Contacts of the strand formed by residues 209 - 214 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLY* 1.3 76.4 - - - +
210A LEU* 1.3 58.6 + - - +
251A VAL* 6.1 5.8 - - + -
252A VAL 5.8 1.8 - - - +
254A ASP 5.6 0.2 - - - -
255A GLU* 3.6 35.0 + - + -
328A ARG* 3.6 2.4 - - - +
329A LEU* 3.2 6.7 - - - +
330A GLU* 2.7 60.2 + - + +
332A LYS* 3.9 27.4 - - + +
13B ARG* 3.4 57.5 - - - +
46B GLU* 4.5 2.6 + - - -
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLY 4.2 1.2 + - - -
209A ARG* 1.3 74.3 - - - +
211A ALA* 1.3 71.3 + - - +
212A TYR* 4.5 0.4 - - + -
251A VAL* 3.8 4.3 - - - +
252A VAL* 2.8 57.7 + - + +
254A ASP 5.4 0.2 + - - -
257A PHE* 3.9 20.4 - - + -
260A VAL* 4.3 22.2 - - + -
287A LEU* 4.4 20.6 - - + -
289A TYR* 3.6 34.1 - - + -
327A PHE* 4.6 6.3 - - + -
328A ARG 3.4 16.8 - - - +
329A LEU* 4.4 9.0 - - + -
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG 4.2 0.2 - - - -
210A LEU* 1.3 75.9 - - - +
212A TYR* 1.3 62.0 + - - +
245A VAL* 3.9 34.3 - - + -
249A TRP* 3.9 7.9 - - + -
250A THR 3.2 11.4 - - - +
251A VAL* 4.3 7.9 - - + -
327A PHE* 3.2 3.6 - - - +
328A ARG* 2.7 40.2 + - + +
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Residues in contact with TYR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 4.5 1.8 - - + -
211A ALA* 1.3 79.1 - - - +
213A LEU* 1.3 59.0 - - - +
214A PRO* 3.7 13.6 - - + +
249A TRP* 3.4 11.7 - - - +
250A THR* 2.9 61.7 + - + +
252A VAL* 3.6 30.0 - - + +
287A LEU* 3.6 31.4 - - + -
289A TYR* 4.5 12.1 + + - -
320A VAL* 5.5 0.3 - - - +
322A VAL* 3.6 35.8 - - + +
324A VAL* 3.4 18.2 - - + -
326A ALA 3.4 12.3 - - - +
327A PHE* 4.1 1.8 - - + -
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 1.3 73.3 - - - +
214A PRO* 1.3 81.2 - - + +
216A GLY 4.5 2.0 - - - +
217A ARG* 4.1 13.5 - - + -
237A HIS* 3.8 28.9 - - + +
248A HIS* 3.7 35.2 - - + +
249A TRP* 3.8 31.0 - - + +
324A VAL* 3.3 3.3 - - - -
325A VAL* 2.9 49.3 + - + +
326A ALA* 2.8 16.7 + - + +
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Residues in contact with PRO 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TYR* 3.7 24.8 - - + +
213A LEU* 1.3 101.5 - - + +
215A VAL* 1.3 55.2 + - - +
216A GLY* 2.7 31.7 + - - +
217A ARG* 3.6 3.3 + - - -
248A HIS 4.7 5.4 - - - +
250A THR* 3.9 15.3 - - - +
322A VAL* 4.5 9.0 - - + -
323A PRO 3.5 13.2 - - - +
324A VAL* 4.2 2.5 - - + -
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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