Contacts of the helix formed by residues 279 - 291 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A ASP* 2.9 15.2 + - - -
277A ARG* 3.3 5.0 + - - +
278A GLU* 1.3 79.5 - - - +
280A LEU* 1.3 60.0 + - - -
281A ILE 3.5 2.5 - - - -
282A GLN 4.2 0.2 - - - -
283A ALA* 2.9 31.2 + - - +
411A ILE* 3.3 32.1 - - - -
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 4.7 19.5 - - + +
247A ASP* 4.3 0.8 + - - -
277A ARG* 5.4 4.7 - - - +
279A GLY* 1.3 69.6 - - - -
281A ILE* 1.3 63.9 + - - +
283A ALA* 3.6 5.0 - - - +
284A ARG* 3.2 57.8 + - - +
301A ASP* 5.2 7.2 - - - +
411A ILE* 3.6 17.4 + - + +
412A TRP* 4.5 25.1 - - + -
415A GLU* 4.8 8.1 - - - +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLY 3.5 0.2 - - - -
280A LEU* 1.3 77.8 - - + +
282A GLN* 1.3 79.9 + - + +
284A ARG* 3.2 20.3 + - - +
285A SER* 3.3 8.8 + - - -
405A TYR* 3.7 31.4 - - + -
409A LEU* 3.5 22.4 - - + -
410A GLN 2.8 29.6 - - - +
411A ILE* 3.7 10.0 + - - +
412A TRP* 4.1 1.8 - - - +
413A GLY 4.1 7.6 - - - +
415A GLU* 3.7 37.9 - - + +
464A ASN* 4.2 0.4 - - - +
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLU* 3.6 31.6 - - + +
279A GLY 3.7 1.8 + - - -
281A ILE* 1.3 90.3 - - + +
283A ALA* 1.3 64.5 + - - +
284A ARG 3.2 0.2 - - - -
285A SER* 3.2 17.9 + - - +
286A ILE* 3.1 29.1 + - + +
405A TYR 4.6 1.1 + - - +
406A ASP 3.4 21.4 + - - -
407A PRO* 3.6 22.3 - - - +
409A LEU 3.0 28.0 + - - +
410A GLN 5.6 1.6 - - - +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A VAL* 3.5 31.6 - - + +
245A ILE* 3.9 13.3 - - + +
247A ASP* 4.1 13.0 - - - +
274A ASN* 4.5 1.3 - - - +
278A GLU* 4.4 1.2 - - - +
279A GLY 2.9 22.9 + - - +
280A LEU 3.6 3.4 - - - +
282A GLN* 1.3 77.2 - - - +
284A ARG* 1.3 61.1 + - - +
286A ILE* 3.3 15.0 + - - +
287A GLY* 3.1 17.8 + - - -
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 4.0 16.1 - - + +
280A LEU* 3.2 44.5 + - + +
281A ILE* 3.2 10.7 + - - +
283A ALA* 1.3 80.2 - - - +
285A SER* 1.3 61.4 + - - +
287A GLY* 3.2 8.8 + - - +
288A ALA 3.2 1.6 + - - -
299A TYR* 3.0 53.6 + - + +
301A ASP* 4.6 5.3 + - - -
389A GLY 3.5 15.3 + - - -
390A GLY* 3.4 31.1 + - - -
392A PHE* 4.6 2.2 - - - -
399A PHE* 5.8 0.2 - - - -
405A TYR* 3.8 26.4 + - + -
415A GLU* 2.8 33.1 + - - +
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ILE 3.3 3.5 + - - -
282A GLN* 3.2 24.7 + - - -
284A ARG* 1.3 77.2 - - - +
286A ILE* 1.3 65.8 + - - +
288A ALA* 3.2 14.0 + - - +
289A GLN* 3.2 23.5 + - - +
299A TYR* 5.0 0.2 - - - -
399A PHE* 5.8 0.4 - - - -
404A LEU* 4.0 15.9 - - - +
405A TYR* 3.6 36.8 + - - +
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ILE* 4.7 4.0 - - + -
274A ASN* 3.6 26.9 - - - +
278A GLU* 3.6 34.1 - - + +
282A GLN* 3.1 16.5 + - + +
283A ALA* 3.3 6.5 + - - +
285A SER* 1.3 76.5 - - - +
287A GLY* 1.3 57.8 + - - +
289A GLN* 3.2 18.6 + - + +
290A LYS* 2.8 56.6 + - + +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 4.1 14.5 - - - +
214A VAL* 6.0 0.2 - - - -
243A VAL* 4.7 0.8 - - - +
245A ILE* 3.8 26.0 - - - -
283A ALA 3.1 11.0 + - - -
284A ARG* 3.2 5.1 + - - -
285A SER 3.1 0.4 - - - -
286A ILE* 1.3 78.1 - - - +
288A ALA* 1.3 60.5 + - - +
290A LYS 3.1 1.5 + - - -
291A ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ARG 3.2 4.8 + - - +
285A SER 3.2 9.8 + - - +
287A GLY* 1.3 77.0 - - - +
289A GLN* 1.3 60.4 + - - +
291A ALA 3.4 3.6 - - - +
297A LEU* 3.6 22.9 - - + -
299A TYR* 3.2 22.1 + - - +
396A ARG* 3.2 27.4 + - - -
400A PHE* 3.7 5.3 - - + -
404A LEU* 3.7 23.1 - - + -
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A SER* 3.2 16.4 - - - +
286A ILE* 3.2 23.2 + - + +
288A ALA* 1.3 78.1 - - - +
290A LYS* 1.3 63.4 + - + +
291A ALA 3.3 0.7 + - - -
292A LYS* 3.7 22.5 - - - +
396A ARG* 3.9 4.6 + - - +
400A PHE* 4.2 21.6 - - + -
404A LEU* 4.4 13.2 - - + +
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLU* 4.7 2.3 - - - +
243A VAL* 4.2 2.2 - - - +
245A ILE* 4.4 6.5 - - + -
272A PHE* 3.3 67.5 - - + -
273A ARG 5.1 4.7 - - - -
274A ASN* 5.1 4.7 - - - +
286A ILE* 2.8 44.9 + - + +
287A GLY 3.1 3.5 + - - +
289A GLN* 1.3 77.1 - - + +
291A ALA* 1.3 59.3 + - - +
292A LYS* 3.8 10.3 + - - +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A SER* 4.0 9.9 + - - -
212A VAL* 3.9 15.9 - - + -
241A GLU* 3.2 16.4 - - - +
243A VAL* 3.6 17.3 - - + -
287A GLY 3.0 14.0 + - - +
288A ALA 3.4 2.1 - - - +
289A GLN 3.2 0.8 - - - -
290A LYS* 1.3 79.5 - - - +
292A LYS* 1.3 59.1 + - - +
297A LEU* 4.3 5.5 - - + +
396A ARG* 3.0 24.0 + - - -
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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