Contacts of the helix formed by residues 235 - 245 (chain E) in PDB entry 2GPV
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 235 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234E TYR* 1.3 87.9 - - + +
236E LYS* 1.3 64.8 + - - +
237E ILE* 2.6 36.7 + - - +
238E VAL* 3.4 20.3 + - + -
239E SER* 3.2 26.2 + - - -
398E ALA* 3.5 31.2 + - - +
401E ASP* 3.8 21.8 + - + +
402E TYR* 5.5 3.4 - - + +
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Residues in contact with LYS 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E ASN* 1.3 79.8 + - - +
237E ILE* 1.3 60.7 + - + +
239E SER* 3.8 4.6 - - - -
240E HIS* 3.1 26.0 + - - +
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Residues in contact with ILE 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E ASN* 2.6 16.3 + - - +
236E LYS* 1.3 75.1 - - + +
238E VAL* 1.3 58.8 + - - +
240E HIS* 3.3 6.7 + - - +
241E LEU* 3.0 33.2 + - + +
287E PRO* 4.2 23.6 - - + -
394E VAL* 3.2 38.8 - - + +
395E LEU* 4.0 21.3 - - + -
397E GLU* 6.1 0.4 - - - +
398E ALA* 4.0 18.2 - - + -
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Residues in contact with VAL 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E TYR* 4.5 8.5 - - + -
235E ASN* 3.4 20.8 + - + +
237E ILE* 1.3 73.8 - - - +
239E SER* 1.3 58.8 + - - +
241E LEU* 3.2 10.5 + - + +
242E LEU* 2.9 31.6 + - + +
364E GLU* 3.6 40.6 - - + +
367E VAL* 5.1 0.4 - - + -
368E THR* 3.5 18.6 - - - +
398E ALA* 4.1 25.8 - - + +
402E TYR* 4.4 12.6 - - + -
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Residues in contact with SER 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E TYR* 3.4 19.4 - - - -
235E ASN 3.2 17.9 + - - -
236E LYS* 3.8 5.6 - - - -
238E VAL* 1.3 79.2 - - - +
240E HIS* 1.3 62.5 + - - +
242E LEU* 3.1 21.9 + - - +
243E VAL* 3.2 19.4 + - - +
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Residues in contact with HIS 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E LYS 3.1 19.1 + - - +
237E ILE* 3.6 8.3 - - - +
238E VAL 3.3 0.4 - - - -
239E SER* 1.3 76.5 - - - +
241E LEU* 1.3 56.7 + - - +
243E VAL* 3.0 30.4 - - + +
244E ALA* 3.2 8.4 + - + +
285E HIS* 3.2 39.5 + - + +
287E PRO* 4.5 15.7 - - + +
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Residues in contact with LEU 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ILE* 3.0 31.5 + - + +
238E VAL* 3.5 7.4 - - - +
240E HIS* 1.3 75.5 - - - +
242E LEU* 1.3 63.5 + - - +
244E ALA* 3.4 7.3 + - + +
245E GLU* 3.3 20.4 + - - +
282E TRP* 4.7 11.2 + - - +
285E HIS 5.0 1.8 - - - +
286E ILE* 4.2 26.9 - - + -
287E PRO* 4.3 14.4 - - + -
367E VAL* 3.8 21.8 - - + +
368E THR* 3.7 38.6 - - + +
371E ALA* 4.0 13.0 - - + -
395E LEU* 4.5 3.8 - - + -
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Residues in contact with LEU 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E TYR* 3.4 32.5 - - + +
238E VAL* 2.9 22.8 + - + +
239E SER* 3.1 17.0 + - - +
241E LEU* 1.3 75.5 - - - +
243E VAL* 1.3 65.3 + - + +
245E GLU* 3.3 19.7 - - - +
363E LYS* 4.2 29.1 - - + -
364E GLU* 4.0 25.4 - - + +
367E VAL* 4.6 6.3 - - + -
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Residues in contact with VAL 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E SER* 3.5 14.6 - - - +
240E HIS* 3.0 33.0 - - + +
242E LEU* 1.3 76.1 - - + +
244E ALA* 1.3 62.7 + - + +
245E GLU 3.2 8.1 + - - +
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Residues in contact with ALA 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E HIS* 3.2 14.7 + - + +
241E LEU* 3.4 11.1 + - + +
243E VAL* 1.3 80.1 - - + +
245E GLU* 1.3 65.2 + - - +
246E PRO* 3.2 4.9 - - - +
282E TRP* 3.5 25.4 - - + +
285E HIS* 3.8 38.7 - - + +
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Residues in contact with GLU 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E LEU 3.3 7.6 + - - +
242E LEU* 3.3 17.2 - - - +
243E VAL 3.2 7.0 - - - +
244E ALA* 1.3 76.3 - - - +
246E PRO* 1.3 86.8 - - - +
247E GLU* 3.8 8.3 + - - +
282E TRP* 4.2 5.9 + - - -
363E LYS* 4.3 22.4 - - - +
366E PHE* 3.3 19.0 - - - -
367E VAL* 3.7 13.0 - - + +
370E LYS* 3.0 35.4 + - - -
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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