Contacts of the helix formed by residues 582 - 586 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B ASP* 3.6 23.1 - - - -
507B ALA 4.8 3.4 - - - -
580B TYR* 3.3 7.1 + - - +
581B LYS* 1.3 79.1 - - - +
583B LEU* 1.3 59.5 + - - -
584B GLY 2.8 12.5 + - - -
585B GLU* 3.1 17.6 + - - +
586B MET* 4.7 7.5 + - - +
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Residues in contact with LEU 583 (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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432B VAL* 4.6 0.7 - - + -
433B GLU 5.2 2.0 - - - +
437B ALA* 4.0 28.7 - - + +
440B SER* 5.2 4.9 + - - -
504B MET* 3.8 32.5 - - + +
505B THR* 3.8 17.7 - - - +
506B ASP* 2.8 25.9 + - - +
540B PRO* 3.6 36.3 - - + -
582B GLY* 1.3 69.6 - - - -
584B GLY* 1.3 60.1 + - - +
585B GLU 3.2 1.5 + - - -
586B MET* 3.3 32.2 + - + +
591B LEU* 4.6 18.8 - - + +
595B THR* 5.7 0.2 - - + -
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Residues in contact with GLY 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102A HIS 4.1 0.9 - - - +
1103A GLY* 3.5 19.3 - - - -
1104A ASN 4.4 2.3 + - - -
1114A ALA* 5.4 0.9 - - - +
1118A TYR* 3.4 44.2 - - - +
1119A THR* 4.4 1.0 - - - +
436B SER* 6.1 1.3 - - - -
437B ALA* 5.4 6.0 - - - +
506B ASP* 4.4 2.0 + - - -
582B GLY 2.8 4.0 + - - -
583B LEU* 1.3 77.1 - - - +
585B GLU* 1.3 56.6 + - - +
586B MET 3.4 1.1 - - - -
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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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1061A LYS* 3.6 23.4 + - - -
1102A HIS* 3.6 25.6 - - - +
1103A GLY 4.2 3.8 - - - -
1118A TYR 4.4 4.2 - - - +
1120A GLU* 3.6 33.1 - - + +
579B ARG 4.0 2.1 - - - +
580B TYR* 3.8 27.1 - - + -
581B LYS* 2.8 46.5 + - - +
582B GLY 3.1 17.3 - - - +
583B LEU 3.2 0.2 - - - -
584B GLY* 1.3 73.1 - - - +
586B MET* 1.3 60.5 + - - +
590B GLN* 3.9 2.1 - - - +
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Residues in contact with MET 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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1103A GLY* 3.1 17.4 - - - -
440B SER* 3.9 11.3 + - - -
540B PRO* 4.1 10.5 - - + -
541B PRO* 3.5 38.1 - - + +
557B TYR* 6.2 0.7 - - - -
580B TYR* 3.8 40.4 - - + +
582B GLY 4.9 2.7 - - - +
583B LEU* 3.3 29.1 + - + +
584B GLY 4.4 0.2 - - - +
585B GLU* 1.3 82.7 - - - +
587B ASN* 1.3 68.3 + - - +
590B GLN* 3.4 10.1 - - + +
591B LEU* 4.3 28.5 - - + -
594B THR* 4.5 7.9 - - - -
595B THR* 4.9 0.9 - - - -
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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
------------------------------------------------------------
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