Contacts of the helix formed by residues 588 - 602 (chain J) in PDB entry 6K71
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 588 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582J LYS* 4.9 1.1 - - - +
586J ASN 3.8 2.4 + - - -
587J ILE* 1.3 81.2 - - - +
589J LEU* 1.3 64.9 + - - +
590J LYS* 3.9 7.3 + - - +
591J GLU* 2.3 40.8 + - - +
592J VAL* 3.4 16.2 + - - +
209P ALA* 5.9 8.3 - - - -
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Residues in contact with LEU 589 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582J LYS* 4.5 16.8 - - - +
588J SER* 1.3 75.7 - - - +
590J LYS* 1.3 60.5 + - + +
591J GLU 2.9 6.5 + - - -
592J VAL* 4.6 2.5 - - - +
593J MET* 3.0 56.4 + - + +
635J TYR* 4.4 13.5 - - + +
638J ARG* 4.9 17.0 - - - +
212P GLN* 3.7 41.5 - - + +
213P GLY 5.7 0.4 - - - +
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Residues in contact with LYS 590 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588J SER* 3.3 6.2 + - - +
589J LEU* 1.3 78.4 - - + +
591J GLU* 1.3 66.4 + - - +
593J MET* 5.6 0.4 - - - -
594J GLN* 2.7 35.6 + - - +
638J ARG* 5.3 10.5 - - - +
644J GLU* 5.2 20.2 + - + -
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Residues in contact with GLU 591 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550J ILE* 3.7 31.2 - - + -
587J ILE* 3.8 9.6 - - + -
588J SER* 2.3 38.4 + - - +
590J LYS* 1.3 86.3 - - - +
592J VAL* 1.3 59.7 + - - +
593J MET 3.4 1.3 - - - -
594J GLN* 3.3 15.3 - - - +
595J VAL* 3.0 33.6 + - - +
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Residues in contact with VAL 592 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553J PHE* 3.6 35.6 - - + -
578J ILE* 5.7 1.6 - - + +
579J ASN* 6.0 0.2 - - - +
582J LYS* 3.7 28.5 - - + -
587J ILE* 3.8 21.8 - - + +
588J SER 3.4 16.6 + - - +
589J LEU* 3.2 5.6 + - - +
591J GLU* 1.3 76.6 - - - +
593J MET* 1.3 56.6 + - - +
595J VAL* 3.2 2.3 + - - +
596J LEU* 3.0 35.8 + - + +
635J TYR* 3.5 19.7 - - - +
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Residues in contact with MET 593 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589J LEU* 3.0 46.1 + - + +
592J VAL* 1.3 75.4 - - - +
594J GLN* 1.3 62.8 + - + +
596J LEU* 3.5 9.0 - - + +
597J SER* 3.0 30.0 + - - -
632J PHE* 4.9 8.3 - - + -
635J TYR* 3.4 48.5 - - + +
636J ILE* 4.9 3.8 - - - -
638J ARG* 5.4 0.4 - - - -
641J ASP* 3.2 41.5 - - - +
645J ALA* 6.0 6.7 - - + -
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Residues in contact with GLN 594 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590J LYS* 2.7 35.4 + - - +
591J GLU* 3.3 13.6 - - - +
593J MET* 1.3 78.4 - - + +
595J VAL* 1.3 60.6 + - + +
597J SER* 3.8 2.1 - - - -
598J HIS* 2.9 32.2 + - - +
645J ALA* 6.4 0.9 - - - +
648J ALA* 4.5 26.3 - - + +
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Residues in contact with VAL 595 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550J ILE* 3.7 26.5 - - + +
553J PHE* 3.8 22.7 - - + +
554J GLN* 3.8 31.6 - - + +
557J VAL* 4.8 5.2 - - + -
591J GLU 3.0 18.3 + - - +
592J VAL 3.2 3.3 + - - +
594J GLN* 1.3 78.3 - - + +
