Contacts of the strand formed by residues 402 - 406 (chain E) in PDB entry 4DVQ
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 LEU 402 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E LEU* 4.2 13.5 - - + -
86E PRO* 6.1 1.1 - - + +
87E ARG 2.9 15.7 + - - +
88E MET* 3.0 27.8 - - + +
89E VAL 2.8 31.2 + - - +
111E MET* 3.6 37.2 - - + -
383E GLU* 3.9 26.0 - - + +
384E ARG 3.7 8.1 - - - +
385E VAL* 3.9 13.9 - - + +
400E GLY 3.7 3.4 + - - -
401E THR* 1.3 71.4 - - - +
403E VAL* 1.3 54.4 + - - +
404E GLN* 4.0 17.3 - - + +
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Residues in contact with VAL 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E VAL* 3.6 11.4 - - + +
91E VAL* 4.3 13.0 - - + -
100E LEU* 3.7 33.1 - - + +
383E GLU* 3.4 3.8 - - - +
384E ARG 2.8 39.2 + - - +
386E VAL* 3.9 14.6 - - + -
392E LEU* 4.1 19.5 - - + -
397E ILE* 4.2 22.2 - - + -
401E THR* 3.7 13.7 - - + +
402E LEU* 1.3 76.0 - - - +
404E GLN* 1.3 64.6 + - - +
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Residues in contact with GLN 404 (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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68E MET* 5.0 2.2 - - - +
88E MET* 4.6 15.5 - - - +
89E VAL 2.9 13.2 + - - +
90E CYS* 3.4 8.4 - - - +
91E VAL* 2.9 26.9 + - - +
381E PHE* 3.6 24.4 - - + -
382E LEU 3.3 6.5 - - - +
383E GLU* 3.0 24.9 - - + +
402E LEU* 4.0 19.1 - - + +
403E VAL* 1.3 78.1 - - - +
405E VAL* 1.3 63.5 + - - +
406E PHE* 3.3 37.6 + - + -
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Residues in contact with VAL 405 (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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91E VAL* 3.4 28.9 - - + +
92E MET* 4.7 0.9 - - - -
93E LEU 5.2 0.4 - - - +
97E VAL* 3.9 28.0 - - + -
100E LEU* 3.7 25.4 - - + -
381E PHE* 3.2 3.5 - - - -
382E LEU* 2.8 47.2 + - + +
404E GLN* 1.3 76.0 - - - +
406E PHE* 1.3 59.6 + - - +
407E LEU* 3.1 16.8 + - + +
410E LEU* 4.2 17.5 - - + -
445E PHE* 5.5 0.4 - - + -
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Residues in contact with PHE 406 (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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64E LEU* 4.6 5.4 - - + -
65E HIS* 5.5 0.7 - - - -
68E MET* 3.5 50.3 - - + -
72E PHE* 4.0 24.2 - + + -
90E CYS* 3.9 17.3 - - + -
91E VAL 3.1 9.3 + - - +
92E MET* 4.1 3.6 - - - +
380E LEU* 3.7 29.4 - - + -
381E PHE* 3.4 25.1 - + + -
404E GLN* 3.3 35.2 - - + -
405E VAL* 1.3 70.3 - - - +
407E LEU* 1.3 60.7 + - - +
408E TYR* 3.2 3.7 + - + +
409E SER* 3.4 9.3 + - - +
410E LEU* 3.1 26.0 + - - +
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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