Contacts of the helix formed by residues 628 - 641 (chain A) in PDB entry 1ZY7
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 CYS 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A GLY 3.1 21.5 - - - +
388A LEU* 3.9 21.8 - - - +
389A ALA 4.2 4.0 - - - +
390A LEU* 3.7 16.1 - - + +
401A ARG* 3.9 0.7 - - - -
624A ALA* 4.0 12.1 - - - -
625A SER* 3.1 27.0 + - - +
626A ARG 3.5 0.2 - - - -
627A LEU* 1.3 79.2 - - - +
629A LYS* 1.3 66.7 + - - +
630A HIS* 3.7 6.5 - - - -
631A ALA* 3.0 18.9 + - - -
632A LEU* 2.9 20.4 + - - +
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Residues in contact with LYS 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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387A GLY* 3.3 17.9 + - - +
389A ALA 5.2 6.6 + - - +
391A ASN* 3.6 24.2 + - - -
401A ARG* 3.6 7.5 - - - +
628A CYS* 1.3 72.5 - - - +
630A HIS* 1.3 57.9 + - - +
632A LEU* 3.2 3.8 + - - +
633A TYR* 2.8 31.7 + - - +
658A TYR* 3.7 18.8 - - + +
662A LYS* 4.2 0.6 - - - +
690A LYS* 6.2 1.0 - - - +
694A GLN* 3.7 27.9 - - - +
695A ASP* 2.9 29.8 + - - +
697A PHE* 3.8 5.2 - - + -
901A IHP 3.0 55.6 + - - +
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Residues in contact with HIS 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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386A ARG* 3.8 13.2 - - - +
387A GLY 2.9 21.9 + - - +
388A LEU* 3.7 24.6 - - + +
628A CYS* 3.8 2.6 - - - -
629A LYS* 1.3 74.0 - - - +
631A ALA* 1.3 61.7 + - - +
633A TYR* 3.3 2.6 + - - +
634A CYS* 2.9 32.8 + - + +
697A PHE* 4.0 16.8 - + - -
698A SER 4.8 4.0 + - - -
699A LEU* 3.5 32.6 - - + +
700A THR 5.0 3.2 + - - -
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Residues in contact with ALA 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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625A SER 3.6 15.7 - - - +
626A ARG* 3.3 26.9 - - - +
628A CYS* 3.0 10.2 + - - +
630A HIS* 1.3 82.3 - - - +
632A LEU* 1.3 63.4 + - - +
634A CYS* 3.3 10.7 + - - +
635A ARG* 3.1 26.2 + - - +
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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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401A ARG* 3.5 42.6 - - + +
404A LEU* 4.0 24.5 - - + -
405A ARG* 4.0 26.9 - - + -
408A TYR* 3.9 23.2 + - + +
532A LEU* 5.5 2.5 - - + -
626A ARG 4.2 8.1 - - - +
627A LEU* 3.5 8.5 - - - +
628A CYS 2.9 15.3 + - - +
629A LYS* 3.8 4.9 - - - +
631A ALA* 1.3 76.2 - - - +
633A TYR* 1.3 59.0 + - - +
635A ARG* 3.1 9.1 + - + +
636A TRP* 2.9 27.5 + - - +
658A TYR* 5.1 4.7 - - + +
901A IHP 4.7 6.1 - - - +
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Residues in contact with TYR 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 3.9 11.4 - - + -
629A LYS 2.8 18.5 + - - +
630A HIS* 3.6 5.6 - - - +
632A LEU* 1.3 75.3 - - - +
634A CYS* 1.3 59.7 + - - +
636A TRP* 3.2 26.6 + + - -
637A MET* 2.8 43.0 + - + +
656A ASN 2.7 32.4 + - - -
657A VAL 3.7 0.5 + - - -
658A TYR* 3.4 43.0 - + + -
661A SER* 2.8 32.0 + - - -
697A PHE* 4.0 8.3 - + - -
699A LEU* 3.7 29.4 - - + -
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Residues in contact with CYS 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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630A HIS* 2.9 21.0 + - + +
631A ALA* 3.3 13.5 - - - +
633A TYR* 1.3 76.3 - - - +
