Contacts of the helix formed by residues 587 - 602 (chain B) in PDB entry 1WZ2
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 PRO 587 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548B LEU* 5.6 4.9 - - + -
553B LYS* 5.1 16.2 - - - +
581B GLU* 4.1 9.9 - - + +
585B GLY 4.4 2.9 - - - +
586B ILE* 1.3 99.5 - - + +
588B ALA* 1.3 62.1 + - - +
589B GLU* 3.0 28.0 - - - +
590B ILE* 3.3 20.5 + - + -
591B ILE* 3.0 15.4 - - - +
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Residues in contact with ALA 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B GLU* 3.6 27.4 - - + +
578B LYS* 3.2 43.3 - - + +
581B GLU* 3.9 11.2 + - - +
586B ILE 3.5 1.7 + - - -
587B PRO* 1.3 67.6 - - - +
589B GLU* 1.3 64.8 + - - +
590B ILE 3.0 1.8 - - - -
591B ILE* 2.8 27.4 + - - +
592B HIS 3.0 10.4 + - - -
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Residues in contact with GLU 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B GLU* 4.9 0.9 - - - -
578B LYS* 4.9 3.3 + - - +
587B PRO* 3.0 25.4 - - - +
588B ALA* 1.3 84.7 + - - +
590B ILE* 1.3 71.3 + - + +
591B ILE 3.3 0.2 - - - -
592B HIS* 3.8 9.8 - - - +
593B GLU* 3.3 24.3 + - - +
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Residues in contact with ILE 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B HIS* 4.7 16.9 - - + +
548B LEU* 4.2 28.0 - - + -
586B ILE* 4.0 9.9 - - + -
587B PRO* 3.3 36.1 - - + +
588B ALA 3.0 0.4 - - - -
589B GLU* 1.3 92.1 - - + +
591B ILE* 1.3 66.2 + - - +
593B GLU* 3.7 15.7 + - - +
594B MET* 3.1 23.0 + - - +
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Residues in contact with ILE 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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563B PHE* 3.7 32.1 - - + -
566B TYR* 3.9 29.4 - - + -
567B ILE* 4.0 3.6 - - + -
577B GLU* 4.8 12.6 - - + +
580B LEU* 4.8 5.2 - - + +
581B GLU* 5.5 0.2 - - - -
584B THR* 4.6 2.0 - - - +
586B ILE* 3.2 34.5 - - + +
587B PRO 3.0 14.6 - - - +
588B ALA* 2.8 12.0 + - - +
590B ILE* 1.3 75.7 - - - +
592B HIS* 1.3 67.7 + - - +
594B MET* 2.8 32.8 + - + +
595B LYS* 2.9 13.0 + - - +
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Residues in contact with HIS 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B TYR* 5.1 0.4 - - - -
572B PHE* 3.6 38.5 - + - -
577B GLU* 3.1 35.8 + - - +
588B ALA 3.0 6.5 + - - +
589B GLU* 3.8 12.6 - - - +
591B ILE* 1.3 76.4 - - - +
593B GLU* 1.3 51.4 + - - +
595B LYS* 3.3 0.7 + - - -
596B GLU* 2.7 56.0 + - + +
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Residues in contact with GLU 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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27B ILE* 6.1 3.1 - - + -
544B HIS* 3.0 33.5 - - - +
589B GLU 3.3 15.9 + - - +
590B ILE* 3.7 17.6 - - - +
591B ILE 3.1 0.2 - - - -
592B HIS* 1.3 78.0 + - - +
594B MET* 1.3 54.2 + - - +
596B GLU* 2.9 17.5 + - + +
597B GLU* 2.7 44.7 + - + +
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Residues in contact with MET 594 (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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541B ILE* 3.2 35.9 - - + +
544B HIS* 3.5 22.0 - - + -
545B ILE* 3.8 23.6 - - - -
548B LEU* 5.8 4.9 - - - -
563B PHE* 3.8 22.4 - - + -
567B ILE* 3.4 35.0 - - + -
586B ILE* 6.3 0.7 - - - -
590B ILE* 3.1 12.3 + - - +
591B ILE* 2.8 24.4 + - + +
593B GLU* 1.3 74.7 - - - +
595B LYS* 1.3 59.2 + - - +
597B GLU* 2.9 24.4 - - - +
598B PHE 3.3 4.2 + - - -
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Residues in contact with LYS 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B TYR* 3.1 34.3 - - + +
567B ILE* 3.4 32.9 - - + +
568B PHE 4.4 4.9 - - - +
569B LEU 4.8 1.1 - - - -
570B GLU 3.1 17.7 - - - -
571B GLU* 4.5 1.3 - - - +
572B PHE* 3.5 41.4 - - + +
591B ILE 2.9 7.4 + - - +
592B HIS* 3.8 2.9 - - - +
594B MET* 1.3 74.1 - - - +
