Contacts of the helix formed by residues 243 - 250 (chain A) in PDB entry 2V3V
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 ASN 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A ASP* 1.3 78.3 - - - +
244A PRO* 1.4 58.5 - - - +
245A ARG* 3.9 8.5 + - - +
246A PHE* 2.9 34.4 + - + +
247A TRP* 3.0 16.6 + - - -
329A ILE 3.0 4.4 + - - +
330A THR 2.8 37.7 + - - +
331A GLY* 3.8 11.2 + - - +
335A ARG* 5.9 1.2 - - - +
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Residues in contact with PRO 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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242A ASP* 3.3 19.1 - - - +
243A ASN* 1.4 88.7 - - - +
245A ARG* 1.3 64.2 + - + +
247A TRP* 3.2 27.8 - - + +
248A GLN* 2.9 49.4 + - - +
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Residues in contact with ARG 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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243A ASN* 3.2 8.6 + - - +
244A PRO* 1.3 83.3 - - + +
246A PHE* 1.3 61.0 + - - +
248A GLN* 4.3 17.6 + - - +
249A ARG* 3.7 17.7 + - - +
250A TYR* 4.6 2.9 - - - -
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Residues in contact with PHE 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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243A ASN* 2.9 28.8 + - - +
245A ARG* 1.3 75.7 - - - +
247A TRP* 1.3 61.6 + - - +
248A GLN 3.2 1.9 + - - -
249A ARG 3.3 1.7 + - - -
250A TYR* 2.9 61.9 + + + +
251A VAL* 4.0 13.9 - - + -
328A LEU* 3.4 32.5 - - + -
331A GLY* 3.5 18.2 - - - -
333A ILE* 3.6 27.8 - - + -
334A CYS* 5.6 0.4 - - + -
580A ARG* 5.5 2.2 - - - -
581A PHE* 3.7 26.0 - + - -
583A PHE* 4.0 13.2 - + - -
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Residues in contact with TRP 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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242A ASP* 3.0 19.9 + - - -
243A ASN 3.0 28.4 + - - -
244A PRO* 3.2 21.0 - - + +
246A PHE* 1.3 77.8 - - - +
248A GLN* 1.3 91.2 + - + +
251A VAL* 3.2 52.8 + - + +
253A PHE* 3.7 18.5 - + + -
263A PHE* 3.2 55.6 - + + -
328A LEU 3.9 7.4 - - - +
329A ILE* 3.5 29.1 - - + +
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Residues in contact with GLN 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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244A PRO* 2.9 35.1 + - - +
245A ARG* 4.3 16.2 + - - +
247A TRP* 1.3 112.7 - - + +
249A ARG* 1.3 56.9 + - - +
590A ARG* 3.1 22.7 + - - +
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Residues in contact with ARG 249 (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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245A ARG 3.7 12.5 + - - +
246A PHE 3.3 0.6 + - - -
248A GLN* 1.3 79.5 - - - +
250A TYR* 1.3 94.5 + - + +
579A ASP* 3.6 30.5 + - - +
590A ARG* 3.3 25.7 + - - +
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Residues in contact with TYR 250 (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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245A ARG 4.7 3.8 - - - -
246A PHE* 2.9 55.7 + + + +
249A ARG* 1.3 106.6 - - + +
251A VAL* 1.3 61.3 + - - +
579A ASP* 3.6 12.8 + - + +
580A ARG* 3.2 35.9 + - + +
581A PHE* 3.5 50.3 - + + -
583A PHE* 4.0 11.4 - + + -
589A GLY 4.9 4.9 - - - -
590A ARG* 3.3 10.4 - - - +
591A ALA* 2.9 24.9 + - - +
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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
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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