Contacts of the helix formed by residues 586 - 596 (chain A) in PDB entry 2EYQ
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 586 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585A HIS* 1.3 89.0 - - - +
587A ARG* 1.3 62.5 + - - +
588A GLU* 2.8 13.2 + - - +
589A GLN* 2.6 37.5 + - + +
590A TYR* 3.1 16.6 + - - +
647A ASP* 4.5 2.5 - - - +
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Residues in contact with ARG 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLU* 6.3 0.8 - - - -
585A HIS* 4.1 23.7 + - + -
586A ASP* 1.3 72.5 - - - +
588A GLU* 1.3 57.6 + - + +
590A TYR* 3.6 27.3 - - - +
591A GLN* 3.0 30.5 + - - +
610A ASN* 4.9 11.3 + - - -
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Residues in contact with GLU 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A ASP* 2.8 13.6 + - - +
587A ARG* 1.3 73.7 - - + +
589A GLN* 1.3 67.2 + - - +
590A TYR 3.1 1.3 - - - -
591A GLN* 3.1 21.6 + - - +
592A LEU* 3.2 21.2 + - + +
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Residues in contact with GLN 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A HIS 4.7 0.2 - - - +
586A ASP* 2.6 34.9 + - + +
588A GLU* 1.3 71.7 - - - +
590A TYR* 1.3 62.6 + - - +
592A LEU* 3.2 25.8 + - - +
593A PHE 3.2 9.4 + - - -
643A PHE* 3.7 14.4 - - + -
647A ASP* 3.3 32.1 + - - +
676A TRP* 3.7 31.5 - - - -
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Residues in contact with TYR 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A HIS* 3.8 31.8 + + + +
586A ASP 3.1 13.7 + - - +
587A ARG* 3.6 28.0 - - - +
588A GLU 3.1 0.2 - - - -
589A GLN* 1.3 77.6 - - - +
591A GLN* 1.3 68.6 + - - +
593A PHE* 2.9 16.9 + + + +
594A CYS* 2.9 32.0 + - - -
609A ILE* 3.8 9.4 - - - +
610A ASN* 5.2 4.1 + - - -
613A LEU* 4.1 15.6 - - + +
640A ARG* 2.6 47.5 + - + -
643A PHE* 3.9 22.6 - + + -
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Residues in contact with GLN 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLU* 3.8 35.4 + - - +
404A ARG* 3.0 46.9 + - - +
587A ARG 3.0 17.5 + - - +
588A GLU* 3.1 11.7 + - - +
590A TYR* 1.3 84.4 - - + +
592A LEU* 1.3 58.1 + - - +
594A CYS* 3.6 9.3 + - + +
595A ASP* 3.2 25.6 + - - +
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Residues in contact with LEU 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A ALA* 5.3 2.4 - - - +
368A LYS 6.0 0.7 - - - +
370A PRO* 4.1 21.3 - - + -
404A ARG* 4.6 8.5 - - - +
588A GLU* 3.2 16.5 + - + +
589A GLN* 3.2 22.4 + - - +
590A TYR 3.0 0.8 + - - -
591A GLN* 1.3 75.3 - - - +
593A PHE* 1.3 68.2 + - - +
595A ASP* 3.0 35.3 + - - +
596A SER* 3.8 4.5 + - - -
676A TRP* 4.0 14.2 + - + -
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Residues in contact with PHE 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A GLN 3.2 2.4 + - - -
590A TYR* 2.9 11.3 + + - +
592A LEU* 1.3 77.5 - - - +
594A CYS* 1.3 65.8 + - - +
596A SER* 2.8 12.1 + - - -
639A MET* 4.3 2.0 - - + -
640A ARG* 4.1 23.8 - - + -
643A PHE* 3.3 56.5 - + + -
672A ARG* 2.7 75.1 + - + -
673A PHE* 3.6 37.9 - + - -
676A TRP* 3.6 21.0 - + - +
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Residues in contact with CYS 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A TYR* 2.9 52.7 + - - -
591A GLN* 3.6 12.8 - - + +
593A PHE* 1.3 81.2 - - - +
595A ASP* 1.3 61.5 + - - +
597A PHE* 2.8 25.8 + - - +
598A PRO* 4.9 0.5 - - - +
640A ARG* 3.6 25.1 - - - +
672A ARG* 4.1 7.9 - - - +
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Residues in contact with ASP 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A VAL* 4.6 13.8 - - + +
365A ALA* 4.2 19.6 - - + +
370A PRO* 4.3 8.3 - - - +
401A LEU* 5.4 3.6 - - - +
404A ARG* 3.4 25.1 + - - -
450A LEU* 6.1 0.2 - - - +
591A GLN* 3.2 9.6 + - - +
592A LEU* 3.0 46.1 + - - +
593A PHE 2.9 1.2 + - - -
594A CYS* 1.3 76.3 - - - +
596A SER* 1.3 56.3 + - - +
597A PHE 3.0 5.0 + - - -
598A PRO* 3.8 15.2 - - - +
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Residues in contact with SER 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A ALA* 3.8 10.3 - - - +
592A LEU 4.1 2.4 + - - -
593A PHE 2.8 13.7 + - - -
595A ASP* 1.3 74.7 - - - +
597A PHE* 1.3 57.8 - - - +
598A PRO* 3.7 6.7 - - - +
672A ARG* 3.6 29.9 + - - -
675A ASN* 3.6 23.6 + - - +
676A TRP* 4.0 14.8 + - - -
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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