Contacts of the helix formed by residues 314 - 328 (chain T) 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 PRO 314 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351Q ALA* 4.5 5.4 - - + -
215T PRO* 4.5 11.2 - - + -
218T HIS* 5.2 3.4 - - - +
262T VAL* 4.4 11.4 - - + -
263T GLU 3.6 26.9 - - - +
264T GLY* 4.4 2.0 - - - -
295T VAL* 3.9 22.2 - - + -
296T THR 3.9 14.8 - - - +
297T GLY* 4.2 1.3 - - - -
313T ILE* 1.4 94.7 - - + +
315T GLN* 1.3 81.3 + - - +
318T ASP* 2.7 19.8 - - - +
319T ILE* 4.8 3.8 - - + -
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Residues in contact with GLN 315 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218T HIS* 4.3 16.5 + - - -
310T ASP* 3.4 30.9 + - + +
311T ASN* 3.7 20.6 + - - +
313T ILE* 3.5 4.8 + - - +
314T PRO* 1.3 90.9 - - - +
316T VAL* 1.3 64.3 + - - +
317T LYS* 3.0 44.0 + - - +
318T ASP* 3.1 21.6 + - - +
319T ILE* 3.7 7.8 + - - +
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Residues in contact with VAL 316 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218T HIS* 2.8 45.6 + - + +
221T GLU* 3.4 29.2 - - + +
222T ALA* 4.1 5.5 - - + +
225T VAL* 5.3 4.3 - - + -
315T GLN* 1.3 73.0 - - - +
317T LYS* 1.3 62.7 + - + +
318T ASP 3.3 0.2 - - - -
319T ILE* 3.7 6.7 + - - +
320T ILE* 3.4 34.6 + - + +
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Residues in contact with LYS 317 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311T ASN* 5.6 1.5 + - - -
315T GLN* 3.0 42.3 + - - +
316T VAL* 1.3 82.1 - - + +
318T ASP* 1.3 73.3 + - - +
319T ILE 3.1 2.2 - - - -
320T ILE* 3.6 11.0 + - + +
321T PHE* 3.0 26.2 + - - +
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Residues in contact with ASP 318 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351Q ALA* 2.8 32.5 - - + +
352Q ASN* 2.9 28.1 + - - +
355Q ILE* 4.0 12.9 - - - +
295T VAL* 3.9 8.0 - - + +
311T ASN* 5.8 0.3 - - - -
313T ILE 4.2 0.5 - - - +
314T PRO 2.7 26.9 - - - +
315T GLN* 3.1 14.4 + - - +
317T LYS* 1.3 94.0 - - - +
319T ILE* 1.3 62.1 + - - +
321T PHE* 3.9 2.3 - - - +
322T ALA* 3.4 11.3 + - - +
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Residues in contact with ILE 319 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209T VAL* 4.6 5.6 - - + -
218T HIS* 4.1 16.4 - - + +
219T CYS* 4.0 25.4 - - - +
222T ALA* 4.4 9.6 - - + -
260T VAL* 5.2 2.0 - - + -
262T VAL* 3.7 46.2 - - + -
295T VAL* 4.3 11.9 - - + -
314T PRO* 4.8 2.9 - - + -
315T GLN 3.9 11.4 - - - +
316T VAL* 3.7 6.5 + - - +
317T LYS 3.1 0.2 - - - -
318T ASP* 1.3 78.4 - - - +
320T ILE* 1.3 66.1 + - - +
322T ALA* 3.2 2.3 + - - +
323T ILE* 2.9 48.1 + - + +
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Residues in contact with ILE 320 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222T ALA* 3.8 19.3 - - + -
225T VAL* 3.9 27.1 - - + -
226T LEU* 4.3 19.6 - - + +
316T VAL* 3.4 32.7 + - + +
317T LYS* 3.6 10.3 + - + +
319T ILE* 1.3 77.2 - - - +
321T PHE* 1.3 64.2 + - - +
323T ILE* 3.2 7.5 + - - +
324T LYS* 3.0 50.0 + - + +
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Residues in contact with PHE 321 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352Q ASN* 3.8 17.7 - - - +
