Contacts of the strand formed by residues 402 - 409 (chain A) in PDB entry 3VEY
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 MET 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A ILE* 3.5 41.5 - - + +
393A MET* 3.9 10.8 - - + -
394A ARG* 3.7 41.6 - - + +
397A ARG* 3.8 22.4 - - + +
399A GLU* 3.7 21.8 - - - +
401A VAL* 1.3 70.4 - - - +
403A ARG* 1.3 63.4 + - - +
404A ILE* 3.8 27.6 + - + +
433A SER 3.0 9.6 + - - +
434A CYS* 3.3 10.7 - - - +
435A GLU 2.9 25.5 + - - +
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Residues in contact with ARG 403 (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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219A GLN* 3.7 38.3 - - - +
397A ARG* 4.3 12.1 + - - +
399A GLU* 5.4 0.8 + - - -
401A VAL* 3.5 11.0 + - + +
402A MET* 1.3 72.5 - - - +
404A ILE* 1.3 60.0 + - - +
435A GLU* 2.8 48.1 + - + +
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Residues in contact with ILE 404 (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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219A GLN* 3.8 11.4 - - - +
221A GLU* 4.2 11.0 - - + +
222A VAL* 3.8 15.5 - - + -
390A ILE* 4.3 11.4 - - + -
393A MET* 3.5 35.0 - - + -
397A ARG* 5.4 2.0 - - - +
402A MET* 3.8 33.4 - - + +
403A ARG* 1.3 74.6 - - - +
405A THR* 1.3 73.8 + - - +
406A VAL* 5.1 0.9 - - + -
435A GLU 3.0 8.6 + - - +
436A ILE* 3.4 24.0 - - + +
437A THR* 3.0 23.8 + - - +
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Residues in contact with THR 405 (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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217A ASP* 2.6 32.7 + - - +
219A GLN* 3.1 12.2 + - - +
220A CYS* 3.3 39.0 - - + -
221A GLU 3.4 8.0 + - - -
222A VAL 3.7 5.0 + - - -
404A ILE* 1.3 77.0 - - - +
406A VAL* 1.3 66.5 + - - +
437A THR* 3.2 21.3 + - - +
439A ILE* 3.6 27.6 - - + -
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Residues in contact with VAL 406 (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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220A CYS* 4.2 1.3 - - - -
222A VAL* 3.6 33.2 - - + -
224A MET* 4.4 8.1 - - + -
386A LEU* 4.2 16.8 - - + -
390A ILE* 4.1 16.6 - - + -
404A ILE* 5.1 2.2 - - + +
405A THR* 1.3 76.6 - - - +
407A GLY* 1.3 65.2 + - - +
408A VAL* 3.9 17.7 + - + +
436A ILE* 3.8 22.7 - - + -
437A THR 2.7 8.9 + - - -
438A PHE* 3.5 13.1 - - + -
439A ILE* 3.0 26.9 + - - +
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Residues in contact with GLY 407 (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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209A THR* 3.7 10.2 - - - +
210A MET* 5.1 0.2 - - - -
213A CYS* 3.8 20.0 - - - -
220A CYS* 3.5 9.1 - - - -
222A VAL 2.8 13.9 + - - -
223A GLY* 3.4 3.5 - - - -
224A MET 2.8 26.9 + - - +
406A VAL* 1.3 71.4 - - - +
408A VAL* 1.4 60.0 + - - +
439A ILE 3.4 5.8 - - - -
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Residues in contact with VAL 408 (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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209A THR* 3.8 4.3 - - - +
224A MET* 3.4 28.5 - - + +
226A VAL* 4.9 0.4 - - + -
406A VAL* 3.9 25.1 - - + +
407A GLY* 1.4 76.9 - - - +
409A ASP* 1.3 68.3 + - - +
413A TYR* 3.5 50.7 - - + +
414A LYS* 4.1 0.5 - - - -
438A PHE* 4.1 10.3 - - + -
439A ILE 2.8 14.2 + - - +
440A GLU* 3.4 9.3 - - + +
441A SER* 2.9 25.9 + - - +
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Residues in contact with ASP 409 (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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209A THR* 3.7 5.5 + - - +
224A MET 3.1 5.3 + - - +
225A ILE* 3.3 26.5 - - + +
226A VAL* 2.9 23.9 + - - +
408A VAL* 1.3 80.0 - - - +
410A GLY* 1.3 70.1 + - - +
413A TYR* 4.6 0.6 - - - +
414A LYS* 2.8 27.8 + - - +
441A SER* 3.4 19.2 + - - +
444A GLY 5.1 5.4 + - - -
445A SER* 5.1 6.9 + - - -
503A AGS 5.5 3.4 + - - -
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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