Contacts of the helix formed by residues 587 - 596 (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 ASN 587 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585A GLU 4.1 0.6 + - - -
586A MET* 1.3 72.3 - - - +
588A ALA* 1.3 62.0 + - - +
589A ASP* 4.2 9.4 - - + +
590A GLN* 2.8 42.8 + - + +
591A LEU* 3.0 10.6 + - - +
1101B MET 3.5 10.5 + - - +
1102B HIS* 3.5 24.3 + - - -
1103B GLY* 3.0 30.6 + - - +
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Residues in contact with ALA 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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440A SER* 3.7 28.0 + - - +
443A GLN* 3.9 20.2 - - + +
444A GLY* 3.8 18.0 - - - +
586A MET 3.8 1.2 + - - -
587A ASN* 1.3 72.5 - - - +
589A ASP* 1.3 62.5 + - - +
591A LEU* 3.4 9.8 + - - +
592A TRP* 3.1 22.5 + - - +
1103B GLY 5.4 1.0 + - - -
1293B ARG* 5.3 3.8 - - + -
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Residues in contact with ASP 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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587A ASN* 4.2 6.7 - - + +
588A ALA* 1.3 79.5 - - - +
590A GLN* 1.3 64.1 + - + +
592A TRP* 3.4 4.7 + - - +
593A GLU* 3.1 23.6 + - - +
1293B ARG* 4.6 20.0 - - + +
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Residues in contact with GLN 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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557A TYR* 2.9 31.2 + - + +
580A TYR* 3.9 12.1 + - - -
585A GLU 4.6 0.2 - - - +
586A MET* 3.9 16.5 - - + -
587A ASN* 2.8 44.5 + - + +
589A ASP* 1.3 72.7 - - + +
591A LEU* 1.3 61.5 + - - +
593A GLU* 3.3 5.6 + - - +
594A THR* 2.7 37.0 + - - +
1102B HIS* 4.0 22.0 - - - -
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Residues in contact with LEU 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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437A ALA* 4.7 2.7 - - + +
440A SER* 3.8 29.4 - - - +
441A ALA* 3.9 17.3 - - + +
444A GLY* 5.6 0.2 - - - -
504A MET* 3.8 18.6 - - + -
583A LEU* 4.9 16.4 - - + +
586A MET* 4.3 20.2 - - + +
587A ASN 3.0 10.1 + - - +
588A ALA* 3.5 11.2 - - - +
590A GLN* 1.3 76.2 - - - +
592A TRP* 1.3 57.0 + - - +
594A THR* 3.9 3.6 - - - -
595A THR* 2.8 51.7 + - + +
596A MET* 3.2 21.6 + - + -
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Residues in contact with TRP 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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444A GLY* 3.3 25.7 + - - +
445A ARG 4.1 0.7 - - - -
446A ASP* 3.9 27.4 - - + -
449A PHE* 5.5 1.1 - + - -
450A GLN* 3.8 20.9 - - - -
588A ALA 3.1 4.6 + - - +
589A ASP 3.7 8.3 - - - +
591A LEU* 1.3 81.0 - - - +
593A GLU* 1.3 69.8 + - + +
594A THR 3.3 0.3 + - - -
596A MET* 3.4 30.8 + - + +
597A ASN* 3.0 67.0 + - + +
598A PRO* 4.0 7.4 - - + -
1293B ARG* 3.2 40.8 - - - +
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Residues in contact with GLU 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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557A TYR* 5.7 4.5 - - + +
589A ASP 3.1 13.3 + - - +
590A GLN* 3.3 6.9 + - - +
592A TRP* 1.3 87.0 - - + +
594A THR* 1.3 63.3 + - + +
597A ASN* 4.8 2.7 - - - +
600A THR* 2.9 31.5 - - - +
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Residues in contact with THR 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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539A LEU 4.7 0.7 - - - +
541A PRO* 3.9 16.1 - - + +
557A TYR* 3.8 47.8 - - + -
559A TRP* 4.0 19.8 - - + -
586A MET* 4.2 2.8 - - - -
590A GLN 2.7 24.6 + - - +
591A LEU* 3.5 1.6 + - - -
593A GLU* 1.3 82.2 - - + +
595A THR* 1.3 76.8 + - - +
596A MET 4.0 0.4 - - - -
600A THR 3.7 4.3 - - - +
601A ARG* 3.6 17.7 - - - -
602A THR 4.3 1.9 + - - -
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Residues in contact with THR 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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430A TYR* 3.7 9.4 + - - -
504A MET* 3.5 23.9 - - - +
538A ALA* 4.1 14.7 - - - +
539A LEU 3.9 13.2 - - - +
540A PRO* 3.6 30.5 - - + +
541A PRO* 3.8 2.7 - - + -
586A MET* 5.0 1.3 - - - -
591A LEU* 2.8 21.4 + - + +
594A THR* 1.3 93.2 - - - +
596A MET* 1.3 58.3 + - - +
601A ARG* 3.6 18.0 - - - +
602A THR 5.9 0.2 - - - -
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Residues in contact with MET 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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430A TYR* 3.7 23.8 - - + -
441A ALA* 4.2 24.7 - - + +
444A GLY* 4.6 4.0 - - - -
445A ARG* 3.9 20.0 - - + -
450A GLN* 3.1 44.5 + - - +
452A ILE* 4.1 17.9 - - + -
504A MET* 4.3 7.0 - - - -
591A LEU* 3.2 32.6 + - + +
592A TRP* 3.8 20.4 - - + -
595A THR* 1.3 82.8 - - - +
597A ASN* 1.3 61.7 + - - +
598A PRO* 3.1 5.4 - - - +
601A ARG* 3.5 8.2 + - - -
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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