596B GLU* 1.3 67.5 + - - +
597B GLU 3.2 0.3 + - - -
598B PHE* 3.3 7.1 + - + +
599B GLU* 2.9 52.4 + - + +
630B ARG* 4.1 11.7 - - - +
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Residues in contact with GLU 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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27B ILE* 3.5 25.9 - - + +
28B ARG* 5.6 2.3 - - - +
572B PHE* 3.7 10.9 - - + -
592B HIS* 2.7 42.0 + - + +
593B GLU* 3.1 18.9 - - - +
595B LYS* 1.3 76.2 - - - +
597B GLU* 1.3 64.5 + - - +
599B GLU* 3.9 3.8 - - - +
600B TYR* 3.1 19.4 + - - +
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Residues in contact with GLU 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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27B ILE* 3.1 34.8 + - + +
28B ARG* 5.4 1.7 + - - -
148B ARG* 3.5 9.9 + - - -
540B THR* 3.2 19.5 - - - +
543B ARG* 4.2 15.2 + - + -
544B HIS* 3.3 36.2 + - + +
593B GLU* 2.7 17.1 + - + +
594B MET 2.9 8.7 - - - +
596B GLU* 1.3 75.6 - - - +
598B PHE* 1.3 55.3 + - - +
600B TYR* 2.5 30.7 + - - +
601B TRP* 2.9 25.8 + - - +
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Residues in contact with PHE 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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537B ALA* 3.3 16.6 - - + -
540B THR* 2.9 33.4 + - + +
541B ILE* 4.7 1.3 - - + -
567B ILE 4.4 3.1 - - - +
568B PHE* 3.3 61.5 - + + -
594B MET 3.3 5.0 + - - +
595B LYS* 3.7 11.2 - - + +
597B GLU* 1.3 77.8 - - - +
599B GLU* 1.3 71.1 + - + +
600B TYR 3.0 0.5 + - - -
602B TYR* 2.9 49.1 + + - +
629B PHE* 3.9 13.7 - + - -
633B HIS* 3.2 37.2 - + - -
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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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32B LYS* 4.4 9.7 - - - +
572B PHE* 4.6 9.1 - - + -
595B LYS* 2.9 45.8 + - + +
596B GLU* 3.9 6.3 - - - +
598B PHE* 1.3 80.5 - - + +
600B TYR* 1.3 62.2 + - - +
602B TYR 3.4 9.7 - - - +
630B ARG* 3.7 19.9 + - - +
632B GLU* 4.0 3.6 - - - +
633B HIS* 3.4 27.0 + - - +
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Residues in contact with TYR 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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27B ILE* 3.2 49.1 - - + -
30B LYS 3.1 4.9 + - - -
31B PRO 3.0 15.9 + - - -
32B LYS* 3.2 49.8 - - + +
35B LYS* 3.9 19.6 - - + +
73B ASN* 2.7 28.6 + - - +
596B GLU 3.1 13.0 + - - +
597B GLU 2.5 16.3 + - - +
599B GLU* 1.3 76.2 - - - +
601B TRP* 1.3 98.3 + + - +
602B TYR 3.3 5.7 + - - +
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Residues in contact with TRP 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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25B PRO* 3.9 15.0 + - + +
27B ILE* 3.8 7.5 - - + +
35B LYS* 3.2 31.8 - - + -
36B PHE 3.6 10.5 - - - -
37B TYR* 3.2 31.8 - - + +
73B ASN* 2.7 32.8 - - - -
75B LEU* 3.2 49.1 - - + +
148B ARG* 3.3 16.6 - - - +
540B THR* 3.7 20.4 - - - +
597B GLU* 2.9 29.7 + - + -
600B TYR* 1.3 99.5 - + - +
602B TYR* 1.3 56.1 + - - +
603B PRO 3.1 13.0 - - - +
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Residues in contact with TYR 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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35B LYS* 4.9 1.2 - - - -
37B TYR* 3.9 17.5 - + - -
534B ILE 4.1 1.0 + - - -
536B MET* 3.0 22.8 - - + +
537B ALA* 2.8 49.6 + - + +
540B THR* 4.4 3.8 - - - -
598B PHE* 2.9 50.7 + + + +
599B GLU 3.4 10.6 - - - +
600B TYR 3.3 11.0 - - - +
601B TRP* 1.3 74.0 - - - +
603B PRO* 1.3 64.9 - - + +
604B LEU* 4.3 6.7 - - + -
625B HIS* 3.5 29.4 + + - -
629B PHE* 4.9 5.7 - + - -
633B HIS* 3.7 32.6 + - + -
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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
------------------------------------------------------------
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