Contacts of the strand formed by residues 241 - 245 (chain A) in PDB entry 2FV7
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 CYS 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ILE* 4.1 8.7 - - + -
234A ILE 3.3 14.1 - - - +
235A THR* 4.0 8.3 - - + -
236A LEU* 4.3 2.9 - - - +
239A GLU 3.5 2.0 + - - -
240A GLY* 1.3 75.9 - - - +
242A VAL* 1.3 60.1 + - - +
253A HIS* 3.2 7.7 - - - -
254A ILE* 2.8 53.6 + - - -
271A PHE* 4.0 9.0 - - + -
291A LEU* 3.9 28.7 - - - -
295A ASN* 3.8 15.3 - - - -
401A ADP 4.4 2.7 - - - +
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Residues in contact with VAL 242 (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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214A ALA* 3.8 25.6 - - + +
217A ALA* 4.0 12.3 - - + +
218A GLY* 4.3 10.8 - - - +
221A ALA* 4.9 1.5 - - + +
232A VAL 3.9 0.9 - - - +
233A ILE* 3.3 5.5 - - - +
234A ILE* 3.0 33.4 + - + +
236A LEU* 3.4 24.2 - - + -
241A CYS* 1.3 77.9 - - - +
243A VAL* 1.3 62.6 + - - +
244A LEU* 3.9 21.5 - - + +
251A PRO* 4.0 12.3 - - + -
252A LYS 3.2 11.7 - - - +
253A HIS* 4.2 6.7 - - + -
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Residues in contact with VAL 243 (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* 3.8 5.2 - - + -
232A VAL 3.4 11.0 - - - +
233A ILE* 4.0 2.2 - - + -
242A VAL* 1.3 73.3 - - - +
244A LEU* 1.3 75.7 + - - +
245A SER* 5.7 0.2 - - - -
250A GLU 3.8 1.9 - - - +
251A PRO* 3.4 1.4 - - - +
252A LYS* 2.8 57.8 + - + +
254A ILE* 4.5 9.4 - - + -
287A LEU* 3.8 26.5 - - + -
288A GLU* 4.4 14.6 - - + +
291A LEU* 3.5 29.6 - - + -
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Residues in contact with LEU 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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218A GLY 4.0 3.8 - - - +
221A ALA* 3.3 26.0 - - + +
222A LEU* 3.5 42.6 - - + +
225A LEU* 4.1 11.7 - - + -
231A VAL* 3.5 7.3 - - - +
232A VAL* 3.1 28.1 + - + +
242A VAL* 3.9 6.5 - - + -
243A VAL* 1.3 77.2 - - - +
245A SER* 1.3 64.4 + - - +
248A GLU* 3.9 8.5 - - - +
249A PRO 3.6 17.0 - - - +
251A PRO* 3.3 40.4 - - + -
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Residues in contact with SER 245 (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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225A LEU* 3.3 10.1 - - - +
230A GLN 3.2 13.7 - - - -
231A VAL* 4.0 12.8 - - - -
243A VAL* 5.7 0.2 - - - -
244A LEU* 1.3 80.4 - - - +
246A GLN* 1.3 60.2 + - - +
247A THR* 3.6 9.0 + - - -
248A GLU* 2.8 38.8 + - - +
249A PRO* 2.9 29.3 - - - +
287A LEU* 5.2 5.2 - - - -
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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