Contacts of the strand formed by residues 253 - 259 (chain C) in PDB entry 3VA2
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 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249C ILE* 3.7 5.4 - - - +
250C GLU* 3.2 45.9 + - + +
251C GLY 3.4 0.6 - - - -
252C THR* 1.3 94.9 - - + +
254C LEU* 1.3 64.3 + - - +
255C SER* 5.6 0.2 - - - -
295C ILE* 4.1 31.3 - - + +
296C SER 3.7 13.5 - - - +
297C ILE* 4.7 8.5 - - + -
298C ILE* 4.0 8.4 - - - +
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C ALA* 4.2 12.6 - - + -
248C GLU 3.5 17.5 - - - +
249C ILE* 4.1 3.4 - - + -
253C ARG* 1.3 72.8 - - - +
255C SER* 1.3 62.1 + - - +
256C ILE* 4.2 10.3 - - + -
276C ILE* 3.7 29.2 - - + -
294C PHE 4.6 0.2 - - - -
295C ILE* 3.2 30.7 - - - +
296C SER* 3.0 19.6 + - - +
298C ILE* 3.7 31.3 - - + +
304C TYR* 4.4 10.1 - - + -
306C VAL* 4.4 10.1 - - + -
331C VAL* 3.6 24.5 - - + -
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Residues in contact with SER 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C THR 3.6 1.0 - - - +
247C ALA* 3.2 4.3 - - - -
248C GLU* 2.8 58.4 + - - -
250C GLU* 6.0 2.9 - - - -
254C LEU* 1.3 74.6 - - - +
256C ILE* 1.3 61.6 + - - +
257C GLN* 3.4 19.5 + - - -
295C ILE* 3.8 21.3 - - - +
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Residues in contact with ILE 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C VAL* 4.8 2.5 - - + -
246C THR 3.4 9.9 - - - +
247C ALA* 4.3 11.2 - - + -
254C LEU* 4.7 10.5 - - + -
255C SER* 1.3 82.9 + - - +
257C GLN* 1.3 69.7 + - - +
258C TRP* 3.9 22.2 - - + -
274C VAL* 4.0 15.7 - - + -
276C ILE* 4.5 13.2 - - + -
293C ALA* 3.3 4.5 - - - +
294C PHE* 2.8 53.5 + - + +
295C ILE* 5.6 0.4 - - - +
296C SER* 5.9 0.4 - - - +
306C VAL* 3.6 39.9 - - + -
308C VAL* 4.7 4.7 - - + -
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Residues in contact with GLN 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ASN 3.2 3.7 - - - +
245C VAL* 3.3 2.9 - - - +
246C THR* 2.5 66.9 + - - +
247C ALA* 4.5 0.4 - - - +
248C GLU* 4.9 6.5 - - - +
255C SER* 3.4 26.5 + - - -
256C ILE* 1.3 76.7 - - - +
258C TRP* 1.3 70.9 + - - +
292C ASN* 3.8 9.2 - - - +
293C ALA* 4.4 8.3 - - + +
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Residues in contact with TRP 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C PRO* 3.6 20.9 - - + -
243C LEU 3.1 13.9 - - - +
244C ASN 3.8 4.3 - - - -
245C VAL* 3.7 19.1 - - + -
256C ILE* 3.9 22.4 - - + -
257C GLN* 1.3 83.0 - - - +
259C GLU* 1.3 77.8 + - - +
272C TYR* 3.4 42.5 - + + -
274C VAL* 4.6 4.7 - - + -
289C LEU* 4.3 10.8 - - + -
291C THR 3.1 22.2 - - - -
292C ASN* 2.3 48.8 + - - -
293C ALA* 3.8 27.1 - - - -
294C PHE* 4.1 10.5 - - + -
308C VAL* 3.8 19.7 - - + -
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Residues in contact with GLU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C PRO* 3.4 2.6 - - - +
243C LEU* 2.5 40.5 + - + +
244C ASN* 2.3 40.9 + - - +
258C TRP* 1.3 84.7 - - - +
260C LYS* 1.3 68.5 + - - +
261C PRO* 3.0 5.9 - - - +
292C ASN* 3.7 6.3 - - - +
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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