Contacts of the helix formed by residues 230 - 241 (chain D) in PDB entry 3VI4
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 GLY 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167D PHE* 4.2 6.9 - - - +
168D VAL 3.0 13.1 + - - -
169D GLU* 3.7 11.3 + - - -
170D LYS 5.0 0.4 - - - -
198D SER* 5.3 2.3 + - - +
229D GLU* 1.3 73.9 - - - +
231D GLY* 1.3 62.9 + - - +
232D PHE 3.2 3.1 - - - -
233D ASP* 3.0 23.7 + - - +
234D ALA* 3.6 4.3 + - - +
263D HIS 5.8 0.2 - - - -
296D TYR* 4.0 22.9 - - - -
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Residues in contact with GLY 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D PHE* 3.7 27.3 - - - -
229D GLU 3.3 6.7 + - - -
230D GLY* 1.3 76.3 - - - +
232D PHE* 1.3 52.8 + - - +
234D ALA* 3.1 4.9 + - - +
235D ILE* 2.8 36.2 + - - +
256D PHE* 3.7 23.2 - - - -
262D PHE* 5.6 1.2 - - - +
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Residues in contact with PHE 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D GLU 5.1 0.2 + - - -
230D GLY 3.2 1.0 - - - -
231D GLY* 1.3 75.7 - - - +
233D ASP* 1.3 64.7 + - - +
235D ILE* 4.2 14.1 - - + -
236D MET* 3.2 17.2 + - - +
256D PHE* 5.1 4.7 - + - -
262D PHE* 3.1 53.6 - + + -
263D HIS 3.7 16.8 + - - +
264D PHE* 4.3 2.7 - - + -
296D TYR* 5.0 2.9 - - + -
297D PRO* 3.3 42.7 - - + +
299D ILE* 3.9 19.3 - - + -
302D LEU* 3.5 32.2 - - + +
328D LEU* 4.0 24.9 - - + -
332D ILE* 5.8 0.2 - - + -
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Residues in contact with ASP 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D LYS* 2.7 38.8 + - - +
198D SER* 4.1 12.9 + - - +
199D TYR* 5.8 0.4 - - + -
230D GLY* 3.0 12.1 + - - +
232D PHE* 1.3 78.0 - - - +
234D ALA* 1.3 62.4 + - - +
236D MET* 3.3 4.8 + - - +
237D GLN* 3.1 26.9 + - - +
277D ASN* 4.0 9.6 + - - +
288D TYR* 3.8 24.9 + - + -
294D TYR 4.8 0.2 - - - +
295D ASP 4.2 0.2 - - - +
296D TYR* 3.6 17.2 + - - -
297D PRO* 3.6 18.6 - - - +
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Residues in contact with ALA 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D LEU* 3.6 17.3 - - + -
167D PHE* 3.6 30.7 - - + -
199D TYR* 3.9 25.9 - - + +
230D GLY 3.6 1.2 + - - +
231D GLY 3.1 8.7 + - - +
233D ASP* 1.3 76.1 - - - +
235D ILE* 1.3 66.9 + - - +
237D GLN* 3.1 3.0 + - - +
238D VAL* 2.8 25.6 + - - +
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Residues in contact with ILE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D LEU* 3.7 8.5 - - + +
231D GLY 2.8 21.1 + - - +
232D PHE* 3.9 15.5 - - + +
234D ALA* 1.3 72.9 - - - +
236D MET* 1.3 64.3 + - - +
238D VAL* 3.1 4.6 + - - +
239D ALA* 2.9 21.2 + - + +
254D LEU* 4.0 19.5 - - + +
256D PHE* 3.7 40.4 - - + -
302D LEU* 3.8 32.3 - - + -
306D LEU* 4.0 19.1 - - + -
313D THR* 5.4 3.4 - - + +
315D PHE* 4.7 9.9 - - + -
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Residues in contact with MET 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D PHE 3.2 11.0 + - - +
233D ASP 3.4 9.9 - - - +
234D ALA 3.2 0.2 - - - -
235D ILE* 1.3 76.8 - - - +
237D GLN* 1.3 73.8 + - - +
239D ALA* 2.9 16.3 + - - +
240D VAL* 3.1 21.2 + - + +
277D ASN* 3.6 20.0 - - - +
279D GLY* 4.0 11.7 - - - -
297D PRO* 3.8 18.2 - - + -
301D HIS* 3.4 42.0 - - + +
302D LEU* 3.8 14.5 - - + +
305D LYS* 3.6 30.1 - - + -
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Residues in contact with GLN 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D TYR* 3.7 22.4 - - + -
233D ASP 3.1 12.9 + - - +
234D ALA 3.1 6.5 + - - +
236D MET* 1.3 88.1 - - - +
238D VAL* 1.3 63.1 + - - +
240D VAL* 4.3 1.0 - - - +
241D CYS* 3.1 46.7 + - - +
245D ILE* 4.3 1.3 - - - -
277D ASN* 5.5 0.8 + - - +
278D ASP* 5.2 0.8 + - - -
280D GLN 3.0 24.7 + - - -
281D CYS* 4.0 0.2 - - - +
282D HIS* 2.9 24.7 + - - +
283D LEU* 4.1 2.0 - - + +
288D TYR* 3.4 47.2 + - + -
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Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TYR* 3.8 29.8 - - + -
128D LEU* 3.9 10.3 - - + -
199D TYR* 3.4 30.5 - - + +
234D ALA 2.8 22.8 + - - +
235D ILE* 3.5 4.0 - - - +
237D GLN* 1.3 71.8 - - - +
239D ALA* 1.3 60.4 + - - +
241D CYS 4.3 0.9 + - - -
245D ILE* 3.4 14.9 - - + +
247D TRP* 3.0 46.2 + - + -
254D LEU* 4.1 18.8 - - + -
311D ILE* 5.5 0.2 - - + -
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Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ILE* 2.9 12.7 + - + +
236D MET* 2.9 11.8 + - - +
238D VAL* 1.3 79.2 - - + +
240D VAL* 1.3 60.8 + - + +
241D CYS 3.7 0.4 - - - -
242D GLY* 5.0 1.8 + - - -
247D TRP* 4.9 5.9 + - - -
254D LEU* 6.1 0.2 - - + -
302D LEU* 6.3 0.4 - - + -
305D LYS* 4.6 9.4 - - + +
306D LEU* 4.6 13.0 - - + -
309D ASN* 2.9 37.7 + - - +
311D ILE* 4.5 21.5 - - + +
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Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D MET* 3.1 24.2 + - + +
237D GLN* 4.1 5.4 - - - +
239D ALA* 1.3 81.9 - - + +
241D CYS* 1.3 61.2 + - - +
242D GLY 3.3 6.1 + - - -
279D GLY 3.3 28.3 - - - +
280D GLN* 3.7 21.3 - - - +
281D CYS* 3.8 12.1 + - - +
305D LYS* 4.0 21.5 - - + -
309D ASN* 3.9 14.8 - - - +
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Residues in contact with CYS 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D GLN* 3.1 40.8 + - - +
238D VAL 4.3 1.0 + - - -
239D ALA 3.7 0.4 - - - -
240D VAL* 1.3 78.3 - - - +
242D GLY* 1.3 66.2 + - - +
243D SER 3.2 1.1 + - - -
244D LEU* 2.9 25.4 + - + +
245D ILE* 3.8 16.6 - - + -
281D CYS* 2.1 49.4 - - - -
283D LEU* 3.6 15.9 - - + -
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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