Contacts of the strand formed by residues 383 - 388 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C ARG* 3.4 24.7 - - - +
356C CYS* 3.5 26.3 - - + -
357C ALA 3.4 11.8 + - - +
360C LYS 3.7 7.4 - - - +
361C THR 3.5 32.3 - - - +
362C LEU* 5.5 0.4 - - + -
378C ALA* 4.5 1.6 - - + -
379C HIS* 3.6 32.1 - - + +
382C PHE* 1.3 78.2 - - - +
384C THR* 1.3 61.6 + - - +
385C SER 4.4 1.6 - - - +
397C THR* 4.0 13.2 - - + +
398C GLY 3.8 8.3 - - - +
399C SER* 3.6 2.2 - - - -
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Residues in contact with THR 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C VAL 3.0 27.5 + - - +
112C THR* 3.8 15.3 - - + +
113C ARG* 5.3 1.0 + - - -
342C ARG* 3.6 53.4 + - - +
356C CYS* 4.0 0.2 - - - -
382C PHE 4.2 0.5 + - - -
383C VAL* 1.3 74.8 - - - +
385C SER* 1.3 66.8 + - - +
398C GLY 2.8 13.5 + - - -
399C SER* 3.3 11.4 - - - -
400C VAL* 3.9 7.7 + - + +
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Residues in contact with SER 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C THR 3.3 7.6 + - - -
113C ARG* 3.3 43.0 + - - -
114C VAL* 3.6 12.8 + - - +
342C ARG 5.1 1.8 - - - -
343C GLY* 5.1 0.9 - - - -
356C CYS* 3.6 8.8 - - - -
383C VAL* 3.6 2.6 - - - +
384C THR* 1.3 85.1 - - - +
386C LEU* 1.3 66.6 + - - +
397C THR* 3.4 4.3 + - - -
398C GLY* 3.1 27.7 + - - +
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Residues in contact with LEU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C VAL* 4.0 8.2 - - - +
343C GLY* 3.4 38.6 - - - -
344C VAL 3.8 2.0 - - - +
345C LEU* 3.8 25.6 - - + +
354C LEU* 3.8 37.0 - - + -
355C SER 4.1 7.0 - - - +
356C CYS* 3.5 18.6 - - + -
362C LEU* 4.4 9.4 - - + -
385C SER* 1.3 76.5 - - - +
387C ASP* 1.3 68.2 + - - +
395C VAL* 5.8 4.0 - - + -
396C VAL 3.1 13.2 - - - +
397C THR* 4.2 8.1 - - - +
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Residues in contact with ASP 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C VAL 3.8 19.3 - - - +
115C ILE* 3.7 6.9 - - - +
116C PHE* 3.0 48.2 + - + +
345C LEU* 3.9 11.6 - - - +
386C LEU* 1.3 80.5 - - - +
388C PHE* 1.3 68.5 + - - +
395C VAL* 3.0 7.1 - - - -
396C VAL* 2.9 33.3 + - + -
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Residues in contact with PHE 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C TRP* 3.7 18.6 - + + -
95C ILE 5.5 4.5 - - - -
96C PRO* 5.3 8.1 - - + -
116C PHE* 3.2 12.2 - - - +
345C LEU* 3.3 20.5 - - + +
346C PHE 5.3 4.5 - - - +
347C HIS* 3.4 50.9 - + - -
348C SER* 3.6 22.2 - - - -
354C LEU* 4.0 28.7 - - + -
387C ASP* 1.3 79.7 + - - +
389C HIS* 1.3 71.8 + - - +
390C LYS 3.8 2.6 + - - -
392C ALA 5.6 0.2 - - - -
393C PRO* 6.5 0.2 - - + -
394C TYR 4.7 4.3 - - - -
395C VAL* 2.9 30.1 - - + -
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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