Contacts of the helix formed by residues 589 - 594 (chain A) in PDB entry 2W3C
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 LEU 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587A HIS* 2.9 28.4 + - + +
588A GLU* 1.3 84.0 - - + +
590A TYR* 1.3 66.4 + - - +
591A SER 3.4 1.6 - - - -
592A ARG* 3.8 16.9 + - + +
593A ALA* 3.4 20.4 + - - +
605A GLU 5.2 0.9 - - - +
606A TYR* 3.7 45.1 - - + +
608A ILE* 4.3 24.2 - - + -
609A PHE* 4.0 9.7 - - + +
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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
----------------------------------------------------------
584A ILE* 3.6 19.3 - - + +
585A SER* 3.2 37.0 - - - +
587A HIS 2.9 9.8 + - - +
589A LEU* 1.3 81.6 - - - +
591A SER* 1.3 69.6 + - - +
593A ALA* 3.2 15.6 + - - +
594A SER* 3.3 13.4 + - - -
609A PHE* 3.9 26.7 - + + -
614A THR* 2.6 50.9 + - + +
617A VAL* 3.5 30.5 - - + +
618A LYS* 3.5 12.5 + - + +
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Residues in contact with SER 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A SER 5.1 1.1 + - - -
587A HIS 4.5 1.6 + - - -
588A GLU 5.0 6.3 - - - -
589A LEU 3.4 0.4 - - - -
590A TYR* 1.3 83.3 - - - +
592A ARG* 1.3 58.3 + - - +
594A SER* 2.6 32.8 + - - -
595A GLN* 3.5 10.5 + - - +
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Residues in contact with ARG 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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588A GLU 5.4 1.1 + - - +
589A LEU* 3.8 17.9 + - + +
590A TYR 3.5 0.4 - - - -
591A SER* 1.3 73.0 - - - +
593A ALA* 1.3 68.0 + - - +
594A SER 3.0 2.9 + - - -
595A GLN* 3.2 45.7 + - - +
596A LYS 4.4 1.4 + - - +
600A ASN* 3.4 41.2 + - + +
602A PRO* 6.2 1.3 - - - -
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Residues in contact with ALA 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LEU 3.4 10.8 + - - +
590A TYR 3.2 12.5 + - - +
592A ARG* 1.3 79.5 - - - +
594A SER* 1.3 56.8 + - - +
595A GLN 3.5 0.3 + - - -
596A LYS 3.6 5.0 - - - +
600A ASN* 6.3 2.0 - - - +
601A PHE* 6.1 2.5 - - + -
609A PHE* 3.6 34.8 - - + +
611A HIS* 3.1 29.9 + - - +
614A THR* 3.7 8.3 - - + -
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Residues in contact with SER 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A TYR* 3.3 16.5 + - - -
591A SER* 2.6 20.6 + - - -
592A ARG 3.0 0.8 - - - -
593A ALA* 1.3 78.9 - - - +
595A GLN* 1.3 62.0 + - - +
611A HIS* 3.3 13.3 - - - -
614A THR* 3.4 25.5 + - - -
615A LYS* 6.0 0.5 - - - +
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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