Contacts of the strand formed by residues 242 - 248 (chain A) in PDB entry 2ZV6
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 SER 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A GLU* 2.9 35.4 + - - -
235A PRO* 3.3 19.5 - - - -
236A TYR* 4.2 1.6 - - - -
240A ASP 5.8 0.4 - - - -
241A LEU* 1.3 74.1 - - - +
243A MET* 1.3 59.9 + - - +
244A ILE* 3.5 10.3 - - - +
373A ILE* 4.6 0.4 - - - -
374A ARG* 3.1 24.3 + - - +
376A ASN* 2.5 40.9 + - - -
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Residues in contact with MET 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TRP* 3.3 29.6 - - + -
234A ILE* 3.0 35.6 + - + +
236A TYR* 3.5 15.4 - - + +
242A SER* 1.3 72.8 - - - +
244A ILE* 1.3 59.4 + - - +
245A VAL* 3.5 28.0 - - - -
284A LEU* 5.2 4.5 - - + -
287A PHE* 4.6 4.3 - - + -
336A VAL* 3.8 29.2 - - + -
371A PHE* 4.0 28.7 - - + -
372A PHE 3.6 4.5 - - - -
373A ILE* 3.5 25.4 - - + +
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Residues in contact with ILE 244 (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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231A VAL* 4.0 4.0 - - + -
232A LEU 3.5 7.9 - - - +
233A GLU* 4.1 16.8 - - + -
242A SER* 3.5 22.9 - - - +
243A MET* 1.3 74.7 - - - +
245A VAL* 1.3 64.7 + - - +
246A LEU* 3.7 10.5 - - + -
270A THR* 3.2 31.0 - - + +
275A MET* 4.9 1.6 - - + -
371A PHE* 3.3 3.1 - - - +
372A PHE* 2.9 54.7 + - + -
374A ARG* 3.1 46.0 - - + +
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A VAL* 3.4 0.9 - - - -
232A LEU 2.9 34.7 + - - +
234A ILE* 3.6 17.5 - - + -
243A MET* 3.5 29.4 - - - -
244A ILE* 1.3 73.7 - - - +
246A LEU* 1.3 74.8 + - - +
284A LEU* 4.9 7.6 - - + -
363A PHE* 3.6 25.0 - - + -
365A CYS* 4.4 5.8 - - - -
369A PHE* 3.4 31.9 - - + -
370A LEU 4.0 2.7 - - - -
371A PHE* 3.8 7.0 - - + -
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Residues in contact with LEU 246 (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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224A LEU* 6.3 0.2 - - + -
229A ALA* 5.7 2.5 - - + -
230A LYS 3.3 2.7 - - - +
231A VAL* 3.2 31.9 - - + -
244A ILE* 3.7 17.5 - - + -
245A VAL* 1.3 86.8 - - - +
247A LEU* 1.3 61.0 + - - +
248A PRO* 3.5 3.2 - - - +
257A LEU* 4.3 16.8 - - + -
261A LEU* 4.1 20.2 - - + -
266A LEU* 5.1 3.4 - - + -
269A TRP* 5.0 8.3 - - + -
270A THR* 4.0 9.0 - - + -
369A PHE* 3.0 22.5 - - - +
370A LEU* 2.7 47.3 + - + +
372A PHE* 4.8 5.2 - - + -
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Residues in contact with LEU 247 (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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229A ALA* 3.3 1.7 - - - -
230A LYS* 2.8 42.0 + - + +
246A LEU* 1.3 72.1 - - - +
248A PRO* 1.3 76.4 - - + +
249A ASN* 3.4 1.4 + - - +
363A PHE* 3.1 39.2 - - + -
364A HIS* 2.7 42.8 - - + +
365A CYS* 3.7 6.1 - - - -
367A HIS* 3.2 38.6 - - + +
368A PRO 3.9 4.3 - - - +
369A PHE* 3.9 8.3 - - + -
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Residues in contact with PRO 248 (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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228A GLN 4.5 0.2 - - - +
229A ALA* 3.5 13.4 - - + -
246A LEU 3.5 9.4 - - - +
247A LEU* 1.3 86.7 - - + +
249A ASN* 1.3 60.1 + - - +
250A GLU 3.9 1.3 - - - +
251A ILE 4.5 0.9 - - - +
253A GLY* 3.3 33.7 - - - +
254A LEU* 3.4 19.5 - - + +
257A LEU* 4.2 7.6 - - + -
367A HIS* 2.6 36.7 + - + +
368A PRO 3.4 24.9 - - - +
369A PHE* 3.8 4.0 - - + -
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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