Contacts of the strand formed by residues 834 - 838 (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 VAL 834 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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787E LYS* 3.8 0.9 - - - +
788E ILE* 2.5 47.4 + - + +
791E MET* 3.8 20.9 - - + -
792E PHE* 4.1 3.1 - - + -
806E ILE* 3.8 25.6 - - + -
810E ILE* 4.5 11.4 - - + -
823E ILE* 3.7 17.9 - - + -
824E ALA 3.5 5.2 - - - +
825E VAL* 3.7 23.1 - - + -
833E CYS* 1.3 79.4 - - - +
835E TYR* 1.3 68.0 + - - +
836E VAL* 4.5 8.1 - - + -
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Residues in contact with TYR 835 (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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786E LEU 3.7 3.6 - - - +
787E LYS* 3.3 37.2 - - + -
822E HIS* 3.9 4.8 + - + +
823E ILE* 3.3 4.9 - - - +
824E ALA* 2.6 55.1 + - + +
825E VAL 5.2 0.2 - - - -
826E ASP* 4.0 21.9 + - + -
833E CYS* 4.0 20.2 - - + +
834E VAL* 1.3 74.0 - - - +
836E VAL* 1.3 63.0 + - - +
866E LEU* 3.7 23.3 - - + -
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Residues in contact with VAL 836 (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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784E PRO 4.0 0.5 - - - +
785E CYS* 3.4 4.2 - - - +
786E LEU* 2.9 44.6 + - + +
788E ILE* 3.6 27.8 - - + -
810E ILE* 4.5 9.6 - - + -
820E ILE* 3.9 15.5 - - + -
822E HIS* 3.3 8.3 - - - +
823E ILE* 3.7 22.9 - - + -
834E VAL* 4.5 2.7 - - + -
835E TYR* 1.3 80.5 - - - +
837E LYS* 1.3 62.5 + - - +
838E CYS* 3.9 24.0 - - - -
847E ALA* 5.6 1.1 - - + -
851E LEU* 5.7 0.9 - - + -
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Residues in contact with LYS 837 (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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784E PRO* 3.6 6.7 - - - +
785E CYS* 3.8 25.6 - - - -
821E VAL* 3.2 30.5 + - + +
822E HIS* 3.0 34.2 + - + +
835E TYR 4.4 0.2 - - - -
836E VAL* 1.3 74.3 - - - +
838E CYS* 1.3 74.0 + - - +
879E LEU* 3.3 37.3 + - + +
880E THR* 4.5 6.5 - - - +
881E SER* 4.9 7.5 + - - +
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Residues in contact with CYS 838 (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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784E PRO* 2.8 23.4 + - - +
786E LEU* 5.0 1.1 - - - -
819E GLY 3.3 12.3 - - - +
820E ILE* 3.8 28.3 - - - -
821E VAL* 4.1 5.7 - - - +
836E VAL* 3.9 12.6 - - - -
837E LYS* 1.3 90.0 - - - +
839E LEU* 1.3 67.4 + - - +
840E SER 3.5 2.9 - - - +
843E TYR* 4.2 4.7 - - + -
844E ALA* 3.8 37.9 - - - +
847E ALA* 4.6 3.8 - - - -
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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