Contacts of the strand formed by residues 383 - 388 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342G ARG* 3.6 10.5 - - - +
356G CYS* 3.3 36.7 - - + -
357G ALA 3.2 20.1 + - - +
360G LYS* 3.9 20.2 - - - +
361G THR 4.3 3.4 - - - +
362G LEU* 5.2 0.4 - - + -
378G ALA* 4.2 7.0 - - + -
379G HIS* 3.2 39.5 - - + -
382G PHE* 1.3 75.3 - - - +
384G THR* 1.3 59.5 + - - +
385G SER 4.4 2.5 - - - +
397G THR* 4.1 18.2 - - - +
398G GLY 4.2 3.6 - - - +
399G SER* 3.7 3.6 - - - -
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Residues in contact with THR 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G VAL 3.2 22.5 + - - +
112G THR* 4.3 13.8 - - + +
113G ARG* 4.9 2.6 + - - -
342G ARG* 3.1 58.1 + - - +
356G CYS* 4.1 4.3 - - - -
382G PHE 3.7 3.6 + - - -
383G VAL* 1.3 73.3 - - - +
385G SER* 1.3 64.1 + - - +
398G GLY 2.6 16.3 + - - -
399G SER* 3.5 12.5 - - - -
400G VAL* 3.8 6.9 - - + +
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Residues in contact with SER 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G VAL* 4.7 0.5 + - - +
112G THR 3.5 1.4 + - - -
113G ARG* 3.1 38.7 + - - -
114G VAL* 3.4 25.8 + - - +
343G GLY* 5.5 1.3 - - - -
356G CYS* 4.0 7.7 - - - -
383G VAL* 3.7 2.7 - - - +
384G THR* 1.3 83.4 - - - +
386G LEU* 1.3 63.9 + - - +
396G VAL 4.5 0.2 - - - -
397G THR* 3.2 5.5 + - - -
398G GLY* 2.6 36.0 + - - -
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Residues in contact with LEU 386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G VAL* 4.6 7.0 - - - +
343G GLY* 3.6 35.4 - - - -
344G VAL 4.0 3.4 - - - +
345G LEU* 4.0 22.4 - - + +
354G LEU* 3.7 35.0 - - + -
355G SER* 4.4 1.6 - - - +
356G CYS* 4.3 7.6 - - + -
362G LEU* 3.9 18.6 - - + -
385G SER* 1.3 79.5 - - - +
387G ASP* 1.3 64.1 + - - +
395G VAL* 4.6 9.4 - - + -
396G VAL* 3.1 12.1 - - - +
397G THR* 4.5 8.1 - - - +
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Residues in contact with ASP 387 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G VAL 4.0 9.6 - - - +
115G ILE* 3.9 23.5 - - - +
116G PHE* 3.6 18.3 + - + +
345G LEU* 4.4 10.6 - - - +
386G LEU* 1.3 76.5 - - - +
388G PHE* 1.3 75.9 + - - +
395G VAL* 3.0 19.8 - - - +
396G VAL* 3.0 33.8 + - + +
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Residues in contact with PHE 388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G TRP* 3.9 21.1 - + + -
95G ILE 4.6 12.1 - - - -
96G PRO* 4.8 13.7 - - + -
116G PHE* 3.8 3.0 - - - -
345G LEU* 3.3 25.0 - - + +
346G PHE 5.9 0.2 - - - +
347G HIS* 3.1 46.0 - + - -
348G SER* 4.4 14.5 + - - -
354G LEU* 4.7 11.2 - - + -
387G ASP* 1.3 85.4 + - - +
389G HIS* 1.3 65.3 + - - +
390G LYS* 3.5 4.5 + - - +
393G PRO 5.7 0.9 - - - -
394G TYR 3.5 15.0 - - - -
395G VAL* 3.2 37.7 - - + -
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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