Contacts of the helix formed by residues 294 - 303 (chain D) in PDB entry 6XAV
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 LEU 294 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271D ALA* 4.6 9.0 - - + +
285D LEU* 6.1 4.7 - - + -
289D VAL* 3.8 29.6 - - + -
290D ASP 4.4 2.6 + - - +
291D ALA 4.5 4.8 + - - +
292D ASN 3.5 0.2 - - - -
293D ALA* 1.3 77.9 - - + +
295D HIS* 1.3 62.8 + - - +
296D ARG 3.5 0.2 - - - -
297D PRO* 3.7 5.2 - - - +
298D LYS* 3.2 33.7 + - - +
330D VAL* 5.4 6.3 - - + +
331D ILE* 4.2 22.2 - - + -
334D GLU* 3.8 37.5 - - + +
335D PHE* 4.1 22.6 - - + -
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Residues in contact with HIS 295 (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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291D ALA 5.0 2.1 + - - +
292D ASN* 3.9 22.7 + - + +
293D ALA 3.3 1.4 - - - -
294D LEU* 1.3 78.6 - - - +
296D ARG* 1.3 82.3 + - - +
298D LYS* 3.9 9.1 - - - +
299D ARG* 3.4 60.7 + - - +
233E ASP 3.9 9.2 + - - -
234E GLU* 4.6 0.8 + - - -
235E PRO* 3.7 42.6 - - + +
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Residues in contact with ARG 296 (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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240D VAL* 4.8 8.1 - - - +
244D GLU* 4.9 18.0 + - - +
274D TYR* 3.5 58.2 + - + -
292D ASN 4.7 7.8 + - - +
293D ALA 4.2 0.4 + - - -
295D HIS* 1.3 95.4 - - - +
297D PRO* 1.3 68.5 - - + +
299D ARG* 3.2 8.2 + - - +
300D PHE* 3.1 20.8 + - - +
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Residues in contact with PRO 297 (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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267D ILE* 4.9 7.1 - - + +
270D LEU* 4.8 8.7 - - + -
271D ALA* 4.3 24.5 - - + +
274D TYR* 3.9 13.2 - - + -
293D ALA 3.2 22.2 - - - +
294D LEU* 3.7 5.8 - - - +
296D ARG* 1.3 93.4 - - + +
298D LYS* 1.3 57.3 + - - +
300D PHE* 3.8 8.5 - - + +
301D PHE* 2.9 32.6 + - - +
335D PHE* 3.9 26.8 - - + -
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Residues in contact with LYS 298 (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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294D LEU* 3.2 26.6 + - - +
295D HIS* 3.9 8.1 - - - +
296D ARG 3.2 0.8 - - - -
297D PRO* 1.3 78.8 - - - +
299D ARG* 1.3 58.5 + - + +
301D PHE* 4.2 5.3 - - - +
302D GLY* 2.9 24.4 + - - -
334D GLU* 5.0 14.9 + - + +
335D PHE* 4.0 20.2 - - + -
338D THR* 4.2 19.0 - - + +
210E ASP* 4.4 11.5 + - - -
232E PHE* 3.2 44.0 + - + +
233E ASP* 4.6 3.0 - - - +
234E GLU 4.4 8.4 + - - -
235E PRO* 5.3 5.3 - - - +
236E ALA 5.6 1.6 - - - +
239E HIS* 5.3 0.8 + - - -
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Residues in contact with ARG 299 (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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251D LYS* 5.4 8.1 - - - +
295D HIS* 3.4 39.5 + - - +
296D ARG* 3.2 9.9 + - - +
298D LYS* 1.3 78.1 - - + +
300D PHE* 1.3 64.8 + - - +
302D GLY* 3.7 1.7 - - - -
303D ALA* 3.0 25.3 + - - +
233E ASP* 3.3 42.4 + - + +
234E GLU* 6.1 1.1 - - - -
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Residues in contact with PHE 300 (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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207D LEU* 3.9 21.5 - - + -
243D ALA* 3.9 15.9 - - + -
246D VAL* 4.8 3.6 - - + -
247D ILE* 3.5 45.8 - - + -
262D ILE* 4.8 15.0 - - + -
264D LEU* 3.6 34.8 - - + -
270D LEU* 4.0 22.4 - - + -
274D TYR* 5.9 2.9 - - + +
296D ARG 3.1 12.8 + - - +
297D PRO* 3.4 10.5 + - + +
299D ARG* 1.3 79.8 - - - +
301D PHE* 1.3 63.9 + - + +
303D ALA* 3.5 8.3 + - - +
315D ILE* 3.4 25.0 - - + +
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Residues in contact with PHE 301 (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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173D ARG* 3.3 50.0 - - + +
174D GLY 3.4 27.8 - - - -
175D LEU* 3.5 27.1 - - + -
264D LEU* 5.5 2.0 - - + -
267D ILE* 4.3 17.7 - - + -
297D PRO 2.9 17.2 + - - +
298D LYS* 4.3 4.0 - - - +
300D PHE* 1.3 84.6 - - + +
302D GLY* 1.3 61.9 + - - +
303D ALA 3.4 0.9 + - - -
304D ALA* 3.8 7.4 + - - +
315D ILE* 4.0 15.6 - - + +
317D ALA* 3.6 21.8 - - + -
335D PHE* 5.0 6.3 - + + -
338D THR* 4.1 20.6 - - + -
339D GLY* 4.2 7.9 - - - -
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Residues in contact with GLY 302 (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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173D ARG* 3.9 13.1 + - - -
298D LYS 2.9 20.3 + - - -
299D ARG* 3.7 2.7 - - - -
300D PHE 3.3 0.2 - - - -
301D PHE* 1.3 75.0 - - - +
303D ALA* 1.3 63.9 + - - +
304D ALA 3.1 11.3 + - - +
305D ARG* 5.0 6.1 + - - -
338D THR* 5.3 0.2 - - - -
213E PRO* 5.2 8.1 - - - +
232E PHE* 4.8 7.5 - - - -
233E ASP* 4.5 21.4 - - - +
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Residues in contact with ALA 303 (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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133D PHE* 3.6 21.8 - - + -
247D ILE* 3.8 23.3 - - + -
251D LYS* 4.4 13.7 - - - -
299D ARG 3.0 16.0 + - - +
300D PHE 3.7 9.4 - - - +
301D PHE 3.2 1.6 - - - -
302D GLY* 1.3 77.6 - - - +
304D ALA* 1.3 61.8 + - - +
305D ARG* 3.3 7.7 + - - +
313D LEU* 3.4 15.3 - - + +
233E ASP* 5.9 0.2 - - - -
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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