Contacts of the strand formed by residues 209 - 214 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F GLY* 1.3 71.4 - - - -
210F LEU* 1.3 63.5 + - - +
211F ALA* 5.3 4.7 - - + +
251F VAL* 4.2 18.9 - - - +
252F VAL 2.8 26.9 + - - -
253F PRO* 3.8 13.7 + - - +
254F ASP 4.1 3.2 + - - -
255F GLU* 3.1 33.7 + - - +
328F ARG* 3.6 4.2 - - + +
329F LEU* 3.3 4.8 - - - -
330F GLU* 2.7 60.4 + - + +
332F LYS* 4.1 24.8 - - - +
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Residues in contact with LEU 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F GLY 4.0 2.2 + - - -
209F ARG* 1.3 80.0 + - - +
211F ALA* 1.3 72.0 + - - +
212F TYR* 4.7 0.9 - - + -
251F VAL* 4.2 0.2 - - - -
252F VAL* 3.0 43.2 + - + +
254F ASP 5.1 0.4 + - - -
257F PHE* 3.9 24.8 - - + -
260F VAL* 4.4 19.5 - - + -
287F LEU* 4.6 19.7 - - + -
289F TYR* 3.6 32.8 - - + -
327F PHE* 4.8 6.1 - - + -
328F ARG 3.4 12.3 - - - +
329F LEU* 4.2 15.9 - - + +
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Residues in contact with ALA 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F ARG* 4.2 5.8 + - + -
210F LEU* 1.3 76.0 - - - +
212F TYR* 1.3 61.6 + - - +
245F VAL* 3.8 36.1 - - + -
249F TRP* 3.8 2.9 - - + -
250F THR 3.5 9.0 - - - +
251F VAL* 4.5 9.0 - - + -
327F PHE* 3.2 3.3 - - - +
328F ARG* 2.6 47.3 + - + +
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Residues in contact with TYR 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F LEU* 4.7 2.7 - - + -
211F ALA* 1.3 77.0 - - - +
213F LEU* 1.3 56.9 + - - +
214F PRO* 3.4 15.3 - - + +
249F TRP* 3.4 10.2 - - - -
250F THR* 2.7 66.5 + - + +
252F VAL* 3.7 29.8 - - + -
287F LEU* 3.6 26.9 - - + -
289F TYR* 4.6 9.1 + + - -
320F VAL* 5.4 1.2 - - - +
322F VAL* 3.3 42.5 - - + +
324F VAL* 3.7 14.1 - - + -
326F ALA 3.5 13.7 - - - +
327F PHE* 4.2 0.9 - - + -
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Residues in contact with LEU 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F TYR* 1.3 73.7 - - - +
214F PRO* 1.3 78.8 - - + +
217F ARG* 4.2 15.9 - - + +
237F HIS* 3.9 28.5 - - + +
248F HIS* 3.6 33.0 - - + +
249F TRP* 3.6 31.1 - - + +
324F VAL* 3.6 2.3 - - - +
325F VAL* 3.1 45.9 + - + +
326F ALA* 3.2 13.6 + - + -
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Residues in contact with PRO 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F TYR* 3.4 26.9 - - + +
213F LEU* 1.3 104.1 - - + +
215F VAL* 1.3 66.7 + - - +
216F GLY 3.2 3.9 + - - +
217F ARG* 3.4 43.5 + - + +
248F HIS 4.6 0.4 - - - +
250F THR* 3.7 15.9 - - - +
322F VAL* 4.3 5.8 - - + -
323F PRO 3.7 11.2 - - - +
325F VAL* 5.1 0.9 - - - +
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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
------------------------------------------------------------
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