596J LEU* 1.3 59.3 + - - +
598J HIS* 3.2 12.7 - - - +
599J VAL* 3.0 32.0 + - + +
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Residues in contact with LEU 596 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553J PHE* 5.3 1.1 - - + -
557J VAL* 4.8 8.1 - - + -
578J ILE* 3.9 33.9 - - + -
592J VAL* 3.0 30.4 + - + +
593J MET* 3.5 5.2 - - - +
595J VAL* 1.3 79.3 - - - +
597J SER* 1.3 69.7 + - - +
599J VAL* 3.4 1.1 + - - +
600J VAL* 3.0 38.8 + - + +
632J PHE* 3.6 36.3 - - + -
635J TYR* 3.5 35.9 - - + +
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Residues in contact with SER 597 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593J MET 3.0 17.4 + - - -
594J GLN* 4.2 2.2 - - - -
596J LEU* 1.3 77.2 - - - +
598J HIS* 1.3 56.9 + - - +
600J VAL* 3.7 6.1 - - - -
601J LEU* 2.9 39.1 + - - +
632J PHE* 3.5 31.9 - - - -
645J ALA* 5.5 7.6 - - - +
649J ILE* 5.4 7.0 - - - -
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Residues in contact with HIS 598 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554J GLN* 4.8 17.5 + - - -
594J GLN 2.9 20.9 + - - +
595J VAL* 3.2 15.6 - - - +
597J SER* 1.3 75.4 - - - +
599J VAL* 1.3 55.1 + - + +
601J LEU* 3.0 7.9 + - - +
602J GLU* 2.8 67.8 + - - +
649J ILE* 5.2 7.2 - - + -
652J PHE* 3.6 32.5 - + + -
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Residues in contact with VAL 599 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554J GLN* 4.3 27.8 - - + +
557J VAL* 4.8 11.0 - - + +
558J LEU* 4.0 31.9 - - + +
561J LEU* 5.3 8.1 - - + -
595J VAL* 3.0 20.5 + - + +
596J LEU 4.2 2.0 - - - +
598J HIS* 1.3 76.7 - - + +
600J VAL* 1.3 60.9 + - + +
602J GLU* 2.8 33.4 + - + +
603J PHE* 3.0 16.0 + - + -
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Residues in contact with VAL 600 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557J VAL* 6.5 0.7 - - + -
561J LEU* 4.4 23.6 - - + -
578J ILE* 6.5 0.4 - - + -
596J LEU* 3.0 22.8 + - + +
597J SER* 3.7 5.8 - - - +
599J VAL* 1.3 78.1 - - + +
601J LEU* 1.3 67.2 + - + +
603J PHE* 3.0 43.2 - - + -
628J TRP* 3.6 41.3 - - + -
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Residues in contact with LEU 601 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597J SER* 2.9 20.7 + - - +
598J HIS 3.0 4.7 + - - +
600J VAL* 1.3 85.4 - - + +
602J GLU* 1.3 58.7 + - - +
603J PHE 3.3 4.7 - - - -
604J PRO* 3.3 16.8 - - + +
621J LEU* 6.3 2.9 - - + -
628J TRP* 6.5 1.1 - - + -
649J ILE* 3.7 37.5 - - + -
652J PHE* 5.9 3.6 - - + -
653J PHE* 4.5 17.0 - - + -
666J VAL* 5.4 13.2 - - + -
670J PHE* 6.0 8.1 - - + -
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Residues in contact with GLU 602 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554J GLN* 5.2 3.3 + - - -
598J HIS* 2.8 60.2 + - - +
599J VAL* 2.8 26.4 + - + +
601J LEU* 1.3 73.1 - - - +
603J PHE* 1.3 63.3 + - - +
604J PRO* 4.0 1.6 - - - -
605J LEU* 4.4 19.5 + - + +
606J GLN* 4.8 4.7 + - - +
652J PHE* 3.1 26.6 - - + -
659J LEU* 6.6 0.2 - - + -
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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