Contacts of the helix formed by residues 317 - 333 (chain D) in PDB entry 1XVP
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 ALA 317 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422C LEU* 4.4 5.6 - - + +
423C PRO* 4.0 19.7 - - + +
426C ARG* 2.7 55.4 + - + +
313D LEU 3.1 16.8 + - - +
314D GLY* 3.5 11.7 - - - +
316D LEU* 1.3 79.3 - - - +
318D GLU* 1.3 57.2 + - - +
320D ARG* 3.4 2.9 + - - +
321D SER 3.3 5.5 + - - -
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Residues in contact with GLU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ASN* 4.3 5.4 + - - +
379C ASP* 4.1 27.4 - - - +
426C ARG* 3.3 22.9 + - - +
241D LEU* 4.4 16.4 - - - +
245D PHE* 3.7 20.6 - - + -
314D GLY 3.7 13.0 - - - +
315D LEU* 2.7 26.3 + - + +
317D ALA* 1.3 76.0 - - - +
319D LEU* 1.3 48.2 + - - +
320D ARG 2.8 6.0 + - - -
321D SER* 2.9 15.4 + - - -
322D ILE* 2.7 40.1 + - + +
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D GLU* 2.8 62.5 - - + +
203D HIS* 3.6 25.1 - - + -
204D ILE* 3.6 30.7 - - + -
245D PHE* 3.5 28.2 - - + -
249D LEU* 6.1 0.4 - - + -
262D LEU* 6.1 2.5 - - + -
315D LEU* 2.9 13.0 + - + +
316D LEU* 4.0 20.9 - - + +
317D ALA 3.6 0.4 - - - -
318D GLU* 1.3 71.8 - - - +
320D ARG* 1.3 56.1 + - - +
322D ILE* 3.9 9.4 - - + +
323D ASN* 2.9 17.2 + - - +
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Residues in contact with ARG 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ARG* 4.9 0.6 - - - +
423C PRO* 3.7 31.8 + - - +
424C ALA 3.9 0.8 - - - +
426C ARG* 3.9 5.8 - - + -
427C SER* 2.7 32.3 + - - +
430C LEU* 3.9 6.9 - - + +
200D GLU* 4.0 10.9 + - - +
265D MET 5.0 1.6 + - - -
269D SER* 3.0 37.6 + - - -
271D ASP* 2.8 30.9 + - - -
272D ARG* 3.3 28.3 - - - +
316D LEU* 3.1 20.1 + - - +
317D ALA 3.4 7.2 - - - +
318D GLU 2.9 0.6 - - - -
319D LEU* 1.3 76.2 - - - +
321D SER* 1.3 68.5 + - - +
322D ILE 3.0 1.1 - - - -
323D ASN* 3.9 2.3 - - - +
324D GLU* 2.9 26.7 + - - +
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Residues in contact with SER 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ARG* 3.4 33.8 + - - -
430C LEU* 4.0 20.2 - - - +
241D LEU* 4.8 7.2 - - - +
317D ALA 3.3 1.2 + - - -
318D GLU* 2.9 17.8 + - - -
320D ARG* 1.3 80.7 - - - +
322D ILE* 1.3 59.0 + - - +
324D GLU* 3.5 3.7 - - - +
325D ALA* 3.5 21.0 + - - +
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Residues in contact with ILE 322 (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 VAL* 5.3 0.4 - - + -
203D HIS* 4.2 26.2 - - + +
238D PHE* 3.9 11.3 - - + -
241D LEU* 3.9 22.7 - - + -
242D LEU* 4.0 20.6 - - + -
245D PHE* 3.7 44.4 - - + -
318D GLU* 2.7 17.4 + - + +
319D LEU* 3.9 11.4 - - + +
321D SER* 1.3 76.4 - - - +
323D ASN* 1.3 69.1 + - - +
324D GLU 3.0 1.8 - - - -
325D ALA* 4.6 3.4 - - - +
326D TYR* 2.9 24.9 + - + +
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Residues in contact with ASN 323 (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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195D LYS 4.9 5.8 + - - +
196D GLY* 3.0 31.4 + - - -
199D VAL* 3.2 36.4 - - + +
200D GLU* 3.4 15.3 - - + +
319D LEU 2.9 23.3 + - - +
320D ARG* 3.9 4.3 - - - +
322D ILE* 1.3 76.5 - - - +
324D GLU* 1.3 63.1 + - - +
326D TYR* 3.8 6.8 - - - +
327D GLY* 3.3 15.8 + - - -
346D ILE* 5.7 1.5 - - - +
347D CYS* 4.6 7.3 - - - -
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Residues in contact with GLU 324 (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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430C LEU* 4.2 37.7 - - + +
434C GLU* 4.0 19.8 - - - +
320D ARG 2.9 18.8 + - - +
321D SER* 3.5 9.4 - - - +
323D ASN* 1.3 78.7 - - - +
325D ALA* 1.3 69.0 + - + +
327D GLY* 3.2 7.8 + - - -
328D TYR* 3.5 9.4 + - - +
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Residues in contact with ALA 325 (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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238D PHE* 3.7 24.7 - - + -
241D LEU* 5.0 6.1 - - + -
321D SER 3.5 12.2 + - - +
322D ILE* 3.4 1.9 + - - -
324D GLU* 1.3 81.9 - - + +
326D TYR* 1.3 63.7 + - - +
