Contacts of the strand formed by residues 319 - 324 (chain H) 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 319 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275H HIS* 3.5 17.8 - - - -
315H SER 3.6 14.3 + - - -
317H ASP* 2.7 45.6 + - + +
318H LYS* 1.3 82.4 - - - +
320H ILE* 1.3 61.7 + - - +
321H LYS* 4.5 0.3 + - - -
333H THR* 3.8 20.3 - - + +
334H LEU 3.8 5.6 - - - -
335H VAL* 3.8 28.7 - - + -
336H GLY 5.2 0.2 - - - +
341H VAL* 4.4 1.3 - - - +
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Residues in contact with ILE 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312H LEU* 4.0 18.2 - - + -
313H SER 3.1 16.2 - - - +
314H GLY* 4.6 0.2 - - - -
319H THR* 1.3 73.5 - - - +
321H LYS* 1.3 61.3 + - - +
332H MET 4.2 0.2 - - - +
333H THR* 3.6 1.7 - - - -
334H LEU* 2.9 46.4 + - + +
341H VAL* 4.2 20.4 - - + -
344H VAL* 3.6 24.9 - - + -
353H ILE* 4.9 1.1 - - + -
355H SER* 3.6 32.8 - - - +
363H ARG* 4.4 2.9 - - - +
365H TRP* 3.6 28.7 - - + +
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Residues in contact with LYS 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H GLU* 3.1 29.8 + - + +
275H HIS* 3.6 22.0 - - + -
312H LEU* 3.3 7.8 - - - +
313H SER* 2.6 44.6 + - - +
317H ASP* 4.2 6.8 + - - -
319H THR* 4.0 0.6 + - - -
320H ILE* 1.3 72.2 - - - +
322H MET* 1.3 59.8 + - - +
323H TRP* 3.5 34.4 - - + +
330H CYS* 4.0 12.8 - - + -
332H MET 3.6 3.6 - - - +
333H THR* 3.0 50.6 + - + +
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Residues in contact with MET 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291H SER* 3.7 19.1 - - - +
294H SER* 5.8 2.7 - - - +
310H PHE* 4.0 29.2 - - + -
311H LEU 3.6 4.5 - - - +
312H LEU* 3.6 20.6 - - + -
320H ILE 4.4 0.2 + - - -
321H LYS* 1.3 73.6 - - - +
323H TRP* 1.3 68.8 + - - +
330H CYS* 3.8 2.8 - - - -
331H LEU* 3.0 51.3 + - + -
332H MET* 3.4 29.3 + - + +
346H PHE* 4.4 13.7 - - + -
353H ILE* 5.2 1.6 - - - -
367H TYR* 4.2 23.6 - - - -
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Residues in contact with TRP 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258H VAL* 5.4 2.5 - - + -
272H LEU* 3.2 63.4 - - + +
273H ARG 4.0 4.0 - - - -
274H GLU* 4.1 15.9 - - + -
275H HIS* 4.7 8.3 - + - -
310H PHE* 2.9 31.3 - - - -
311H LEU* 3.1 35.4 + - + +
313H SER* 3.2 26.3 + - - -
321H LYS* 3.5 33.1 - - + +
322H MET* 1.3 84.3 - - - +
324H ASP* 1.3 64.9 + - - +
325H VAL 4.0 0.5 + - - -
328H GLY 4.2 7.6 - - - -
329H MET 3.4 25.6 - - - +
330H CYS* 4.1 5.4 - - + -
331H LEU* 4.6 2.5 - - - +
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Residues in contact with ASP 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308H GLY* 5.1 1.2 - - - -
309H PRO* 3.1 16.6 - - + +
310H PHE* 3.1 25.5 - - + -
323H TRP* 1.3 74.5 - - - +
325H VAL* 1.3 56.3 + - - +
326H SER* 3.4 13.9 + - - +
327H THR* 2.9 25.0 + - - +
328H GLY* 2.8 32.9 + - - -
329H MET 3.7 5.8 + - - +
331H LEU* 3.1 24.6 - - - +
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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