Contacts of the helix formed by residues 628 - 637 (chain A) in PDB entry 5ZR1
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 THR 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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626A GLY 4.9 3.8 - - - +
627A TYR* 1.3 77.6 - - - +
629A HIS* 1.3 69.1 + - - +
630A GLU* 3.7 7.5 + - - +
631A GLU* 3.1 35.3 + - - +
632A LEU* 3.1 21.8 + - - +
697A ALA* 3.9 3.6 - - - -
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Residues in contact with HIS 629 (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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628A THR* 1.3 80.2 - - - +
630A GLU* 1.3 102.5 + - + +
632A LEU* 3.5 0.6 + - - -
633A LYS* 3.3 20.6 + - + +
690A GLU* 4.2 5.6 - - - -
693A SER* 3.4 33.3 - - - +
694A ARG* 3.5 42.9 + - - -
697A ALA* 3.7 13.9 - - + +
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Residues in contact with GLU 630 (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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628A THR* 3.3 7.0 + - - +
629A HIS* 1.3 108.8 + - + +
631A GLU* 1.3 62.5 + - + +
633A LYS* 3.6 18.7 + - - +
634A ASN* 2.9 32.5 + - - +
690A GLU* 4.3 11.1 - - - +
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Residues in contact with GLU 631 (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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451A ALA* 3.9 33.1 - - + +
452A ARG* 4.3 4.4 + - - -
627A TYR* 3.2 25.5 - - + -
628A THR* 3.1 37.1 + - - +
630A GLU* 1.3 77.4 - - + +
632A LEU* 1.3 62.6 + - - +
633A LYS 3.3 0.2 - - - -
634A ASN* 3.3 8.0 + - - +
635A ILE* 3.2 28.9 + - - +
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Residues in contact with LEU 632 (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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627A TYR* 3.6 23.8 - - + +
628A THR 3.1 23.0 + - - +
629A HIS 3.7 5.4 - - - +
630A GLU 3.4 0.2 - - - -
631A GLU* 1.3 76.7 - - - +
633A LYS* 1.3 57.3 + - - +
635A ILE* 3.3 8.4 + - + +
636A ILE* 3.0 33.4 + - - +
693A SER* 3.5 39.9 - - - +
696A VAL* 3.9 15.7 - - + -
697A ALA* 3.9 11.2 - - + +
701A GLY 4.5 7.2 - - - +
702A ASP 4.7 5.4 - - - +
703A ALA* 5.4 2.7 - - - -
706A ALA* 3.7 31.0 - - + -
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Residues in contact with LYS 633 (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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629A HIS* 3.3 10.6 + - + +
630A GLU* 3.8 26.4 + - - +
631A GLU 3.3 0.8 - - - -
632A LEU* 1.3 77.7 - - - +
634A ASN* 1.3 61.5 + - - +
635A ILE 3.2 0.4 - - - -
636A ILE* 4.4 0.2 - - - +
637A ASP* 3.1 40.3 + - - +
686A ALA* 4.3 23.2 + - - +
689A ILE* 4.2 18.1 - - + +
690A GLU* 3.3 32.5 - - - +
693A SER* 3.6 17.9 - - - +
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Residues in contact with ASN 634 (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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450A PRO* 3.4 24.2 - - + +
451A ALA* 6.3 0.4 - - + -
630A GLU* 2.9 23.0 + - - +
631A GLU* 3.3 9.5 + - - +
632A LEU 3.3 0.4 - - - -
633A LYS* 1.3 78.5 + - - +
635A ILE* 1.3 59.1 + - - +
637A ASP* 5.2 2.3 - - - +
638A LEU* 3.3 22.4 - - - +
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Residues in contact with ILE 635 (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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450A PRO* 4.5 6.3 - - + -
451A ALA* 5.0 1.3 - - + -
627A TYR* 4.2 17.9 - - + -
631A GLU 3.2 19.2 + - - +
632A LEU* 3.7 11.2 - - + +
633A LYS 3.2 0.6 - - - -
634A ASN* 1.3 82.3 - - - +
636A ILE* 1.3 66.3 + - + +
637A ASP 3.5 0.4 - - - -
638A LEU* 3.5 6.0 + - - +
639A ARG* 3.3 25.8 + - - +
703A ALA* 4.1 18.4 - - + +
707A LEU* 4.4 21.3 - - + -
2001A AGS 3.9 53.6 - - + +
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Residues in contact with ILE 636 (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 LEU* 4.5 5.4 - - + +
632A LEU 3.0 17.3 + - - +
635A ILE* 1.3 78.5 - - + +
637A ASP* 1.3 62.3 + - - +
639A ARG* 3.2 13.2 + - - +
640A LEU* 3.4 29.6 - - + +
684A MET* 6.2 0.4 - - + -
689A ILE* 3.8 24.2 - - + +
692A ALA* 5.1 3.1 - - + -
693A SER* 3.9 15.7 - - - +
706A ALA* 3.8 28.5 - - + +
707A LEU* 4.3 16.6 - - + -
710A CYS* 3.8 34.8 - - + -
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Residues in contact with ASP 637 (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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633A LYS* 3.1 26.3 + - - +
634A ASN* 5.2 2.2 - - - +
636A ILE* 1.3 75.5 - - - +
638A LEU* 1.3 62.1 + - - +
640A LEU* 3.5 19.7 + - - +
641A LYS* 3.5 16.0 + - - +
644A ASN* 4.0 20.2 + - - +
689A ILE* 4.9 14.0 - - + +
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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