354Q TRP* 3.7 30.5 - + + -
355Q ILE* 6.2 0.7 - - + -
317T LYS* 3.0 18.6 + - + +
318T ASP* 4.0 6.7 - - - +
319T ILE 3.3 0.2 - - - -
320T ILE* 1.3 78.4 - - - +
322T ALA* 1.3 57.3 + - - +
324T LYS* 3.5 6.7 + - + +
325T LYS* 2.9 65.4 + - + +
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Residues in contact with ALA 322 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352Q ASN* 4.1 3.1 - - + +
354Q TRP* 4.0 25.4 - - + -
260T VAL* 4.1 4.8 - - + +
293T VAL* 4.1 10.0 - - + +
295T VAL* 3.6 22.0 - - + -
318T ASP 3.4 15.1 + - - +
319T ILE 3.2 3.8 + - - +
321T PHE* 1.3 77.6 - - - +
323T ILE* 1.3 64.4 + - - +
325T LYS* 3.8 0.9 - - - +
326T THR* 2.7 30.5 + - - -
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Residues in contact with ILE 323 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207T ILE* 4.3 12.5 - - + +
209T VAL* 3.7 30.3 - - + -
222T ALA* 5.3 4.7 - - + -
226T LEU* 3.6 26.5 - - + -
231T VAL* 4.6 0.9 - - + -
233T CYS* 3.9 12.1 - - - -
260T VAL* 4.5 17.5 - - + -
319T ILE* 2.9 36.2 + - + +
320T ILE* 3.7 3.8 - - - +
322T ALA* 1.3 79.2 - - - +
324T LYS* 1.3 59.2 + - + +
326T THR* 3.1 5.2 + - - -
327T LEU* 3.0 45.8 + - + +
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Residues in contact with LYS 324 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226T LEU* 4.1 12.3 - - + -
229T GLU* 3.4 33.6 + - - -
320T ILE* 3.0 33.3 + - + +
321T PHE* 3.8 6.3 - - + +
323T ILE* 1.3 74.3 - - + +
325T LYS* 1.3 67.5 + - - +
327T LEU 3.3 0.5 + - - -
328T ASN* 2.9 18.4 + - - -
329T ILE* 3.0 53.0 + - + +
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Residues in contact with LYS 325 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354Q TRP* 3.2 50.8 - - + +
321T PHE* 2.9 50.0 + - + +
322T ALA* 3.8 5.4 - - - +
324T LYS* 1.3 80.0 - - - +
326T THR* 1.3 57.2 + - - +
328T ASN* 3.0 20.1 + - - +
329T ILE 4.9 0.7 - - - -
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Residues in contact with THR 326 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354Q TRP* 5.0 0.2 - - - -
207T ILE* 4.2 6.5 - - + -
258T HIS* 3.3 36.4 + - + -
259T LEU 4.5 3.1 - - - +
260T VAL* 3.6 9.4 - - + +
290T ALA* 3.5 17.3 - - + +
291T PRO 4.0 19.5 - - - +
293T VAL* 3.2 24.4 - - - +
322T ALA 2.7 21.2 + - - -
323T ILE 3.1 6.1 + - - -
325T LYS* 1.3 71.2 - - - +
327T LEU* 1.3 58.5 + - - +
328T ASN* 3.1 5.7 + - - +
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Residues in contact with LEU 327 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206T HIS* 3.4 28.9 - - + +
207T ILE* 4.3 7.9 - - + -
231T VAL* 3.7 30.1 - - + -
258T HIS* 3.2 37.0 - - + +
323T ILE* 3.0 26.5 + - + +
326T THR* 1.3 73.8 - - - +
328T ASN* 1.3 69.4 + - - +
329T ILE* 2.9 36.6 - - + +
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Residues in contact with ASN 328 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324T LYS 2.9 4.3 + - - -
325T LYS* 3.0 15.2 + - - +
326T THR 3.1 2.7 - - - +
327T LEU* 1.3 81.8 - - - +
329T ILE* 1.3 62.6 + - - +
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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