Contacts of the helix formed by residues 580 - 595 (chain B) in PDB entry 4JWE
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 ASP 580 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532B LEU* 4.0 2.9 - - - -
575B ALA 5.5 0.2 + - - -
578B GLY* 3.6 4.6 + - - -
579B GLU* 1.3 76.8 - - - +
581B LYS* 1.4 61.1 + - - +
582B ALA* 3.3 13.4 + - - +
583B ALA* 2.8 41.8 + - + +
584B ILE* 3.2 25.8 + - - +
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Residues in contact with LYS 581 (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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531B GLU* 5.0 10.5 - - + +
532B LEU* 3.9 12.4 - - + +
534B GLN* 6.4 0.4 - - - +
535B THR* 3.3 35.6 - - + +
579B GLU 3.8 3.6 + - - -
580B ASP* 1.4 69.0 + - - +
582B ALA* 1.3 66.9 + - - +
584B ILE* 3.3 4.5 + - - +
585B GLU* 3.0 55.7 + - - +
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Residues in contact with ALA 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B ASP* 3.3 10.1 + - - +
581B LYS* 1.3 77.3 - - - +
583B ALA* 1.4 53.1 + - - +
585B GLU* 3.2 13.3 + - - +
586B ALA* 2.7 38.1 + - - +
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Residues in contact with ALA 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B ALA* 3.9 11.2 - - + +
580B ASP* 2.8 34.6 + - + +
581B LYS 3.4 0.2 - - - -
582B ALA* 1.4 71.1 - - - +
584B ILE* 1.4 62.2 + - + +
586B ALA* 3.5 7.7 + - - +
587B LYS* 3.3 30.1 + - - +
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Residues in contact with ILE 584 (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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532B LEU* 3.7 24.2 - - + -
535B THR* 3.8 14.6 - - + +
536B ARG* 3.8 19.3 - - + -
572B LEU* 3.7 8.9 - - + +
575B ALA* 3.4 34.8 - - - +
576B LEU* 3.8 23.3 - - + -
578B GLY 4.2 5.2 - - - +
580B ASP 3.2 15.8 + - - +
581B LYS 3.3 5.8 + - - +
583B ALA* 1.4 73.4 - - - +
585B GLU* 1.4 62.5 + - - +
587B LYS* 3.2 3.5 + - - +
588B MET* 3.2 40.0 + - + +
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Residues in contact with GLU 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B THR* 3.9 8.7 + - + +
538B GLN* 4.9 6.0 - - - +
581B LYS* 3.0 51.8 + - - +
582B ALA* 3.6 13.1 - - - +
584B ILE* 1.4 75.6 - - - +
586B ALA* 1.4 60.6 + - - +
588B MET* 3.2 24.5 + - + +
589B GLN* 3.1 21.8 + - - +
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Residues in contact with ALA 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B ALA 2.7 21.0 + - - +
583B ALA* 3.6 10.5 - - - +
584B ILE 3.3 0.4 - - - -
585B GLU* 1.4 70.5 - - - +
587B LYS* 1.3 67.1 + - + +
589B GLN* 3.3 9.4 + - - +
590B GLU* 3.3 29.2 + - - +
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Residues in contact with LYS 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ALA 4.4 6.9 - - - +
571B ALA* 3.8 23.5 - - + +
572B LEU* 3.8 24.5 - - + +
575B ALA* 3.6 17.0 - - + -
583B ALA* 3.3 13.9 + - - +
584B ILE 3.2 8.6 + - - +
586B ALA* 1.3 76.5 - - - +
588B MET* 1.3 64.6 + - - +
590B GLU* 2.9 43.1 + - - +
591B LEU* 3.5 18.7 + - - +
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Residues in contact with MET 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B THR* 4.1 11.7 - - + +
538B GLN* 4.2 13.9 - - + +
539B GLY* 3.9 17.3 - - - -
542B LEU* 3.8 28.1 - - + +
572B LEU* 3.7 16.8 - - + -
584B ILE* 3.2 34.7 + - + +
585B GLU* 3.2 36.8 + - + +
587B LYS* 1.3 74.4 - - - +
589B GLN* 1.4 62.4 + - - +
591B LEU* 3.3 5.2 - - - +
592B ALA* 3.2 21.4 + - - +
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Residues in contact with GLN 589 (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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585B GLU 3.1 11.5 + - - +
586B ALA* 3.4 12.6 - - - +
588B MET* 1.4 74.3 - - - +
590B GLU* 1.4 59.1 + - + +
592B ALA* 3.2 11.0 + - - +
593B GLN* 3.0 68.7 + - - +
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Residues in contact with GLU 590 (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 ALA* 4.1 10.6 - - + +
571B ALA* 4.6 6.6 - - + +
586B ALA* 3.3 13.6 + - - +
587B LYS* 2.9 50.6 + - - +
588B MET 3.4 0.2 - - - -
589B GLN* 1.4 76.7 - - + +
591B LEU* 1.3 62.4 + - - +
593B GLN* 3.6 25.1 - - - +
594B VAL* 3.6 17.0 + - - +
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Residues in contact with LEU 591 (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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542B LEU* 3.8 28.5 - - + -
543B LEU* 5.0 0.9 - - - -
546B THR* 3.3 33.7 - - + +
565B ILE* 5.1 2.2 - - + +
568B ALA* 3.8 26.2 - - + +
569B LEU* 3.8 34.1 - - + -
572B LEU* 4.4 9.6 - - + -
587B LYS 3.5 8.1 + - - +
588B MET 3.3 9.6 + - - +
589B GLN 3.2 0.2 - - - -
590B GLU* 1.3 74.9 - - - +
592B ALA* 1.4 67.9 + - - +
594B VAL* 3.1 15.6 + - + +
595B SER* 3.0 23.5 + - - +
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Residues in contact with ALA 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU* 5.7 5.8 - - + -
588B MET 3.2 9.6 + - - +
589B GLN* 3.2 19.5 + - - +
591B LEU* 1.4 80.7 - - + +
593B GLN* 1.4 60.6 + - - +
595B SER* 3.3 24.6 + - - +
596B GLN* 4.5 5.2 + - - +
599B MET* 6.2 3.8 - - + -
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Residues in contact with GLN 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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589B GLN* 3.0 52.4 + - - +
590B GLU* 3.6 19.7 - - - +
591B LEU 3.1 0.2 + - - -
592B ALA* 1.4 75.9 - - - +
594B VAL* 1.3 62.7 + - + +
595B SER 3.4 0.6 + - - -
596B GLN* 4.8 8.0 + - - +
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Residues in contact with VAL 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B ASP* 4.4 13.7 - - - +
564B ALA* 3.4 47.3 - - + +
565B ILE* 3.3 23.8 - - + +
568B ALA* 4.1 6.1 - - + -
590B GLU 3.6 13.5 - - - +
591B LEU 3.1 14.6 + - - +
593B GLN* 1.3 79.8 - - + +
595B SER* 1.4 57.3 + - - +
596B GLN 3.6 3.7 + - - -
597B LYS 5.3 0.2 + - - -
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Residues in contact with SER 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B THR* 4.1 1.2 - - - +
565B ILE* 3.4 22.7 - - - +
591B LEU* 3.0 30.7 + - - +
592B ALA* 3.3 16.0 + - - +
594B VAL* 1.4 75.3 - - - +
596B GLN* 1.3 62.6 + - - +
597B LYS 3.8 1.3 - - - +
598B LEU* 3.8 22.7 - - - +
599B MET* 3.1 28.5 - - - +
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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