Contacts of the helix formed by residues 307 - 317 (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 PHE 307 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394C GLU* 3.3 30.7 - - + -
397C TYR* 3.6 33.0 - - + -
398C ALA* 3.6 26.2 - - + -
401C GLU* 3.6 23.1 - - + -
415C PHE* 4.1 17.5 - + - -
305D ASP* 3.7 1.8 - - - +
306D ARG* 1.3 112.3 - - + +
308D LEU* 1.3 63.1 + - - +
309D TYR* 3.1 3.4 - - - +
310D ALA* 3.0 20.5 + - + +
311D LYS* 3.0 28.6 + - - +
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Residues in contact with LEU 308 (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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252D LEU* 3.8 40.8 - - + +
254D LEU* 4.2 14.4 - - + -
258D GLU* 4.4 8.3 - - - +
296D ILE* 4.0 30.5 - - + -
299D GLN* 5.2 1.6 - - - +
304D ARG* 4.2 25.4 - - + +
305D ASP* 3.2 33.3 + - - +
306D ARG 2.8 6.4 + - - +
307D PHE* 1.3 75.8 - - - +
309D TYR* 1.3 63.8 + - - +
311D LYS* 3.1 7.4 + - - +
312D LEU* 3.0 31.7 + - + +
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Residues in contact with TYR 309 (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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415C PHE* 6.2 2.2 - + - -
416C ALA* 3.5 30.7 - - + +
419C LEU* 5.5 2.5 - - + -
420C LEU* 3.5 15.8 - - - +
265D MET* 3.6 6.1 - - + +
289D ALA* 3.4 27.6 - - - +
292D LEU* 3.2 33.0 - - + -
293D GLN* 3.5 25.2 + - + -
296D ILE* 3.3 17.9 - - + +
306D ARG 4.5 0.8 + - - +
307D PHE* 3.1 1.7 - - - -
308D LEU* 1.3 80.2 - - - +
310D ALA* 1.3 63.9 + - - +
312D LEU* 3.0 17.5 + - + +
313D LEU* 3.1 44.9 + - + +
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Residues in contact with ALA 310 (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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397C TYR* 3.4 45.9 + - + -
415C PHE* 5.0 2.2 - - + -
419C LEU* 4.1 20.4 - - + +
422C LEU* 5.2 3.8 - - - +
307D PHE* 3.0 24.8 + - + +
309D TYR* 1.3 78.1 - - - +
311D LYS* 1.3 57.5 + - - +
313D LEU* 3.6 6.1 + - - +
314D GLY* 3.1 19.9 + - - -
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Residues in contact with LYS 311 (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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390C GLU* 3.9 17.2 + - - +
393C ARG* 6.1 0.2 - - - +
394C GLU* 2.9 31.6 + - - -
397C TYR* 4.5 10.8 - - + +
252D LEU* 4.4 18.8 - - + -
305D ASP* 2.9 48.6 + - - +
307D PHE* 3.0 20.6 - - - +
308D LEU* 3.4 4.9 - - - +
309D TYR 3.1 0.4 - - - -
310D ALA* 1.3 74.5 - - - +
312D LEU* 1.3 59.9 + - - +
313D LEU 3.1 1.6 - - - -
314D GLY* 3.0 3.2 + - - +
315D LEU* 2.8 36.5 + - + +
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Residues in contact with LEU 312 (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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249D LEU* 5.6 0.7 - - + -
252D LEU* 3.9 24.9 - - + -
254D LEU* 4.2 21.8 - - + -
258D GLU* 4.9 4.7 - - + +
262D LEU* 3.6 38.7 - - + +
292D LEU* 3.8 30.7 - - + -
296D ILE* 4.5 8.7 - - + -
308D LEU* 3.0 23.2 + - + +
309D TYR* 3.0 9.1 + - + +
311D LYS* 1.3 76.3 - - - +
313D LEU* 1.3 58.5 + - + +
315D LEU* 3.7 8.6 - - + +
316D LEU* 2.9 31.2 + - - +
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Residues in contact with LEU 313 (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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416C ALA 4.1 0.2 - - - +
419C LEU* 3.4 50.3 - - + +
420C LEU* 3.5 13.0 - - + +
422C LEU* 4.5 4.3 - - + +
423C PRO* 3.9 13.9 - - + +
262D LEU* 5.6 0.2 - - + -
265D MET* 3.8 19.5 - - + -
309D TYR* 3.1 56.1 + - + +
310D ALA 3.9 6.1 - - - +
312D LEU* 1.3 74.6 - - + +
314D GLY* 1.3 63.7 + - - +
315D LEU 3.0 4.9 - - - -
316D LEU* 3.3 13.6 + - + +
317D ALA* 3.1 23.0 + - - +
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Residues in contact with GLY 314 (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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377C ASN* 5.5 1.0 - - - +
379C ASP* 4.7 4.8 - - - +
393C ARG* 3.9 24.6 + - - -
422C LEU* 5.1 5.1 - - - +
426C ARG* 5.7 0.2 + - - -
310D ALA 3.1 13.7 + - - -
311D LYS* 3.0 9.9 + - - -
313D LEU* 1.3 76.5 - - - +
315D LEU* 1.3 59.2 + - - +
317D ALA* 3.5 16.8 - - - +
318D GLU* 3.7 14.4 + - - +
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Residues in contact with LEU 315 (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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379C ASP* 4.9 7.0 - - - +
245D PHE* 3.8 26.1 - - + -
248D THR* 3.6 26.2 - - + -
249D LEU* 3.6 38.6 - - + -
252D LEU* 4.5 13.2 - - + -
262D LEU* 5.4 5.8 - - + -
311D LYS* 2.8 19.6 + - + +
312D LEU* 3.7 10.3 - - + +
314D GLY* 1.3 77.8 - - - +
316D LEU* 1.3 55.0 + - - +
317D ALA 2.9 5.8 - - - -
318D GLU* 2.7 34.3 + - + +
319D LEU* 2.9 14.7 + - + +
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Residues in contact with LEU 316 (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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423C PRO* 4.1 14.6 - - + -
200D GLU* 4.1 3.9 - - - +
204D ILE* 4.8 0.2 - - + -
262D LEU* 3.7 39.3 - - + +
265D MET* 3.7 46.7 - - + +
266D ALA* 4.3 9.6 - - + -
312D LEU 2.9 19.1 + - - +
313D LEU* 3.3 13.2 + - + +
315D LEU* 1.3 77.3 - - - +
317D ALA* 1.3 59.4 + - - +
319D LEU* 3.7 26.7 + - + +
320D ARG* 3.1 23.4 + - - +
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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