Contacts of the strand formed by residues 274 - 278 (chain C) in PDB entry 2VM8
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 VAL 274 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C ILE* 4.3 10.3 - - + -
250C LEU* 3.3 33.2 - - + +
252C ILE* 4.3 6.5 - - + -
264C ILE* 4.3 14.4 - - + +
267C ALA* 4.3 3.4 - - + -
268C ARG* 3.5 41.1 + - + +
272C THR* 3.0 34.1 + - + +
273C VAL* 1.3 74.9 - - - +
275C TYR* 1.3 82.9 + - - +
327C GLN* 4.0 2.1 + - - -
481C ARG* 5.1 0.6 - - - +
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Residues in contact with TYR 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ILE* 5.9 2.7 - - + -
249C PRO* 5.3 1.8 - - + -
250C LEU 3.0 15.1 + - - +
251C TYR* 3.5 23.2 - + + -
252C ILE* 2.8 31.3 + - - +
264C ILE* 4.7 1.6 - - - -
273C VAL* 4.1 15.5 - - + -
274C VAL* 1.3 88.1 - - - +
276C GLY* 1.3 54.5 + - - +
327C GLN* 3.1 26.5 - - + +
328C VAL* 4.7 5.2 - - + -
391C VAL* 3.9 20.2 - - + -
477C PHE* 3.5 26.6 + + - -
478C VAL* 3.1 33.6 - - + +
481C ARG* 2.9 29.9 + - - -
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Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C TYR* 5.6 0.4 - - - -
252C ILE 3.9 3.4 - - - -
264C ILE* 4.2 15.5 - - - +
275C TYR* 1.3 74.6 - - - +
277C GLU* 1.3 60.2 + - - -
278C PRO* 3.5 12.3 - - - +
326C LEU* 4.0 15.9 - - - -
327C GLN* 2.7 22.4 + - - -
328C VAL* 3.0 19.1 - - - +
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Residues in contact with GLU 277 (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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72C VAL* 3.3 17.9 - - + +
73C HIS* 3.0 36.4 + - - +
107C HIS* 5.7 0.2 + - - -
196C GLN* 5.4 0.2 + - - -
251C TYR* 2.6 39.3 + - + +
252C ILE 3.0 17.0 + - - +
253C THR* 3.6 3.2 - - - -
254C LYS* 2.8 25.8 + - - -
255C VAL* 2.7 23.7 + - - +
276C GLY* 1.3 71.8 - - - -
278C PRO* 1.3 71.5 - - - +
279C ILE* 3.7 10.0 - - + +
328C VAL* 3.7 5.8 - - + +
330C GLY 4.1 1.6 - - - +
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Residues in contact with PRO 278 (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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255C VAL* 3.4 19.5 - - + +
276C GLY 3.5 9.0 - - - +
277C GLU* 1.3 89.1 - - - +
279C ILE* 1.3 60.5 + - - +
282C SER* 3.6 9.0 - - - +
283C LEU* 4.0 22.9 - - + -
317C LEU* 4.6 3.4 - - + -
321C LEU* 4.1 15.0 - - + -
326C LEU* 4.0 28.3 - - + -
328C VAL 3.3 16.2 - - - +
329C THR* 3.5 5.0 - - + -
330C GLY 3.2 19.8 + - - -
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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
------------------------------------------------------------
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