Contacts of the helix formed by residues 584 - 597 (chain B) in PDB entry 2C7A
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 CYS 584 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567B CYS* 3.3 10.2 - - + +
570B CYS* 3.7 4.7 - - - -
572B ASP* 4.0 10.3 - - + +
573B GLU 3.3 26.5 - - - +
574B ALA* 3.8 0.9 - - - +
575B SER* 3.9 3.4 - - - +
578B HIS* 4.1 0.5 - - - -
583B THR* 1.3 89.2 + - - +
585B GLY* 1.3 64.5 + - - +
586B SER* 3.1 27.4 - - - -
587B CYS 3.4 5.4 - - - -
588B LYS* 3.3 11.3 + - - +
616B ARG* 3.9 3.8 - - - -
1639B ZN 2.3 34.3 - - - -
14C T 5.9 0.2 - - - -
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Residues in contact with GLY 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B GLU 4.9 0.2 + - - -
575B SER* 3.7 16.8 + - - -
584B CYS* 1.3 74.9 - - - +
586B SER* 1.3 61.5 + - - +
588B LYS* 3.2 12.3 - - - +
589B VAL* 3.2 24.6 + - - +
14C T 3.7 17.2 + - - -
15C T 5.8 6.3 - - - -
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Residues in contact with SER 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ASP* 4.9 0.2 + - - -
584B CYS* 3.1 7.9 - - - -
585B GLY* 1.3 74.4 - - - +
587B CYS* 1.3 59.3 + - - +
589B VAL* 3.4 8.9 + - - +
590B PHE* 2.9 29.8 + - - +
616B ARG* 3.0 29.5 + - - -
623B ARG* 3.2 12.2 + - - -
13C G 3.6 42.2 + - - -
14C T 3.9 5.8 + - - -
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Residues in contact with CYS 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B CYS* 4.2 2.5 - - - -
569B ILE* 3.7 33.7 - - + -
570B CYS* 3.9 5.4 - - - -
583B THR* 4.2 5.8 - - + -
584B CYS* 3.4 3.6 - - - -
586B SER* 1.3 78.1 + - - +
588B LYS* 1.3 58.6 + - - +
590B PHE* 3.7 4.4 - - - +
591B PHE* 2.9 32.9 + - - +
623B ARG* 3.3 28.0 - - - +
627B CYS* 4.6 3.1 - - - -
632B MET* 4.0 3.7 - - - +
1639B ZN 2.3 35.9 - - - -
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Residues in contact with LYS 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B HIS* 3.7 37.9 - - + +
579B TYR* 3.7 20.9 + - + -
583B THR* 4.0 3.7 + - - -
584B CYS 3.3 13.9 + - - +
585B GLY* 3.2 14.8 - - - +
586B SER 3.1 0.2 - - - -
587B CYS* 1.3 79.2 - - - +
589B VAL* 1.3 72.1 + - + +
591B PHE* 3.8 0.7 - - - +
592B LYS* 3.2 15.1 + - - +
632B MET* 4.6 6.7 - - - -
15C T 5.3 1.2 + - - -
3D A 3.7 30.5 - - - -
4D G 2.6 43.1 + - - -
5D A 4.5 7.3 + - - +
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Residues in contact with VAL 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B GLY 3.2 7.4 - - - +
586B SER* 3.8 7.4 - - - +
588B LYS* 1.3 81.9 - - + +
590B PHE* 1.3 59.6 + - - +
592B LYS* 3.3 7.7 + - + +
593B ARG* 2.8 76.2 + - + +
13C G 4.4 2.7 - - + +
14C T 3.2 43.1 - - + +
5D A 5.4 6.5 - - - +
6D A 5.0 2.9 - - - +
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Residues in contact with PHE 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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586B SER 2.9 20.7 + - - +
587B CYS 3.7 2.5 - - - +
589B VAL* 1.3 78.7 - - - +
591B PHE* 1.3 56.8 + - - +
593B ARG* 3.6 6.6 - - + +
594B ALA* 2.7 53.4 + - + +
601B TYR* 4.5 6.7 - + - -
617B LYS* 6.5 0.2 - - - -
