Contacts of the strand formed by residues 383 - 388 (chain T) in PDB entry 1VYH
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 383 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342T ARG* 3.3 12.6 - - - +
356T CYS* 4.0 15.7 - - + +
357T ALA 2.9 22.3 + - - +
358T ASP* 4.4 0.3 - - - +
360T LYS* 3.8 19.5 - - - +
361T THR 4.5 6.1 - - - +
362T LEU* 6.1 1.3 - - + -
378T ALA* 4.3 6.3 - - + -
379T HIS* 3.3 37.2 - - + +
382T PHE* 1.3 72.5 - - - +
384T THR* 1.3 58.6 + - - +
385T SER 4.2 0.4 - - - +
397T THR* 3.1 33.7 - - + +
398T GLY 2.9 17.9 - - - +
399T SER* 3.3 4.0 - - - -
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Residues in contact with THR 384 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111T VAL 3.7 24.5 - - - +
112T THR* 3.9 15.0 - - + +
113T ARG* 4.6 3.7 + - - +
342T ARG* 3.2 64.3 + - - +
382T PHE* 3.9 14.7 + - - -
383T VAL* 1.3 72.2 + - - +
385T SER* 1.3 59.0 + - - +
398T GLY 2.4 21.5 + - - -
399T SER* 3.6 4.2 - - - +
400T VAL* 4.0 7.8 - - + +
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Residues in contact with SER 385 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111T VAL 4.4 2.1 + - - -
112T THR* 3.0 31.5 + - - -
113T ARG* 3.2 27.1 + - - -
114T VAL* 3.5 12.8 - - - +
342T ARG 5.0 2.2 - - - -
343T GLY* 5.6 0.4 - - - -
356T CYS* 3.6 8.3 - - - -
384T THR* 1.3 80.8 - - - +
386T LEU* 1.3 55.9 - - - +
397T THR* 2.7 23.0 + - - -
398T GLY* 2.9 20.2 + - - -
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Residues in contact with LEU 386 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114T VAL* 5.0 4.0 + - - +
343T GLY* 3.5 40.1 - - - +
344T VAL 4.0 0.2 - - - +
345T LEU* 3.4 23.8 - - + +
354T LEU* 3.6 39.7 - - + +
355T SER* 4.0 0.7 - - - +
356T CYS* 3.8 8.1 - - + +
362T LEU* 3.8 20.6 - - + -
385T SER* 1.3 72.7 - - - +
387T ASP* 1.3 64.4 + - - +
395T VAL* 4.5 4.7 - - + -
396T VAL 3.5 6.7 - - - +
397T THR* 3.2 17.7 - - - +
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Residues in contact with ASP 387 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114T VAL 4.0 17.5 - - - +
115T ILE* 4.1 5.4 - - - +
116T PHE* 3.0 47.3 + - + +
345T LEU* 4.0 9.9 - - - +
386T LEU* 1.3 79.0 - - - +
388T PHE* 1.3 66.9 + - - +
395T VAL* 3.4 4.4 - - - -
396T VAL* 2.9 42.5 + - + -
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Residues in contact with PHE 388 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94T TRP* 3.7 19.5 - + + -
95T ILE 4.0 16.4 - - - -
96T PRO* 4.4 7.6 - - + -
116T PHE* 3.8 7.2 - - - +
345T LEU* 3.7 28.3 - - + +
347T HIS* 3.2 38.6 - + - +
354T LEU* 4.4 9.0 - - + -
387T ASP* 1.3 83.4 - - - +
389T HIS* 1.3 86.2 + - - +
390T LYS 3.8 1.0 + - - -
392T ALA 4.0 8.3 - - - -
393T PRO 3.5 18.4 - - - -
394T TYR 3.0 20.6 - - - -
395T VAL* 3.5 30.5 - - + +
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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