Contacts of the helix formed by residues 582 - 586 (chain A) in PDB entry 4Z4Q
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 GLY 582 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A ASP* 3.7 21.5 - - - -
507A ALA 5.0 2.7 - - - -
580A TYR* 3.4 6.5 - - - +
581A LYS* 1.3 80.0 - - - +
583A LEU* 1.3 63.8 + - - -
584A GLY 3.1 5.4 + - - -
585A GLU* 3.4 17.4 + - - +
586A MET* 4.0 12.2 - - - +
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Residues in contact with LEU 583 (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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432A VAL* 4.7 0.4 - - + -
433A GLU 4.5 4.0 - - - +
437A ALA* 3.9 28.6 - - + +
440A SER* 5.1 3.5 + - - -
504A MET* 3.8 30.5 - - + +
505A THR* 3.7 18.8 - - - +
506A ASP* 3.1 21.1 + - - +
540A PRO* 3.7 36.6 - - + -
582A GLY* 1.3 71.7 - - - -
584A GLY* 1.3 63.3 + - - +
585A GLU 3.2 0.4 - - - -
586A MET* 3.1 35.3 + - + +
591A LEU* 4.9 18.3 - - + +
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Residues in contact with GLY 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A SER* 6.1 1.3 - - - -
437A ALA* 5.1 8.0 - - - +
440A SER* 6.0 1.3 - - - -
506A ASP* 4.6 1.4 + - - -
582A GLY* 3.1 2.4 - - - -
583A LEU* 1.3 79.5 - - - +
585A GLU* 1.3 56.3 + - - +
586A MET 3.2 3.5 + - - -
1102B HIS 4.1 1.0 - - - +
1103B GLY* 3.4 17.7 - - - -
1104B ASN 4.3 2.8 + - - -
1114B ALA* 5.5 0.7 - - - +
1118B TYR* 3.4 39.4 - - - +
1119B THR* 4.6 0.9 - - - +
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Residues in contact with GLU 585 (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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579A ARG 4.9 0.7 - - - +
580A TYR* 3.9 21.0 - - + -
581A LYS* 2.9 52.3 + - - +
582A GLY* 3.4 11.3 + - - +
583A LEU 3.2 1.4 + - - -
584A GLY* 1.3 75.8 - - - +
586A MET* 1.3 57.2 + - - +
590A GLN* 4.6 0.7 - - - +
1061B LYS* 3.3 18.3 + - - -
1102B HIS* 3.6 27.6 + - - +
1103B GLY 4.1 4.3 - - - -
1118B TYR 3.5 16.2 - - - +
1120B GLU* 3.6 35.9 - - + +
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Residues in contact with MET 586 (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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440A SER* 3.8 14.0 + - - -
540A PRO* 4.7 2.0 - - + -
541A PRO* 4.3 22.9 - - + +
580A TYR* 3.9 37.2 - - + +
582A GLY 4.0 12.8 - - - +
583A LEU* 3.1 29.5 + - + +
584A GLY 3.2 1.2 - - - -
585A GLU* 1.3 77.9 - - - +
587A ASN* 1.3 63.3 + - - +
588A ALA 3.8 0.5 + - - -
590A GLN* 3.9 21.8 - - + +
591A LEU* 4.3 23.6 - - + +
594A THR* 4.2 19.3 - - - -
595A THR* 5.0 1.3 - - - -
1103B GLY* 3.5 12.3 - - - -
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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