Contacts of the strand formed by residues 361 - 365 (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 THR 361 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337G HIS* 3.7 12.0 + - - +
355G SER 4.0 0.2 - - - +
356G CYS* 3.3 21.4 - - - +
357G ALA 3.3 8.2 + - - -
359G ASP* 2.6 37.1 + - - +
360G LYS* 1.3 77.9 + - - +
362G LEU* 1.3 66.4 + - - +
363G ARG* 3.5 20.5 + - + +
375G THR* 3.8 16.3 - - + +
376G LEU 3.5 13.2 + - - +
377G ASN* 4.4 9.0 + - - -
383G VAL* 4.3 3.5 - - - +
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Residues in contact with LEU 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G PRO 5.2 3.6 - - - +
354G LEU* 4.1 14.6 - - + -
355G SER 3.1 19.1 - - - +
356G CYS* 4.1 6.1 - - + +
361G THR* 1.3 73.0 - - - +
363G ARG* 1.3 68.2 + - - +
364G VAL* 5.0 2.8 - - + +
376G LEU* 2.9 61.1 + - + +
378G ALA* 4.2 11.2 - - + +
383G VAL* 5.2 0.4 - - + -
386G LEU* 3.9 23.1 - - + -
395G VAL* 5.2 10.1 - - + -
397G THR* 4.0 19.1 - - - +
407G TRP* 4.5 19.3 - - + +
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Residues in contact with ARG 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318G LYS 5.1 0.4 + - - -
320G ILE* 4.4 4.9 - - - +
336G GLY* 4.6 2.5 - - - -
337G HIS* 3.2 51.6 - - + +
338G ASP 3.1 23.4 - - - +
339G ASN 4.1 5.1 + - - -
341G VAL* 3.4 31.3 - - - +
354G LEU* 3.4 3.3 - - - -
355G SER* 2.7 61.2 + - - +
356G CYS 4.1 0.4 + - - -
357G ALA* 3.7 9.1 - - - +
359G ASP* 2.6 27.9 + - - -
361G THR* 3.5 11.7 - - + +
362G LEU* 1.3 79.2 - - - +
364G VAL* 1.3 61.3 + - - +
365G TRP* 3.6 16.5 - - + +
372G CYS* 4.6 0.9 - - - -
374G LYS 3.7 7.0 - - - +
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Residues in contact with VAL 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G PRO* 3.7 33.0 - - + +
352G PHE* 4.6 9.6 - - + -
353G ILE 3.9 2.7 - - - -
354G LEU* 3.5 35.2 - - + -
362G LEU* 5.0 5.2 - - + +
363G ARG* 1.3 72.6 - - - +
365G TRP* 1.3 65.4 + - - +
372G CYS* 4.0 0.9 - - - -
373G MET* 3.1 39.7 + - + -
374G LYS* 3.2 28.1 + - + +
376G LEU* 5.8 4.9 - - + -
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Residues in contact with TRP 365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G ILE* 3.6 17.7 - - + +
334G LEU* 3.2 44.9 - - + -
335G VAL 3.3 31.9 - - - -
336G GLY* 3.7 17.0 - - - -
337G HIS* 4.2 13.5 - + - -
352G PHE* 3.5 27.2 - - - +
353G ILE* 2.7 34.9 + - + +
355G SER* 3.5 19.7 + - - -
363G ARG* 3.6 22.1 - - + +
364G VAL* 1.3 78.2 - - - +
366G ASP* 1.3 62.9 + - - +
367G TYR 4.1 1.1 - - - +
370G LYS 4.0 10.5 - - - -
371G ARG 3.7 17.7 - - - -
372G CYS* 3.8 21.1 - - + -
373G MET* 4.2 1.3 - - - +
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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
------------------------------------------------------------
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