Contacts of the helix formed by residues 822 - 829 (chain A) in PDB entry 4YZC
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 SER 822 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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680A HIS* 5.9 1.6 - - - -
754A THR* 5.4 3.8 - - - +
757A ILE* 3.9 3.8 - - - -
820A ARG 3.9 1.2 + - - -
821A PRO* 1.3 77.0 - - - +
823A ALA* 1.3 65.1 + - - +
824A LYS* 3.4 10.9 + - - +
825A HIS* 2.9 43.0 + - - -
826A VAL* 3.0 11.6 + - - +
962A PHE* 4.3 4.9 - - - -
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Residues in contact with ALA 823 (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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673A THR* 3.6 13.2 - - + +
676A LEU* 4.5 4.0 - - + -
677A ALA* 3.7 33.4 - - + +
680A HIS* 4.1 15.5 + - + +
757A ILE* 3.4 22.3 - - + +
822A SER* 1.3 72.9 - - - +
824A LYS* 1.3 61.8 + - - +
826A VAL* 3.2 6.3 + - - +
827A LEU* 3.0 27.0 + - - +
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Residues in contact with LYS 824 (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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677A ALA* 4.4 17.0 - - + -
681A SER* 5.0 18.2 - - - -
822A SER* 3.1 8.8 + - - +
823A ALA* 1.3 75.3 - - - +
825A HIS* 1.3 64.9 + - - +
827A LEU* 3.2 22.3 + - + +
828A LYS* 3.3 17.5 + - - +
962A PHE* 3.5 42.0 - - + -
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Residues in contact with HIS 825 (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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821A PRO* 3.5 20.1 - - + +
822A SER* 2.9 34.6 + - - +
824A LYS* 1.3 77.7 - - - +
826A VAL* 1.3 62.5 + - - +
828A LYS* 3.1 13.4 + - + +
829A HIS* 3.4 10.9 + - - +
945A TYR* 5.2 1.2 + - - -
962A PHE* 3.3 52.2 + + + -
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Residues in contact with VAL 826 (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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673A THR* 4.0 13.0 - - + -
757A ILE* 4.6 4.7 - - + -
764A PHE* 4.0 14.4 - - + -
808A LEU* 4.1 9.6 - - + -
812A MET* 3.5 34.5 - - + -
821A PRO* 3.6 17.9 - - + +
822A SER 3.0 15.1 + - - +
823A ALA* 3.2 10.3 + - - +
825A HIS* 1.3 75.7 - - - +
827A LEU* 1.3 62.8 + - - +
829A HIS* 3.1 17.9 + - - +
832A PHE* 3.2 25.8 - - + -
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Residues in contact with LEU 827 (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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670A GLN* 3.9 37.1 + - + +
673A THR* 3.9 18.4 - - + -
674A SER* 3.9 15.0 - - - +
677A ALA* 4.2 21.8 - - + -
823A ALA 3.0 17.9 + - - +
824A LYS* 3.2 15.7 + - + +
826A VAL* 1.3 78.4 - - - +
828A LYS* 1.3 60.7 + - + +
829A HIS 3.4 1.9 + - - +
832A PHE* 3.8 17.4 - - + +
833A TRP* 5.3 1.7 + - - -
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Residues in contact with LYS 828 (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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824A LYS 3.3 12.1 + - - +
825A HIS 3.1 9.9 + - - +
827A LEU* 1.3 77.2 - - + +
829A HIS* 1.3 59.9 + - - +
833A TRP* 2.9 21.6 + - - +
837A LYS* 6.4 0.2 - - - +
945A TYR* 3.5 4.1 + - - +
958A GLN* 3.3 16.7 + - - +
959A PRO* 3.4 24.6 + - - +
960A TYR 3.4 20.6 - - - +
961A TYR* 3.4 28.7 - - - +
962A PHE* 3.8 17.5 - - + +
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Residues in contact with HIS 829 (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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804A ILE* 3.5 28.9 - - + -
807A GLU* 2.5 30.8 + - - -
808A LEU* 3.5 34.9 - - + +
825A HIS 3.4 7.3 + - - +
826A VAL 3.1 17.4 + - - +
827A LEU 3.2 0.4 - - - -
828A LYS* 1.3 79.7 - - - +
830A PRO* 1.3 86.3 - - + +
831A PHE* 2.9 27.0 + - + +
832A PHE* 3.1 14.6 + - - +
833A TRP* 3.3 7.3 - - - -
945A TYR* 4.1 7.4 - + - -
946A ARG* 3.8 14.8 - - - -
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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