Contacts of the helix formed by residues 685 - 694 (chain A) in PDB entry 1ZUC
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 PRO 685 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683A LEU 3.4 9.6 - - - +
684A ILE* 1.4 90.3 - - + +
686A PRO* 1.3 75.9 - - + +
687A LEU 3.2 0.2 - - - -
688A ILE* 3.1 30.8 + - + +
689A ASN* 3.1 8.7 + - - +
851A GLU* 3.1 22.0 - - - +
854A LYS* 4.1 26.9 - - + +
858A LEU* 4.0 14.8 - - + -
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Residues in contact with PRO 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A ILE 3.4 4.5 - - - +
685A PRO* 1.3 85.3 - - + +
687A LEU* 1.3 57.2 + - - +
689A ASN* 3.2 10.0 + - + +
690A LEU* 2.9 27.4 + - - +
854A LYS* 5.9 2.2 - - - +
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Residues in contact with LEU 687 (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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685A PRO 3.2 1.0 - - - -
686A PRO* 1.3 81.2 - - - +
688A ILE* 1.3 57.8 + - - +
690A LEU* 3.2 11.3 + - + +
691A LEU* 2.8 29.3 + - + +
737A PRO* 3.6 33.9 - - + -
847A SER* 5.1 7.6 - - - +
848A TYR* 3.8 34.8 - - + +
851A GLU* 3.6 35.8 + - + +
854A LYS* 5.8 0.7 - - - +
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Residues in contact with ILE 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A ILE* 3.9 9.4 - - + -
685A PRO* 3.1 27.0 + - + +
687A LEU* 1.3 73.2 - - - +
689A ASN* 1.3 67.5 + - - +
691A LEU* 3.2 8.8 + - + +
692A MET* 3.0 28.5 + - + +
816A GLU* 3.6 35.4 - - + +
819A LEU* 4.8 4.0 - - + -
820A CYS* 3.9 9.6 - - - -
851A GLU* 3.4 44.6 + - + +
855A ALA* 4.0 21.1 - - + +
858A LEU* 4.8 0.7 - - + -
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Residues in contact with ASN 689 (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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684A ILE* 4.7 6.8 - - + +
685A PRO 3.1 12.0 + - - +
686A PRO* 3.4 14.0 + - + +
688A ILE* 1.3 77.2 - - - +
690A LEU* 1.3 63.9 + - - +
692A MET* 3.2 28.5 + - + +
693A SER* 3.1 24.3 + - - -
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Residues in contact with LEU 690 (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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686A PRO 2.9 13.4 + - - +
687A LEU* 3.2 13.9 + - + +
689A ASN* 1.3 79.5 - - - +
691A LEU* 1.3 66.0 + - + +
693A SER* 2.9 27.9 + - - +
694A ILE* 3.1 25.6 + - + -
735A SER 3.9 6.3 - - - +
737A PRO* 3.5 42.4 - - + -
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Residues in contact with LEU 691 (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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687A LEU* 2.8 23.2 + - + +
688A ILE* 3.2 11.9 + - + +
690A LEU* 1.3 78.1 - - - +
692A MET* 1.3 62.2 + - - +
694A ILE* 3.5 16.5 + - + +
695A GLU* 3.5 19.9 + - - +
732A TRP* 5.1 4.6 + - + +
736A LEU* 3.5 32.5 - - + -
737A PRO* 4.6 4.7 - - + -
819A LEU* 3.9 43.2 - - + +
820A CYS* 4.3 15.5 - - - +
823A VAL* 3.9 6.3 - - + -
848A TYR* 4.0 21.8 - - + +
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Residues in contact with MET 692 (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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684A ILE* 3.7 27.6 - - + -
688A ILE* 3.0 16.9 + - + +
689A ASN* 3.2 48.7 + - - +
691A LEU* 1.3 75.6 - - - +
693A SER* 1.3 61.1 + - - +
695A GLU* 3.4 19.4 - - - +
815A GLN* 3.7 25.4 - - - +
816A GLU* 5.3 7.2 - - + +
819A LEU* 3.5 22.4 - - + +
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Residues in contact with SER 693 (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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689A ASN* 3.1 14.3 + - - -
690A LEU* 2.9 21.9 + - - +
692A MET* 1.3 78.7 - - - +
694A ILE* 1.3 65.3 + - - +
695A GLU 3.4 3.7 + - - +
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Residues in contact with ILE 694 (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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690A LEU* 3.4 38.8 - - + +
691A LEU* 3.6 18.6 - - + +
693A SER* 1.3 85.0 - - - +
695A GLU* 1.3 67.7 + - - +
696A PRO* 3.4 2.4 - - - +
732A TRP* 3.5 42.3 - - + +
735A SER* 3.8 35.4 - - - +
736A LEU* 3.9 13.9 - - - +
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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