Contacts of the strand formed by residues 209 - 214 (chain C) in PDB entry 3VZC
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 ARG 209 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C GLY* 1.3 71.7 - - - -
210C LEU* 1.3 64.0 + - - +
211C ALA* 3.9 0.9 + - - +
251C VAL* 6.0 4.5 - - + -
252C VAL 5.8 0.9 - - - +
255C GLU* 3.8 29.3 + - + +
328C ARG* 3.5 4.9 - - - +
329C LEU* 4.2 2.9 - - - -
330C GLU* 2.8 75.4 + - + +
332C LYS* 3.5 43.1 - - - +
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Residues in contact with LEU 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C GLY 3.8 4.2 + - - -
209C ARG* 1.3 73.5 - - - +
211C ALA* 1.3 85.6 + - - +
212C TYR* 4.4 1.1 - - + -
251C VAL* 4.1 4.2 - - - +
252C VAL* 3.2 36.3 + - + +
254C ASP 5.4 0.2 + - - -
255C GLU* 5.3 0.2 - - - +
257C PHE* 3.7 21.5 - - + -
260C VAL* 4.3 24.7 - - + -
287C LEU* 4.4 18.6 - - + -
289C TYR* 3.3 46.4 - - + -
327C PHE* 4.7 4.9 - - + -
328C ARG 3.5 8.5 - - - +
329C LEU* 4.2 9.4 - - + +
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Residues in contact with ALA 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ARG 3.9 0.9 + - - +
210C LEU* 1.3 79.3 - - - +
212C TYR* 1.3 66.0 + - - +
245C VAL* 3.9 28.0 - - + -
249C TRP* 4.0 2.0 - - + -
250C THR 3.5 12.1 - - - +
251C VAL* 4.2 14.8 - - + -
327C PHE* 3.3 0.9 - - - -
328C ARG* 2.7 39.9 + - + +
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Residues in contact with TYR 212 (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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210C LEU* 4.4 2.2 - - + -
211C ALA* 1.3 80.5 - - - +
213C LEU* 1.3 62.0 + - - +
214C PRO* 3.6 25.5 - - + +
249C TRP* 3.3 13.8 - - - +
250C THR* 2.9 57.6 + - - +
252C VAL* 3.5 29.0 - - + +
287C LEU* 3.8 27.8 - - + -
289C TYR* 4.6 10.5 + + - -
320C VAL* 5.5 0.2 - - - +
322C VAL* 3.5 32.0 - - + +
324C VAL* 3.6 14.4 - - + -
326C ALA 3.4 14.4 - - - +
327C PHE* 4.0 1.1 - - + -
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C TYR* 1.3 75.3 - - - +
214C PRO* 1.4 72.8 - - + +
217C ARG* 4.7 11.4 - - + +
237C HIS* 3.5 37.7 - - + -
248C HIS* 3.5 44.9 - - + +
249C TRP* 3.5 32.3 - - + +
324C VAL* 3.5 1.5 - - - +
325C VAL* 3.0 39.7 + - + +
326C ALA* 3.0 12.6 + - + +
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Residues in contact with PRO 214 (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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212C TYR* 3.6 21.5 - - + +
213C LEU* 1.4 100.3 - - + +
215C VAL* 1.3 64.9 + - - +
216C GLY 3.4 4.1 + - - +
217C ARG* 3.5 53.3 + - + +
250C THR* 3.8 0.2 - - - +
322C VAL* 3.8 19.7 - - + -
323C PRO 3.4 8.3 - - - +
324C VAL* 4.1 3.1 - - + -
325C VAL* 4.8 2.6 - - - +
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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