Contacts of the strand formed by residues 319 - 324 (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 THR 319 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275C HIS* 3.3 20.1 - - - -
315C SER* 3.7 10.6 + - - -
317C ASP* 2.5 39.7 + - + +
318C LYS* 1.3 84.8 - - + +
320C ILE* 1.3 62.5 + - - +
321C LYS* 4.6 3.7 + - - +
333C THR* 4.5 15.7 - - + -
334C LEU 3.9 5.8 - - - -
335C VAL* 4.0 29.6 - - + -
341C VAL* 4.0 1.3 - - - +
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Residues in contact with ILE 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LEU* 4.5 7.6 - - + -
313C SER 3.4 13.7 - - - +
314C GLY* 4.5 0.4 - - - -
318C LYS 5.5 0.2 - - - +
319C THR* 1.3 73.8 - - - +
321C LYS* 1.3 71.6 + - - +
322C MET* 6.1 0.7 - - + -
333C THR* 3.6 1.5 - - - -
334C LEU* 2.9 52.5 + - + +
341C VAL* 4.0 19.1 - - + -
344C VAL* 3.9 26.5 - - + -
353C ILE* 5.1 4.9 - - + -
355C SER* 3.4 35.2 - - - +
363C ARG* 4.5 5.2 - - - +
365C TRP* 4.5 14.6 - - + +
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Residues in contact with LYS 321 (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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274C GLU* 2.9 31.5 + - - +
275C HIS* 3.8 24.2 + - + +
312C LEU* 3.2 27.2 - - - +
313C SER* 3.2 10.7 + - - +
317C ASP* 4.7 1.0 + - - -
319C THR* 4.0 5.4 + - - +
320C ILE* 1.3 77.7 - - - +
322C MET* 1.3 62.4 + - - +
323C TRP* 3.4 39.0 - - + +
330C CYS* 3.8 18.2 - - + -
332C MET* 3.8 4.3 - - - -
333C THR* 3.4 31.1 + - + +
334C LEU* 6.1 0.7 - - - -
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Residues in contact with MET 322 (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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291C SER* 4.7 13.5 - - - +
310C PHE* 4.7 19.7 - - + -
311C LEU 3.6 2.7 - - - -
312C LEU* 3.7 15.0 - - + -
320C ILE* 6.1 0.4 - - + -
321C LYS* 1.3 73.0 - - - +
323C TRP* 1.3 68.5 + - - +
330C CYS* 3.6 2.6 - - - -
331C LEU* 2.8 46.3 + - + -
332C MET* 3.5 34.1 + - + +
334C LEU* 5.8 3.6 - - + -
346C PHE* 3.9 26.7 - - - -
353C ILE* 4.6 11.0 - - + -
367C TYR* 4.8 13.9 - - - -
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Residues in contact with TRP 323 (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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258C VAL* 5.4 2.2 - - + +
272C LEU* 3.5 60.1 - - + +
273C ARG 4.1 2.2 - - - -
274C GLU* 3.7 26.7 - - + -
275C HIS* 4.4 9.0 - + - -
309C PRO 3.8 0.2 - - - +
310C PHE* 3.0 11.3 - - - +
311C LEU* 2.7 57.1 + - + +
313C SER* 2.5 28.5 + - - -
321C LYS* 3.4 33.0 - - + +
322C MET* 1.3 84.2 - - - +
324C ASP* 1.3 63.0 + - - +
325C VAL 3.9 0.4 + - - -
328C GLY 4.3 4.7 - - - -
329C MET 3.7 7.2 - - - +
330C CYS* 3.9 25.8 - - + -
331C LEU* 4.5 2.2 - - - +
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Residues in contact with ASP 324 (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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308C GLY* 4.9 4.9 - - - -
309C PRO 3.5 4.3 - - - +
310C PHE* 3.3 28.0 - - + -
323C TRP* 1.3 72.3 - - - +
325C VAL* 1.3 52.5 + - - +
326C SER* 2.9 22.5 + - - -
327C THR* 2.5 38.5 + - - +
328C GLY* 2.6 33.5 + - - -
329C MET 3.3 7.1 + - - -
331C LEU* 4.0 22.2 - - + +
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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