Contacts of the helix formed by residues 583 - 594 (chain B) in PDB entry 4Q9Z
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 583 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581B GLY 4.0 1.9 - - - -
582B GLN* 1.3 79.1 - - - +
584B GLU* 1.3 63.7 + - - +
585B GLU* 3.3 17.0 + - - +
586B GLU* 3.1 21.7 + - - +
587B LEU* 3.0 24.0 + - - +
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Residues in contact with GLU 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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543B PRO* 3.6 28.0 - - + +
583B ASP* 1.3 74.8 - - - +
585B GLU* 1.3 54.5 + - - +
587B LEU* 4.1 7.6 - - + -
588B PHE* 2.7 69.2 + - + -
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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
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583B ASP* 3.3 15.5 + - - +
584B GLU* 1.3 76.9 - - - +
586B GLU* 1.3 56.5 + - - +
588B PHE* 3.7 7.2 + - - +
589B HIS* 3.2 26.0 + - - +
592B ARG* 5.1 1.6 + - - -
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Residues in contact with GLU 586 (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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580B HIS 4.0 3.3 - - - +
581B GLY* 3.6 15.1 - - - -
582B GLN* 2.9 29.6 + - - +
583B ASP* 3.1 19.2 + - - +
585B GLU* 1.3 72.8 - - - +
587B LEU* 1.3 60.9 + - - +
589B HIS* 3.3 10.6 + - + +
590B SER* 3.0 27.7 + - - -
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Residues in contact with LEU 587 (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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543B PRO* 3.7 25.1 - - + +
544B ASP* 3.3 27.4 - - - +
579B PHE* 3.4 37.5 - - + +
580B HIS* 3.7 10.8 - - - +
581B GLY* 3.9 8.2 - - - +
583B ASP 3.0 17.7 + - - +
584B GLU* 3.6 10.1 - - + +
586B GLU* 1.3 77.2 - - - +
588B PHE* 1.3 58.6 + - + +
590B SER* 3.3 2.4 + - - -
591B ILE* 3.0 43.4 + - + +
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Residues in contact with PHE 588 (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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539B PHE* 4.1 23.1 - + - -
543B PRO* 4.1 27.1 - - + -
546B ILE* 4.2 7.4 - - + -
551B LEU* 3.3 36.0 - - + +
584B GLU* 2.7 64.6 + - + +
585B GLU* 4.1 5.4 - - - +
587B LEU* 1.3 71.2 - - + +
589B HIS* 1.3 60.8 + - - +
591B ILE* 4.0 7.2 - - + -
592B ARG* 3.0 46.9 + - - +
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Residues in contact with HIS 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 3.2 15.8 + - - +
586B GLU* 3.3 15.8 + - + +
588B PHE* 1.3 74.1 - - - +
590B SER* 1.3 62.7 + - - +
592B ARG* 3.3 23.0 + - - +
593B MET* 2.9 56.6 + - + +
594B ASP* 4.6 10.3 + - - -
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Residues in contact with SER 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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578B PRO 4.7 0.7 + - - -
579B PHE* 3.3 18.8 - - - +
580B HIS 3.4 39.3 + - - -
586B GLU 3.0 8.0 + - - -
587B LEU 3.5 6.7 - - - -
589B HIS* 1.3 77.7 + - - +
591B ILE* 1.3 62.3 + - - +
594B ASP* 3.0 54.2 + - - +
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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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543B PRO 3.3 26.2 - - - +
544B ASP 4.4 4.9 - - - +
546B ILE 3.3 25.8 - - - +
548B PRO* 4.0 10.4 - - + +
551B LEU* 3.6 13.0 - - + -
563B TRP* 4.0 19.9 - - + +
579B PHE* 3.7 27.8 - - + -
587B LEU* 3.0 26.4 + - + +
588B PHE* 3.7 23.1 - - + +
590B SER* 1.3 75.0 - - - +
592B ARG* 1.3 57.5 + - - +
616B ARG* 3.0 22.7 + - - -
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Residues in contact with ARG 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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548B PRO* 4.8 9.4 - - + -
551B LEU* 4.1 25.8 + - + +
552B LEU* 3.8 35.1 - - + +
585B GLU 5.1 1.6 + - - -
588B PHE* 3.0 47.4 + - - +
589B HIS* 3.6 29.4 - - - +
590B SER 3.3 0.2 - - - -
591B ILE* 1.3 77.9 - - - +
593B MET* 1.3 71.1 + - + +
616B ARG* 2.8 25.8 + - - +
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Residues in contact with MET 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 HIS* 2.9 50.4 + - + +
590B SER 3.4 0.4 + - - -
592B ARG* 1.3 95.4 - - + +
594B ASP* 1.3 68.3 + - - +
595B ASN* 3.6 6.1 + - - +
616B ARG* 3.8 7.3 + - - -
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Residues in contact with ASP 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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579B PHE* 3.4 8.1 - - + -
589B HIS* 4.6 11.5 + - - -
590B SER* 3.0 43.0 + - - +
593B MET* 1.3 79.2 - - - +
595B ASN* 1.3 65.7 + - - +
616B ARG* 2.7 23.2 + - - -
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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