Contacts of the strand formed by residues 395 - 399 (chain D) 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 395 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D ILE 5.5 0.2 - - - +
96D PRO* 4.4 18.8 - - + +
116D PHE* 4.3 1.1 - - - -
354D LEU* 4.5 4.7 - - + -
362D LEU* 5.0 7.0 - - + -
386D LEU* 4.3 14.6 - - + -
387D ASP 3.0 24.5 - - - +
388D PHE* 3.5 35.7 - - + -
394D TYR* 1.3 75.5 - - - +
396D VAL* 1.3 67.1 + - - +
406D VAL* 3.4 3.5 - - - +
407D TRP* 2.5 61.0 + - + +
408D GLU 5.3 2.2 - - - +
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Residues in contact with VAL 396 (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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114D VAL* 3.7 21.8 - - + -
115D ILE 4.9 0.9 - - - +
116D PHE* 3.3 33.2 - - + -
123D MET* 4.0 25.6 - - + -
137D TYR* 5.4 0.4 - - + -
386D LEU* 3.2 8.7 - - - +
387D ASP* 3.1 33.2 + - + +
395D VAL* 1.3 78.7 - - - +
397D THR* 1.3 61.6 + - - +
404D VAL* 4.0 10.1 - - + -
405D LYS 3.4 14.1 - - - +
406D VAL* 4.0 17.3 - - + -
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Residues in contact with THR 397 (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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114D VAL* 4.0 5.3 - - - +
362D LEU* 4.0 15.9 - - - +
378D ALA* 4.7 1.8 - - + +
379D HIS* 2.6 31.2 - - + +
383D VAL* 4.0 12.3 - - - +
385D SER 3.5 8.2 + - - -
386D LEU* 4.3 4.0 - - - +
396D VAL* 1.3 79.6 + - - +
398D GLY* 1.3 56.6 + - - +
404D VAL* 3.4 2.8 - - - +
405D LYS* 2.7 29.7 + - + -
407D TRP* 3.1 32.6 + - + +
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Residues in contact with GLY 398 (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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111D VAL* 4.3 8.1 - - - -
114D VAL* 3.6 17.4 - - - +
379D HIS* 4.3 2.2 - - - -
383D VAL* 3.6 1.3 - - - +
384D THR* 2.6 36.9 + - - -
385D SER* 3.2 11.6 + - - +
397D THR* 1.3 75.8 - - - +
399D SER* 1.3 55.5 + - - -
403D THR 3.6 11.0 - - - -
404D VAL* 4.4 1.1 - - - -
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Residues in contact with SER 399 (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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111D VAL* 2.7 36.8 + - - +
379D HIS* 2.8 28.0 + - - -
381D HIS 3.5 6.3 - - - -
382D PHE 2.7 21.8 - - - -
383D VAL* 3.7 0.4 - - - -
384D THR* 3.7 5.2 - - - +
398D GLY* 1.3 73.6 - - - -
400D VAL* 1.3 63.1 + - - +
401D ASP* 2.3 25.3 + - - -
402D GLN 3.8 1.7 + - - -
403D THR* 3.4 7.4 + - - -
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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