Contacts of the strand formed by residues 834 - 838 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787D LYS* 3.9 0.3 - - - -
788D ILE* 2.5 53.1 + - + +
791D MET* 3.7 18.2 - - + -
792D PHE* 3.5 22.4 - - + -
806D ILE* 3.7 22.0 - - + -
807D GLN* 6.0 0.9 - - + -
810D ILE* 4.6 14.1 - - + -
823D ILE* 5.0 4.0 - - + -
824D ALA 3.5 14.1 - - - +
825D VAL* 3.6 15.0 - - + -
833D CYS* 1.3 77.6 - - - +
835D TYR* 1.3 70.2 + - - +
836D VAL* 4.8 5.6 - - + -
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Residues in contact with TYR 835 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786D LEU 3.4 4.0 - - - +
787D LYS* 3.3 47.8 + - + -
823D ILE* 3.3 4.3 - - - +
824D ALA 2.8 40.8 + - - +
826D ASP* 3.9 29.5 + - + -
833D CYS* 4.1 14.1 - - + +
834D VAL* 1.3 77.1 - - - +
836D VAL* 1.3 62.5 + - - +
866D LEU* 3.6 27.4 - - + -
871D TYR* 3.3 19.5 + - + -
874D ARG* 4.0 28.2 + - - -
875D PHE* 3.4 29.8 - + + -
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Residues in contact with VAL 836 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784D PRO 4.1 0.2 - - - +
785D CYS* 3.3 4.0 - - - -
786D LEU* 2.8 46.5 + - + +
788D ILE* 3.5 28.9 - - + -
810D ILE* 4.1 12.8 - - + -
820D ILE* 4.1 15.0 - - + -
822D HIS 3.6 2.9 - - - -
823D ILE* 3.5 27.4 - - + -
834D VAL* 4.8 4.7 - - + -
835D TYR* 1.3 76.9 - - - +
837D LYS* 1.3 61.9 + - - +
838D CYS* 4.0 22.0 - - - -
847D ALA* 5.4 1.3 - - + -
851D LEU* 5.2 1.1 - - + -
871D TYR* 3.5 6.0 - - - -
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Residues in contact with LYS 837 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784D PRO* 3.8 2.9 - - + -
785D CYS* 3.9 15.7 - - - -
820D ILE* 3.7 3.6 - - - +
821D VAL* 3.0 36.3 + - + +
822D HIS* 2.8 18.1 + - + +
836D VAL* 1.3 72.7 - - - +
838D CYS* 1.3 73.1 + - - +
868D LEU* 4.1 12.6 - - + -
871D TYR* 3.3 21.5 + - + +
872D HIS* 3.0 24.3 + - - +
878D ALA* 2.7 41.5 + - + +
879D LEU 4.4 4.0 + - - -
881D SER 3.6 11.3 + - - -
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Residues in contact with CYS 838 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784D PRO* 2.8 24.8 + - - +
786D LEU* 4.9 2.0 - - - -
817D ASN* 4.5 0.7 - - - -
819D GLY 3.2 11.4 - - - +
820D ILE* 3.9 24.2 - - - -
821D VAL* 4.4 4.6 - - - +
836D VAL* 4.0 11.2 - - - -
837D LYS* 1.3 89.1 - - - +
839D LEU* 1.3 66.5 + - - +
840D SER 3.9 3.6 - - - +
843D TYR 4.0 5.8 - - - -
844D ALA* 3.6 39.5 - - - +
847D ALA* 4.4 4.3 - - - -
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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