328D TYR* 2.9 19.6 + - - +
329D GLN* 3.0 16.9 + - + +
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Residues in contact with TYR 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D PHE* 4.4 4.3 - + - -
165D ASN* 2.8 30.4 + - - -
199D VAL* 3.9 19.1 - - + -
203D HIS* 5.2 1.1 - - - +
234D PHE* 4.5 4.5 - + - -
238D PHE* 3.5 28.8 - + + -
322D ILE* 2.9 20.3 + - + +
323D ASN* 3.8 6.3 - - - +
325D ALA* 1.3 75.2 - - - +
327D GLY* 1.3 65.6 + - - +
329D GLN* 3.1 13.8 + - - +
330D ILE* 3.2 31.9 + - + +
340D MET* 3.6 12.5 - - - +
343D LEU* 3.9 5.2 - - + +
347D CYS* 3.7 24.9 - - - -
1003D CID 3.2 46.4 - + - -
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Residues in contact with GLY 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D ASN 3.3 6.5 + - - -
324D GLU 3.2 8.8 + - - -
326D TYR* 1.3 79.1 - - - +
328D TYR* 1.3 58.8 + - - +
330D ILE* 2.9 25.9 - - - +
331D GLN* 3.1 11.4 - - - +
347D CYS* 3.8 30.5 - - - -
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Residues in contact with TYR 328 (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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441A LEU* 4.2 41.1 - - + +
442A ILE* 6.1 0.2 - - - -
458C PRO 5.8 3.4 - - - -
459C HIS* 3.9 13.0 + - - -
462C THR* 3.6 45.5 + - + +
235D GLN* 4.8 0.2 - - - -
324D GLU 3.5 6.8 + - - +
325D ALA* 2.9 14.1 + - - +
327D GLY* 1.3 75.8 - - - +
329D GLN* 1.3 72.4 + - - +
331D GLN* 2.8 35.6 + - + +
332D HIS* 3.0 28.7 + - + +
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Residues in contact with GLN 329 (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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234D PHE* 3.7 23.3 - - + -
235D GLN* 3.0 53.4 + - - +
238D PHE* 3.5 35.3 - - + +
325D ALA* 3.0 18.2 + - + +
326D TYR* 3.1 7.4 + - - +
328D TYR* 1.3 94.0 - - - +
330D ILE* 1.3 62.2 + - - +
332D HIS* 3.0 21.2 + - - +
333D ILE* 3.0 19.1 + - + +
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Residues in contact with ILE 330 (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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234D PHE* 5.3 2.0 - - + -
326D TYR* 3.2 43.2 + - + +
327D GLY 2.9 21.8 - - - +
329D GLN* 1.3 74.8 - - - +
331D GLN* 1.3 73.3 + - - +
333D ILE 3.2 18.9 - - - +
336D LEU* 4.3 13.9 - - + +
337D SER* 3.5 26.1 + - - +
340D MET* 3.8 20.6 - - + -
343D LEU* 4.5 9.9 - - + +
344D GLN* 4.7 7.4 - - - -
347D CYS* 3.9 26.2 - - + -
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Residues in contact with GLN 331 (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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440A LYS 6.0 2.5 - - - +
441A LEU* 6.5 0.4 - - + -
327D GLY 3.1 22.0 - - - +
328D TYR* 2.8 21.0 + - + +
330D ILE* 1.3 90.5 - - - +
332D HIS* 1.3 66.6 + - - +
333D ILE 3.1 7.5 + - - +
334D GLN* 4.5 1.6 + - - -
337D SER* 3.2 22.9 + - - -
344D GLN* 5.8 2.0 - - - +
347D CYS 4.1 12.1 - - - +
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Residues in contact with HIS 332 (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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462C THR* 2.7 52.1 + - + +
233D GLY 4.4 13.4 + - - -
235D GLN* 3.7 23.4 - - + +
328D TYR* 3.0 29.7 + - + +
329D GLN* 3.3 18.9 + - - +
331D GLN* 1.3 77.9 - - - +
333D ILE* 1.3 58.9 + - - +
334D GLN* 3.5 7.4 + - - +
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Residues in contact with ILE 333 (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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158D VAL* 5.3 3.8 - - + -
232D VAL* 4.0 15.3 - - + +
233D GLY* 3.2 46.4 - - - +
234D PHE* 3.5 25.4 - - + +
329D GLN* 3.0 15.6 + - + +
330D ILE 3.2 14.1 - - - +
331D GLN 3.1 3.8 - - - +
332D HIS* 1.3 78.4 - - + +
334D GLN* 1.3 70.6 + - - +
335D GLY 3.5 0.5 + - - -
336D LEU* 3.3 36.7 + - + -
337D SER* 4.0 1.7 + - - -
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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
------------------------------------------------------------
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