Contacts of the helix formed by residues 317 - 329 (chain X) in PDB entry 3F6E
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 ASP 317 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149X ALA* 4.9 7.8 - - - +
181X SER* 3.4 25.8 + - - +
182X SER* 4.1 13.6 + - - -
183X VAL* 3.0 21.1 + - - +
214X ALA* 5.8 1.6 - - - +
300X CYS* 4.9 3.1 - - - -
316X ALA* 1.3 74.1 - - - +
318X ILE* 1.3 64.3 + - - +
319X GLY* 3.1 8.6 + - - -
320X ALA* 2.8 28.8 + - + +
321X MET* 3.0 31.9 + - - +
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Residues in contact with ILE 318 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X ASP* 3.7 41.7 - - + +
211X VAL* 3.9 15.3 - - + -
214X ALA* 4.1 4.7 - - + -
216X ALA* 4.2 4.7 - - + -
273X ILE* 3.8 18.4 - - + -
274X GLY* 3.7 10.5 - - - +
298X VAL* 3.6 37.9 - - + +
299X THR 4.0 0.9 - - - -
300X CYS* 3.9 23.5 - - + +
316X ALA 4.1 0.2 - - - +
317X ASP* 1.3 73.0 + - - +
319X GLY* 1.3 61.0 + - - +
321X MET* 4.0 2.0 - - - +
322X ALA* 2.9 29.3 + - - +
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Residues in contact with GLY 319 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214X ALA* 3.6 23.0 - - - +
216X ALA* 4.2 9.0 - - - -
219X ASP* 4.5 2.5 - - - +
317X ASP* 3.1 7.5 + - - -
318X ILE* 1.3 78.1 - - - +
320X ALA* 1.3 62.1 + - - +
322X ALA* 4.1 0.9 - - - +
323X SER* 3.0 26.3 + - - -
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Residues in contact with ALA 320 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182X SER* 4.5 7.0 - - - +
183X VAL 3.6 28.3 - - - +
184X ARG* 4.0 15.1 - - + +
317X ASP* 2.8 18.5 + - + +
319X GLY* 1.3 72.6 - - - +
321X MET* 1.4 56.7 + - - +
323X SER* 3.8 3.6 - - - -
324X ALA* 3.0 29.6 + - - +
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Residues in contact with MET 321 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184X ARG* 3.6 8.1 - - + -
185X LEU* 3.5 40.4 - - + -
190X LEU* 4.1 13.2 - - + -
193X LEU* 4.1 25.4 - - + -
273X ILE* 5.9 0.7 - - + -
298X VAL* 3.8 28.7 - - + -
314X ILE* 4.2 12.1 - - + -
316X ALA* 3.5 18.6 - - + -
317X ASP 3.0 21.2 + - - +
318X ILE 4.0 1.6 - - - +
320X ALA* 1.4 73.8 - - - +
322X ALA* 1.3 60.7 + - - +
324X ALA* 3.3 2.0 + - - +
325X LEU* 2.9 44.2 + - + +
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Residues in contact with ALA 322 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216X ALA* 3.7 23.8 - - + -
219X ASP* 3.7 10.9 - - + +
220X CYS* 4.1 16.4 - - - -
223X LEU* 5.3 3.0 - - - +
273X ILE* 5.0 9.0 - - + +
318X ILE* 2.9 25.3 + - + +
319X GLY 4.1 0.4 - - - +
321X MET* 1.3 73.7 - - - +
323X SER* 1.3 63.6 + - - +
325X LEU* 4.1 6.4 - - - +
326X ALA* 3.0 27.4 + - - +
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Residues in contact with SER 323 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219X ASP* 3.4 24.8 + - - -
319X GLY 3.0 19.0 + - - -
320X ALA* 3.8 5.6 - - - -
322X ALA* 1.3 78.0 - - - +
324X ALA* 1.3 63.0 + - - +
326X ALA* 3.9 0.2 - - - +
327X ASN* 2.8 39.7 + - - +
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Residues in contact with ALA 324 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184X ARG* 4.9 12.6 - - + +
190X LEU* 4.1 26.2 - - + -
320X ALA 3.0 18.9 + - - +
321X MET* 3.3 5.8 + - - +
323X SER* 1.3 75.1 + - - +
325X LEU* 1.3 63.5 + - - +
327X ASN* 3.2 3.8 + - - +
328X LEU* 3.0 35.1 + - + +
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Residues in contact with LEU 325 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X LEU* 3.9 11.2 - - + -
193X LEU* 3.9 29.2 - - + -
194X VAL* 3.9 24.0 - - + -
197X LEU* 4.0 12.6 - - + -
223X LEU* 4.0 18.6 - - + -
271X LEU* 4.3 23.1 - - + -
273X ILE* 4.8 6.7 - - + -
298X VAL* 4.8 7.2 - - + -
321X MET* 2.9 32.2 + - + +
322X ALA* 4.1 2.7 - - - +
324X ALA* 1.3 77.0 - - - +
326X ALA* 1.3 64.7 + - - +
328X LEU* 4.7 1.8 - - - -
329X VAL* 3.1 30.7 + - + +
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Residues in contact with ALA 326 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219X ASP* 3.2 35.2 - - + +
222X MET* 3.3 23.8 - - + +
223X LEU* 4.0 18.1 - - + +
226X ARG* 2.8 19.1 + - - +
322X ALA 3.0 19.5 + - - +
323X SER 3.9 2.9 - - - +
325X LEU* 1.3 77.7 - - - +
327X ASN* 1.3 60.6 + - - +
329X VAL* 4.3 2.6 - - - +
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Residues in contact with ASN 327 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219X ASP* 4.6 5.7 + - - -
222X MET* 3.8 19.4 - - - +
226X ARG* 3.4 18.4 + - - +
323X SER* 2.8 38.1 + - - +
324X ALA* 4.0 3.6 - - - +
325X LEU 3.1 0.6 - - - -
326X ALA* 1.3 83.1 - - - +
328X LEU* 1.3 63.9 + - + +
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Residues in contact with LEU 328 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X LEU* 3.7 35.0 - - + -
191X ASP* 5.1 9.0 - - - +
194X VAL* 3.8 28.2 - - + +
198X ASN* 5.0 0.9 + - - -
324X ALA* 3.0 24.0 + - + +
327X ASN* 1.3 84.0 - - + +
329X VAL* 1.3 66.5 + - - +
330X GLU* 3.7 1.4 + - - +
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Residues in contact with VAL 329 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194X VAL* 4.1 14.4 - - + -
197X LEU* 4.0 27.6 - - + -
198X ASN* 3.6 11.2 - - - +
223X LEU* 3.8 23.6 - - + -
226X ARG* 2.6 57.3 + - + +
227X LEU* 4.1 8.3 - - + -
325X LEU 3.1 22.4 + - - +
326X ALA 4.3 1.6 - - - +
328X LEU* 1.3 80.5 - - - +
330X GLU* 1.3 65.3 + - - +
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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