Contacts of the helix formed by residues 279 - 291 (chain D) in PDB entry 6IWQ
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 279 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247D ASP* 2.6 23.4 + - - -
277D ARG* 3.3 4.3 + - - +
278D GLU* 1.3 75.1 - - - +
280D LEU* 1.3 60.3 + - - -
281D ILE 3.5 2.7 - - - -
282D GLN 4.2 0.7 - - - -
283D ALA* 2.9 31.1 + - - +
411D ILE* 3.5 27.1 - - - -
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Residues in contact with LEU 280 (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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214D VAL* 4.7 20.4 - - + +
247D ASP* 5.7 0.2 - - - -
277D ARG* 5.4 1.7 - - - +
279D GLY* 1.3 70.3 - - - -
281D ILE* 1.3 65.7 + - - +
283D ALA* 3.6 4.8 - - - +
284D ARG* 3.2 56.1 + - - +
301D ASP* 5.2 7.2 - - - +
411D ILE* 3.9 12.2 - - + +
412D TRP* 4.2 31.9 - - + +
415D GLU* 4.7 8.3 - - - +
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Residues in contact with ILE 281 (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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279D GLY 3.5 0.6 - - - -
280D LEU* 1.3 77.2 - - + +
282D GLN* 1.3 81.4 + - + +
284D ARG* 3.2 19.9 + - - +
285D SER* 3.3 8.5 + - - -
405D TYR* 3.7 30.7 - - + -
409D LEU* 3.5 20.6 - - + -
410D GLN 2.9 30.5 - - - +
411D ILE* 5.3 0.4 - - - +
412D TRP* 4.1 7.2 - - - +
413D GLY* 3.3 20.0 - - - +
415D GLU* 3.7 29.4 - - + +
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Residues in contact with GLN 282 (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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278D GLU* 4.0 33.2 - - + +
279D GLY 3.7 1.8 + - - -
280D LEU 3.5 0.2 - - - -
281D ILE* 1.3 90.2 - - + +
283D ALA* 1.3 65.0 + - - +
285D SER* 3.2 18.1 + - - +
286D ILE* 3.1 28.8 + - + +
405D TYR 4.6 1.1 + - - +
406D ASP 3.4 21.2 + - - -
407D PRO* 3.6 21.3 - - - +
409D LEU 3.0 27.9 + - - +
410D GLN* 5.8 1.1 - - - -
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Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D VAL* 3.5 31.1 - - + +
245D ILE* 4.1 8.2 - - + +
247D ASP* 3.8 15.7 - - - +
274D ASN* 4.7 3.4 - - - +
278D GLU* 4.5 0.4 - - - +
279D GLY 2.9 21.6 + - - +
280D LEU 3.6 3.4 - - - +
281D ILE 3.2 0.2 - - - -
282D GLN* 1.3 78.5 - - - +
284D ARG* 1.3 60.9 + - - +
286D ILE* 3.3 14.5 + - - +
287D GLY* 3.1 18.0 + - - -
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Residues in contact with ARG 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D VAL* 4.0 16.1 - - + +
280D LEU* 3.2 44.6 + - - +
281D ILE* 3.2 11.2 + - - +
283D ALA* 1.3 79.6 - - - +
285D SER* 1.3 61.4 + - - +
287D GLY* 3.2 8.1 + - - +
288D ALA 3.2 1.7 + - - -
299D TYR* 3.0 52.8 + - + -
301D ASP* 4.6 4.9 + - - -
389D GLY 3.5 14.6 + - - -
390D GLY* 3.4 31.9 + - - -
392D PHE* 4.6 2.5 - - - -
405D TYR* 3.8 23.1 + - + -
415D GLU* 3.3 38.0 + - - +
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Residues in contact with SER 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ILE 3.3 4.1 + - - -
282D GLN* 3.2 24.5 + - - -
284D ARG* 1.3 76.0 - - - +
286D ILE* 1.3 64.9 + - - +
288D ALA* 3.2 14.0 + - - +
289D GLN* 3.2 23.5 + - - +
299D TYR* 5.0 0.4 - - - -
399D PHE* 5.8 0.9 - - - -
404D LEU* 4.0 16.8 - - - +
405D TYR* 3.6 36.4 + - - +
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Residues in contact with ILE 286 (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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245D ILE* 4.7 6.1 - - + -
274D ASN* 3.6 34.8 - - - +
278D GLU* 3.8 26.5 - - + +
282D GLN* 3.1 15.9 + - + +
283D ALA* 3.6 8.1 - - - +
285D SER* 1.3 76.8 - - - +
287D GLY* 1.3 57.2 + - - +
289D GLN* 3.2 17.6 + - + +
290D LYS* 2.8 56.6 + - + +
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Residues in contact with GLY 287 (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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212D VAL* 3.8 24.6 - - - +
243D VAL* 4.7 0.9 - - - +
245D ILE* 3.8 17.9 - - - -
283D ALA 3.1 10.6 + - - -
284D ARG 3.2 5.1 + - - -
285D SER 3.1 0.6 - - - -
286D ILE* 1.3 78.2 - - - +
288D ALA* 1.3 61.6 + - - +
290D LYS* 3.1 10.0 + - - +
291D ALA* 3.1 18.7 + - - +
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Residues in contact with ALA 288 (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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284D ARG 3.2 4.5 + - - +
285D SER 3.2 10.0 + - - +
287D GLY* 1.3 77.9 - - - +
289D GLN* 1.3 57.9 + - - +
291D ALA 3.7 3.5 + - - +
297D LEU* 3.6 22.2 - - + -
299D TYR* 3.2 22.1 + - - +
396D ARG* 3.0 28.8 + - - -
400D PHE* 3.7 5.7 - - + -
404D LEU* 3.7 22.7 - - + -
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Residues in contact with GLN 289 (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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285D SER* 3.2 16.0 - - - +
286D ILE* 3.2 23.2 + - + +
288D ALA* 1.3 78.0 - - - +
290D LYS* 1.3 63.1 + - + +
291D ALA 3.1 1.9 + - - -
292D LYS* 4.4 2.9 + - - +
396D ARG* 3.7 13.4 + - - +
400D PHE* 4.2 18.0 - - + -
404D LEU* 4.4 13.0 - - + +
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Residues in contact with LYS 290 (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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241D GLU* 4.7 1.7 - - - +
243D VAL* 4.2 4.2 - - + +
245D ILE* 4.7 1.8 - - + -
270D LYS* 5.3 0.7 - - - +
272D PHE* 3.6 69.1 - - + +
273D ARG 5.3 2.9 - - - -
274D ASN* 5.1 4.9 - - - -
286D ILE* 2.8 45.4 + - + +
287D GLY* 3.1 5.6 + - - +
289D GLN* 1.3 76.6 - - + +
291D ALA* 1.3 59.7 + - - +
292D LYS 3.7 2.7 + - - -
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Residues in contact with ALA 291 (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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210D SER* 4.0 13.9 + - - -
212D VAL* 4.1 10.5 - - + -
241D GLU* 3.5 18.1 - - - +
243D VAL* 3.6 15.7 - - + -
287D GLY 3.1 15.7 + - - +
288D ALA 3.7 1.1 + - - +
289D GLN 3.1 2.0 - - - -
290D LYS* 1.3 80.6 - - - +
292D LYS* 1.3 61.9 + - - +
293D LEU 3.5 2.9 + - - -
294D GLY 4.6 0.3 + - - -
297D LEU* 4.3 5.8 - - + +
396D ARG* 3.2 20.8 + - - -
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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