Contacts of the helix formed by residues 315 - 327 (chain V) in PDB entry 3EXG
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 GLN 315 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218V HIS* 5.7 0.7 - - - -
310V ASP* 3.1 34.9 + - + +
311V ASN* 4.1 15.9 + - - +
313V ILE* 4.2 2.9 + - + +
314V PRO* 1.3 78.1 - - - +
316V VAL* 1.3 58.8 + - + +
317V LYS* 2.7 29.6 + - + +
318V ASP* 2.5 57.5 + - - +
319V ILE* 3.1 7.7 + - - -
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Residues in contact with VAL 316 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218V HIS* 3.7 36.0 - - + +
221V GLU* 3.7 30.3 - - + +
222V ALA* 3.9 18.3 - - + +
225V VAL* 5.4 2.0 - - + -
315V GLN* 1.3 73.6 - - + +
317V LYS* 1.3 58.9 + - - +
319V ILE* 3.6 13.6 + - - +
320V ILE* 3.1 32.8 + - + +
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Residues in contact with LYS 317 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311V ASN* 5.7 1.9 + - - -
315V GLN* 2.7 39.7 + - + +
316V VAL* 1.3 75.2 - - - +
318V ASP* 1.3 64.3 + - - +
320V ILE* 3.7 11.2 - - + +
321V PHE* 2.7 35.4 + - - +
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Residues in contact with ASP 318 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295V VAL* 4.4 4.0 - - + +
315V GLN* 2.5 56.6 + - - +
317V LYS* 1.3 80.2 - - - +
319V ILE* 1.3 59.3 + - + +
321V PHE* 4.1 2.8 - - - +
322V ALA* 3.0 24.6 + - - +
351W ALA* 3.7 25.0 - - + +
352W ASN* 3.3 22.3 + - - +
355W ILE* 3.6 19.7 - - - +
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Residues in contact with ILE 319 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209V VAL* 4.7 2.2 - - + -
215V PRO* 5.8 0.2 - - + -
218V HIS* 4.0 34.3 - - + +
219V CYS* 4.3 8.1 - - - -
222V ALA* 4.3 10.5 - - + -
260V VAL* 5.5 1.6 - - + -
262V VAL* 3.8 37.2 - - + -
295V VAL* 4.2 18.6 - - + -
314V PRO* 4.9 3.8 - - + -
315V GLN 3.1 12.1 + - - +
316V VAL* 3.7 10.3 - - - +
318V ASP* 1.3 74.6 - - - +
320V ILE* 1.3 68.6 + - - +
322V ALA* 3.0 6.6 + - - +
323V ILE* 2.8 42.8 + - + +
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Residues in contact with ILE 320 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222V ALA* 3.8 21.1 - - + +
225V VAL* 3.6 37.9 - - + -
226V LEU* 4.4 13.0 - - + +
316V VAL* 3.1 23.4 + - + +
317V LYS* 3.7 9.0 - - + +
319V ILE* 1.3 78.2 - - - +
321V PHE* 1.3 56.3 + - - +
323V ILE* 2.9 9.3 + - - +
324V LYS* 2.6 61.8 + - + +
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Residues in contact with PHE 321 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317V LYS 2.7 22.4 + - - +
318V ASP* 3.7 7.9 - - - +
320V ILE* 1.3 75.5 - - - +
322V ALA* 1.3 59.9 + - - +
324V LYS* 3.7 5.9 - - + +
325V LYS* 2.9 45.7 + - + +
352W ASN* 3.9 14.4 - - - +
354W TRP* 3.6 42.0 - + + -
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Residues in contact with ALA 322 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260V VAL* 4.7 5.4 - - + -
293V VAL* 4.3 10.9 - - + +
295V VAL* 3.6 24.5 - - + -
318V ASP 3.0 17.1 + - - +
319V ILE 3.0 5.1 + - - +
321V PHE* 1.3 76.0 - - - +
323V ILE* 1.3 63.3 + - - +
325V LYS* 3.1 3.6 + - - +
326V THR* 3.0 26.0 + - - -
352W ASN* 4.6 2.2 - - - +
354W TRP* 4.0 23.6 - - + -
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Residues in contact with ILE 323 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207V ILE* 3.5 37.7 - - + -
209V VAL* 3.7 26.2 - - + -
222V ALA* 5.2 4.9 - - + -
226V LEU* 3.6 31.2 - - + -
233V CYS* 4.1 7.6 - - - -
260V VAL* 4.5 9.2 - - + -
319V ILE* 2.8 32.1 + - + +
320V ILE* 3.5 5.4 - - - +
322V ALA* 1.3 76.5 - - - +
324V LYS* 1.3 62.7 + - - +
326V THR* 3.3 2.9 + - - -
327V LEU* 3.1 31.3 + - + +
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Residues in contact with LYS 324 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226V LEU* 4.2 10.8 - - + -
229V GLU* 3.1 38.5 + - - -
320V ILE* 2.6 39.2 + - + +
321V PHE* 3.9 6.3 - - + +
323V ILE* 1.3 73.8 - - - +
325V LYS* 1.3 61.5 + - - +
327V LEU* 4.9 0.7 - - - -
328V ASN 3.4 1.6 + - - -
329V ILE* 3.2 66.5 + - + +
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Residues in contact with LYS 325 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321V PHE* 2.9 36.2 + - + +
322V ALA 3.1 5.1 + - - +
324V LYS* 1.3 78.7 - - - +
326V THR* 1.3 61.4 + - - +
328V ASN* 3.4 14.5 + - - +
354W TRP* 3.1 60.9 - - + +
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Residues in contact with THR 326 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207V ILE* 4.5 8.5 - - + -
258V HIS* 3.5 40.9 + - + -
259V LEU 4.7 4.0 - - - +
260V VAL* 4.1 1.7 - - - +
290V ALA* 3.8 25.2 - - + +
291V PRO 4.1 10.4 + - - +
293V VAL* 3.6 32.7 - - - +
322V ALA 3.0 8.9 + - - -
323V ILE 3.3 3.8 + - - -
325V LYS* 1.3 74.9 - - - +
327V LEU* 1.3 57.8 + - - +
328V ASN* 3.0 12.1 + - - +
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Residues in contact with LEU 327 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206V HIS* 3.9 24.2 - - + +
207V ILE* 4.1 13.9 - - + -
231V VAL* 3.6 38.1 - - + -
258V HIS* 3.7 35.0 - - + +
323V ILE* 3.1 26.7 + - + +
325V LYS 3.5 0.2 - - - -
326V THR* 1.3 74.1 - - - +
328V ASN* 1.3 56.8 + - - +
329V ILE* 2.8 47.1 + - + +
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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