Contacts of the strand formed by residues 820 - 825 (chain E) in PDB entry 5ZOJ
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 ILE 820 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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810E ILE* 5.5 4.5 - - + +
811E LEU* 4.2 16.4 - - + -
814E CYS* 3.6 37.7 - - + +
817E ASN* 3.3 24.8 + - + +
818E ASP 3.7 1.0 - - - -
819E GLY* 1.3 75.0 - - - +
821E VAL* 1.3 54.6 + - - +
822E HIS 4.3 0.9 - - - +
823E ILE* 3.5 31.0 - - + -
836E VAL* 3.9 19.5 - - + -
838E CYS* 3.8 19.7 - - - -
847E ALA* 4.4 6.7 - - + -
884E PRO* 3.2 3.1 - - - +
885E LEU 2.6 37.8 + - - +
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Residues in contact with VAL 821 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819E GLY 3.3 14.4 - - - +
820E ILE* 1.3 75.2 - - - +
822E HIS* 1.3 64.9 + - + +
837E LYS* 3.2 25.3 + - + +
838E CYS 4.1 10.5 - - - +
839E LEU* 3.7 20.4 - - + +
881E SER* 3.5 35.3 - - - +
882E ASN 4.0 5.4 - - - +
883E THR* 3.5 28.3 - - - +
884E PRO* 3.8 8.1 - - + -
885E LEU* 4.1 13.4 - - - +
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Residues in contact with HIS 822 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820E ILE* 3.8 2.0 - - - +
821E VAL* 1.3 84.1 - - + +
823E ILE* 1.3 70.4 + - - +
824E ALA* 3.9 27.8 + - + +
835E TYR* 4.7 5.0 + - + -
836E VAL* 3.3 7.1 - - - +
837E LYS* 3.0 51.1 + - + +
878E ALA* 4.6 21.0 + - + +
881E SER* 4.5 16.4 - - - +
885E LEU* 4.4 4.4 - - - +
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Residues in contact with ILE 823 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807E GLN* 3.7 45.5 + - + +
810E ILE* 4.8 7.6 - - + -
811E LEU* 3.6 22.9 - - + -
820E ILE* 3.5 24.7 - - + -
822E HIS* 1.3 83.6 + - - +
824E ALA* 1.3 64.0 + - - +
825E VAL* 4.3 0.2 - - + -
834E VAL* 3.7 25.4 - - + -
835E TYR 3.3 3.6 - - - +
836E VAL* 3.7 15.3 - - + -
885E LEU* 3.6 27.0 - - + +
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Residues in contact with ALA 824 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807E GLN* 4.7 2.2 - - - +
822E HIS* 3.9 19.7 - - + +
823E ILE* 1.3 75.4 - - - +
825E VAL* 1.3 62.7 + - - +
834E VAL* 3.5 0.6 - - - -
835E TYR* 2.6 53.1 + - + +
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Residues in contact with VAL 825 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792E PHE* 4.4 10.3 - - + -
802E TRP* 5.1 2.7 - - + -
803E HIS* 3.5 35.0 - - + +
806E ILE* 4.1 11.2 - - + -
807E GLN* 3.8 27.6 - - + +
824E ALA* 1.3 79.5 - - - +
826E ASP* 1.3 59.0 + - - +
827E LYS* 3.3 17.7 + - + +
833E CYS 3.6 9.0 - - - +
834E VAL* 3.7 25.1 - - + -
835E TYR* 5.2 0.4 - - - -
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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