Contacts of the helix formed by residues 273 - 280 (chain C) in PDB entry 2VF7
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 273 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271C SER* 3.9 1.2 - - - -
272C ALA* 1.3 83.8 - - - +
274C MET* 1.3 55.2 + - - +
275C LYS 3.1 5.2 - - - -
276C LYS* 3.7 19.9 + - - +
277C ARG* 3.4 21.5 + - - +
596C ARG* 6.1 0.9 - - - +
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Residues in contact with MET 274 (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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185C PRO* 5.1 7.0 - - + -
261C HIS* 4.1 17.0 - - - +
265C THR* 3.6 31.2 - - + +
269C THR* 3.8 12.3 - - - -
271C SER* 3.1 21.3 + - - +
273C SER* 1.3 77.2 - - - +
275C LYS* 1.3 59.8 + - - +
277C ARG* 3.8 41.7 - - - +
278C VAL* 3.6 20.8 + - + +
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Residues in contact with LYS 275 (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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157C LEU* 6.1 3.6 - - - +
266C PHE* 3.6 47.8 + - + +
269C THR* 4.5 9.2 - - - +
271C SER* 3.2 12.4 + - - +
272C ALA* 3.9 16.4 - - - +
274C MET* 1.3 79.4 - - - +
276C LYS* 1.3 60.2 + - + +
277C ARG 3.2 1.6 - - - -
278C VAL* 3.7 3.6 + - - +
279C GLN* 3.2 46.3 + - - +
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Residues in contact with LYS 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ALA 3.9 9.5 + - - +
273C SER* 3.7 20.6 + - - +
274C MET 3.6 0.2 - - - -
275C LYS* 1.3 79.2 - - + +
277C ARG* 1.3 64.9 + - - +
279C GLN* 3.5 21.8 - - + +
280C GLY* 3.7 4.7 + - - -
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Residues in contact with ARG 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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182C ALA 4.9 2.9 + - - -
183C ALA 4.4 5.7 + - - -
184C TRP 3.9 24.4 + - - -
185C PRO* 4.0 0.4 - - - +
186C GLN* 3.7 55.1 - - - +
261C HIS* 3.9 15.6 - - - -
273C SER 3.4 15.3 + - - +
274C MET* 3.8 37.1 - - - +
275C LYS 3.2 0.4 - - - -
276C LYS* 1.3 79.8 - - - +
278C VAL* 1.3 73.2 + - - +
280C GLY* 3.3 11.3 + - - -
281C TYR* 3.4 31.4 - - + +
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Residues in contact with VAL 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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183C ALA 5.4 2.2 - - - +
261C HIS* 4.8 3.6 - - + -
262C VAL* 3.5 37.8 - - + +
265C THR* 3.8 22.7 - - + -
266C PHE* 3.7 22.7 - - + +
274C MET* 3.6 18.3 + - + +
275C LYS* 4.1 2.7 - - - +
276C LYS 3.5 0.2 - - - -
277C ARG* 1.3 95.8 - - - +
279C GLN* 1.3 64.2 + - - +
280C GLY 3.2 1.6 + - - -
281C TYR* 3.3 18.9 + - + +
282C MET* 3.3 13.5 - - - +
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Residues in contact with GLN 279 (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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161C TYR* 3.5 30.7 + - + -
266C PHE* 3.0 33.2 - - + -
275C LYS* 3.2 37.7 + - - +
276C LYS* 3.5 17.6 - - + +
277C ARG 3.2 0.2 - - - -
278C VAL* 1.3 76.6 - - - +
280C GLY* 1.3 62.0 + - - +
281C TYR 3.1 1.8 + - - -
282C MET* 3.1 27.4 + - - +
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Residues in contact with GLY 280 (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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167C SER* 4.4 2.8 - - - +
276C LYS 3.7 5.0 + - - -
277C ARG 3.3 10.4 + - - -
278C VAL 3.2 1.6 - - - -
279C GLN* 1.3 78.4 - - - +
281C TYR* 1.3 66.3 + - - +
282C MET 3.4 5.3 + - - +
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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