620B PRO* 3.5 41.3 - - + -
623B ARG* 3.4 48.0 - - + +
624B LEU* 3.5 27.1 - - + -
627B CYS* 4.3 7.2 - - - -
12C T 5.6 8.5 - - - -
13C G 5.1 0.9 - - - +
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Residues in contact with PHE 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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579B TYR* 3.8 20.0 - + + -
587B CYS 2.9 18.3 + - - +
588B LYS 3.8 1.3 - - - +
590B PHE* 1.3 81.5 - - - +
592B LYS* 1.3 66.9 + - - +
594B ALA* 3.1 3.1 + - - -
595B MET* 3.0 55.1 + - + +
624B LEU* 4.1 5.2 - - + -
627B CYS* 3.6 23.3 - - + -
628B CYS* 4.1 12.3 - - - -
632B MET* 3.5 45.1 - - + -
633B VAL* 3.8 7.9 - - - -
634B LEU* 3.6 35.9 - - + -
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Residues in contact with LYS 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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579B TYR* 3.5 22.9 + - + +
588B LYS 3.2 10.1 + - - +
589B VAL* 3.7 11.2 - - + +
591B PHE* 1.3 81.1 - - - +
593B ARG* 1.3 65.9 + - + +
595B MET* 4.1 1.7 - - - +
596B GLU* 2.9 56.9 + - + +
634B LEU* 3.7 22.0 - - + -
4D G 3.2 47.2 + - - +
5D A 4.5 5.3 + - - -
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Residues in contact with ARG 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 VAL* 2.8 50.1 + - + +
590B PHE* 3.7 6.2 - - + +
592B LYS* 1.3 75.7 - - + +
594B ALA* 1.3 63.3 + - - +
596B GLU* 3.9 4.2 - - - +
597B GLY 3.2 20.3 + - - -
599B HIS* 3.4 13.6 + - - +
601B TYR* 6.0 0.4 - - - +
12C T 3.8 31.4 + - - +
13C G 2.7 53.1 + - - -
6D A 4.1 6.1 - - - +
7D C 4.4 2.6 - - - +
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Residues in contact with ALA 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B PHE* 2.7 33.9 + - + +
591B PHE 3.7 3.4 - - - +
593B ARG* 1.3 73.6 - - - +
595B MET* 1.3 57.6 + - - +
597B GLY 3.0 19.8 - - - +
598B GLN* 5.0 3.5 + - - -
599B HIS* 3.7 13.7 + - - +
601B TYR* 3.9 20.9 - - + -
624B LEU* 3.7 27.9 - - + +
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Residues in contact with MET 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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591B PHE* 3.0 49.1 + - + +
594B ALA* 1.3 75.2 - - - +
596B GLU* 1.3 65.6 + - - +
597B GLY 3.7 2.9 - - - +
598B GLN* 4.1 11.0 - - - +
624B LEU* 3.8 23.6 - - + -
628B CYS* 4.3 17.0 - - - -
632B MET 5.8 0.2 - - - +
634B LEU* 3.6 28.2 - - + +
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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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592B LYS* 2.9 50.0 + - + +
593B ARG* 3.9 5.4 - - - +
594B ALA 3.2 0.2 - - - -
595B MET* 1.3 79.3 - - - +
597B GLY* 1.3 65.0 + - - +
598B GLN* 3.9 1.0 + - - +
634B LEU* 3.5 20.6 - - - +
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Residues in contact with GLY 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 ARG 3.2 7.5 + - - -
594B ALA 3.0 21.0 - - - +
595B MET 3.7 3.5 - - - +
596B GLU* 1.3 79.8 - - - +
598B GLN* 1.3 63.8 + - - -
599B HIS* 3.5 19.8 + - - -
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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