Contacts of the helix formed by residues 276 - 285 (chain A) in PDB entry 2VRB
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 PRO 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A GLN* 5.1 8.5 - - - +
274A LEU 3.4 8.2 - - - +
275A THR* 1.3 86.6 - - - +
277A LEU* 1.3 65.6 + - - +
278A LYS* 4.4 7.2 - - + +
279A GLU* 3.2 43.9 + - + +
280A THR* 3.4 5.0 + - - -
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Residues in contact with LEU 277 (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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144A THR* 3.8 29.4 - - + -
148A VAL* 3.9 16.4 - - + -
204A TRP* 3.7 51.1 - - + +
208A GLU* 4.5 2.5 - - - +
209A LEU* 4.3 11.4 - - + +
212A ILE* 3.5 26.9 - - + -
275A THR 3.6 2.5 + - - -
276A PRO* 1.3 73.9 - - - +
278A LYS* 1.3 63.1 + - - +
280A THR* 3.1 7.0 + - - -
281A VAL* 2.9 30.1 + - + +
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Residues in contact with LYS 278 (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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212A ILE* 3.7 27.9 - - + +
215A GLU* 2.6 47.0 + - - +
216A VAL* 3.9 18.1 - - + +
276A PRO* 3.3 4.6 - - + +
277A LEU* 1.3 78.7 - - - +
279A GLU* 1.3 55.9 + - - +
281A VAL* 3.2 2.3 + - - +
282A LYS* 2.9 48.7 + - - +
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Residues in contact with GLU 279 (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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275A THR* 3.4 19.6 + - + +
276A PRO* 3.2 35.0 + - + +
278A LYS* 1.3 79.1 - - - +
280A THR* 1.3 60.2 + - - +
282A LYS* 3.4 15.4 - - + +
283A GLN* 3.3 37.8 + - + +
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Residues in contact with THR 280 (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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144A THR* 4.0 21.7 - - + +
145A ASP* 5.6 3.6 - - - +
148A VAL* 3.9 20.9 - - + +
174A THR* 3.7 20.1 - - + +
275A THR* 3.4 22.3 + - - +
276A PRO 3.4 4.3 + - - -
277A LEU* 3.1 12.1 + - - -
279A GLU* 1.3 74.8 - - - +
281A VAL* 1.3 60.8 + - - +
283A GLN* 3.5 11.8 + - + +
284A ALA* 3.0 27.0 + - - +
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Residues in contact with VAL 281 (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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148A VAL* 3.7 17.5 - - + -
152A LEU* 4.8 4.0 - - + -
209A LEU* 3.7 28.5 - - + -
212A ILE* 3.8 14.1 - - + -
213A LEU* 4.2 18.4 - - + -
216A VAL* 4.2 17.3 - - + -
277A LEU* 2.9 20.8 + - + +
278A LYS 3.2 6.7 + - - +
280A THR* 1.3 76.1 - - - +
282A LYS* 1.3 63.5 + - - +
284A ALA* 3.2 4.5 + - - +
285A LEU* 3.1 38.8 + - + +
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Residues in contact with LYS 282 (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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216A VAL* 4.0 26.2 - - + +
278A LYS* 2.9 45.9 + - - +
279A GLU* 3.4 21.1 - - + +
281A VAL* 1.3 78.6 - - - +
283A GLN* 1.3 61.5 + - + +
285A LEU* 3.3 21.0 - - - +
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Residues in contact with GLN 283 (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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275A THR* 4.8 4.9 - - - +
279A GLU* 3.3 39.8 + - + +
280A THR* 3.6 14.0 + - + +
282A LYS* 1.3 78.6 - - + +
284A ALA* 1.3 63.2 + - - +
285A LEU 3.2 5.7 + - - -
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Residues in contact with ALA 284 (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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148A VAL* 4.0 9.2 - - + +
149A ASN* 3.6 37.7 - - - +
150A GLU* 3.7 10.1 + - - +
152A LEU* 5.0 0.9 - - + -
153A ARG* 3.2 18.0 + - - -
280A THR 3.0 14.4 + - - +
281A VAL 3.2 9.6 + - - +
283A GLN* 1.3 77.1 - - - +
285A LEU* 1.3 62.7 + - + +
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Residues in contact with LEU 285 (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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149A ASN 4.6 2.7 - - - +
152A LEU* 4.1 23.1 - - + +
153A ARG* 2.7 52.0 + - + +
156A THR* 5.2 2.5 - - - +
213A LEU* 3.7 25.1 - - + -
216A VAL* 4.0 16.2 - - + -
217A SER* 5.1 8.3 - - - -
281A VAL* 3.1 29.9 + - + +
282A LYS* 3.3 16.8 - - - +
283A GLN 3.7 4.9 - - - -
284A ALA* 1.3 83.7 - - + +
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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