635A ARG* 1.3 63.3 + - + +
637A MET* 3.3 3.5 + - - +
638A ARG* 3.1 33.1 + - - +
699A LEU* 3.9 17.6 - - + +
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Residues in contact with ARG 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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405A ARG* 3.8 38.2 + - + +
408A TYR* 3.5 30.0 - - + +
409A THR* 2.9 41.4 + - - +
412A GLU* 3.2 22.4 + - - +
626A ARG 6.0 0.7 - - - +
631A ALA 3.1 14.6 + - - +
632A LEU* 3.4 9.4 - - + +
634A CYS* 1.3 80.2 - - + +
636A TRP* 1.3 64.1 + - - +
638A ARG* 3.2 38.4 + - - +
639A VAL* 3.2 24.1 + - - +
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Residues in contact with TRP 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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408A TYR* 3.5 25.7 - + - +
532A LEU* 2.9 51.9 + - + +
535A ILE* 3.8 23.5 - - + +
536A PHE* 3.2 33.7 - + - -
632A LEU 2.9 9.8 + - - +
633A TYR* 3.2 29.6 + + + +
635A ARG* 1.3 76.2 - - - +
637A MET* 1.3 67.4 + - - +
639A VAL* 3.2 4.7 + - - +
640A HIS* 2.8 51.3 + + + -
652A ILE* 4.1 12.8 - - + -
655A PRO* 3.5 34.3 - - + -
661A SER* 4.7 1.8 - - - -
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Residues in contact with MET 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 TYR* 2.8 53.3 + - + +
634A CYS 3.7 5.2 - - - +
635A ARG 3.3 0.2 - - - -
636A TRP* 1.3 81.4 - - + +
638A ARG* 1.3 63.7 + - - +
640A HIS* 3.2 6.3 + - - +
641A GLY* 3.1 19.8 + - - -
655A PRO* 3.6 40.8 - - + +
656A ASN* 4.9 1.6 - - - +
699A LEU* 3.7 24.2 - - + +
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Residues in contact with ARG 638 (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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412A GLU* 2.7 42.1 + - - +
634A CYS* 3.1 22.1 + - - +
635A ARG* 3.4 40.5 - - - +
637A MET* 1.3 78.8 - - - +
639A VAL* 1.3 60.3 + - - +
641A GLY* 3.5 5.4 + - - -
642A LYS* 3.5 22.0 + - + +
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Residues in contact with VAL 639 (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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408A TYR* 4.0 22.0 - - + +
411A LEU* 4.5 10.3 - - + -
412A GLU* 3.8 29.2 - - + +
415A LEU* 3.9 12.3 - - + -
536A PHE* 3.5 28.5 - - + -
635A ARG 3.2 12.6 + - - +
636A TRP 3.2 7.7 + - - +
638A ARG* 1.3 73.0 - - - +
640A HIS* 1.3 61.4 + - - +
642A LYS* 2.8 24.1 + - - +
643A VAL* 3.1 24.9 + - + +
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Residues in contact with HIS 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PHE* 3.6 14.3 - + + -
636A TRP* 2.8 49.5 + + + +
637A MET* 3.2 13.2 + - - +
639A VAL* 1.3 77.1 - - - +
641A GLY* 1.3 63.6 + - - +
642A LYS 3.2 1.2 + - - -
643A VAL* 3.5 16.4 + - - +
648A LEU* 4.2 14.5 - - + +
652A ILE* 2.9 31.3 + - + +
653A THR 4.0 7.0 - - - -
655A PRO* 3.5 26.0 - - + +
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Residues in contact with GLY 641 (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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637A MET 3.1 12.7 + - - -
638A ARG 3.5 4.0 + - - -
639A VAL 3.2 0.4 - - - -
640A HIS* 1.3 79.3 + - - +
642A LYS* 1.3 63.6 + - - +
643A VAL 3.6 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
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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