + -
632B LEU* 3.8 52.5 - - + +
635B LEU* 4.3 14.4 - - + -
637B LEU* 4.3 4.7 - - + -
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Residues in contact with GLU 599 (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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492B LEU* 3.7 27.6 - - + +
495B LYS* 3.7 43.5 + - - +
496B VAL* 3.9 7.4 - - + +
595B VAL* 3.0 37.8 + - + +
596B GLY* 3.2 16.5 - - - +
598B LEU* 1.3 71.9 - - - +
600B TRP* 1.4 60.2 + - - +
602B PHE* 3.3 6.1 + - - +
603B ALA* 3.0 29.8 + - - +
635B LEU* 5.2 1.3 - - + +
637B LEU* 4.3 18.2 - - + +
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Residues in contact with TRP 600 (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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496B VAL* 3.7 28.1 - - + +
499B ALA* 3.4 31.6 - - + -
500B LEU* 4.2 25.3 - - + +
593B ASN* 4.2 4.5 - - - -
596B GLY* 2.9 34.4 + - - -
597B THR* 3.3 40.8 + - + +
599B GLU* 1.4 73.7 - - + +
601B MET* 1.4 93.5 + - - +
603B ALA* 3.8 0.2 - - - +
604B THR* 2.9 32.2 + - + +
2648B GLU* 3.7 38.5 + - + -
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Residues in contact with MET 601 (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* 3.1 25.0 + - + +
600B TRP* 1.4 96.6 - - + +
602B PHE* 1.4 56.3 + - - +
604B THR* 3.4 10.3 + - - +
605B ILE* 2.8 60.4 + - + +
613B PRO* 4.3 6.7 - - + -
616B PHE* 3.6 40.6 - - + -
617B VAL* 3.7 26.0 - - + -
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Residues in contact with PHE 602 (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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492B LEU* 4.4 9.4 - - + -
598B LEU 2.8 23.5 + - - +
599B GLU 3.7 3.8 - - - +
601B MET* 1.4 71.8 - - - +
603B ALA* 1.3 63.4 + - - +
605B ILE* 3.6 1.9 + - - +
606B GLY* 3.2 19.0 + - - +
612B ARG* 5.2 9.0 - - - -
613B PRO* 4.0 22.5 - - + +
632B LEU* 3.7 27.1 - - + -
637B LEU* 3.5 50.5 - - + -
638B ARG* 3.9 7.9 - - - -
639B LEU* 3.7 40.3 - - + +
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Residues in contact with ALA 603 (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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492B LEU* 5.2 1.3 - - + -
493B MET* 3.9 30.7 - - + -
496B VAL* 4.1 14.8 - - + -
542B LEU* 4.6 2.0 - - + -
546B TRP* 3.0 31.3 + - + -
599B GLU 3.0 17.5 + - - +
600B TRP 3.8 3.8 - - - +
602B PHE* 1.3 76.5 - - + +
604B THR* 1.3 58.4 + - + +
606B GLY* 3.2 8.1 + - - -
639B LEU* 3.7 11.2 - - - +
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Residues in contact with THR 604 (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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496B VAL* 4.8 1.8 - - + -
500B LEU* 4.2 23.8 - - + -
538B LEU* 4.9 4.3 - - + -
542B LEU* 4.0 24.5 - - + -
545B LYS* 3.1 26.6 + - - +
600B TRP* 2.9 22.5 + - - +
601B MET* 3.4 18.2 + - - +
603B ALA* 1.3 72.3 - - + +
605B ILE* 1.4 67.6 + - - +
606B GLY 3.1 1.6 - - - -
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Residues in contact with ILE 605 (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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545B LYS* 3.8 2.5 + - - +
549B GLN* 3.0 22.3 + - - -
601B MET* 2.8 55.4 + - + +
602B PHE 4.1 3.1 - - - +
604B THR* 1.4 72.8 + - - +
606B GLY* 1.3 60.7 + - - +
608B SER* 3.5 12.0 - - - -
611B LEU* 3.5 57.7 - - + +
613B PRO* 4.0 30.3 - - + -
616B PHE* 5.4 5.2 - - + -
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Residues in contact with GLY 606 (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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546B TRP* 3.5 16.4 - - - -
549B GLN* 3.7 0.4 - - - -
602B PHE* 3.2 13.9 + - - +
603B ALA 3.2 14.6 + - - -
604B THR 3.1 2.2 - - - -
605B ILE* 1.3 77.1 - - - +
607B TYR* 1.3 57.7 + - - -
608B SER* 3.0 13.1 + - - -
613B PRO* 6.1 0.2 - - - +
639B LEU* 3.6 17.0 - - - +
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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