Contacts of the helix formed by residues 279 - 290 (chain C) in PDB entry 2WTK
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276C GLY* 4.6 4.6 + - - -
277C ASP 3.6 1.0 - - - -
278C CYS* 1.3 79.5 - - - +
280C PRO* 1.3 77.8 - - - +
281C PRO* 3.5 5.2 - - - -
282C LEU 3.4 3.3 + - - -
283C SER* 3.0 25.3 + - - -
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Residues in contact with PRO 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C GLY* 1.3 82.4 - - - +
281C PRO* 1.4 78.2 - - + +
283C SER* 3.3 6.9 + - - +
284C ASP* 3.1 23.5 + - - +
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Residues in contact with PRO 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C GLY* 3.7 3.4 - - - -
280C PRO* 1.4 101.2 - - + +
282C LEU* 1.3 62.4 + - - +
284C ASP* 3.3 4.0 + - + -
285C LEU 3.4 0.3 + - - -
306C HIS* 3.2 28.4 - - + -
307C SER* 4.8 9.6 - - - +
308C TRP* 3.9 30.0 - - + +
311C LYS* 5.8 11.2 - - + +
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Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C VAL* 4.8 7.9 - - + -
245C LEU* 3.9 28.7 - - + -
249C THR* 3.9 28.9 - - + +
278C CYS* 4.1 28.7 - - - +
279C GLY 3.4 6.1 + - - +
280C PRO 3.3 0.2 - - - -
281C PRO* 1.3 76.9 - - - +
283C SER* 1.3 66.4 + - - +
285C LEU* 3.4 3.4 + - + +
286C LEU* 3.0 34.5 + - + +
308C TRP* 3.6 42.0 - - + +
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Residues in contact with SER 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C ILE* 3.6 36.0 - - - +
278C CYS* 4.4 5.3 - - - +
279C GLY 3.0 19.3 + - - -
280C PRO* 3.3 9.7 + - - +
282C LEU* 1.3 76.4 - - - +
284C ASP* 1.3 58.0 + - - +
286C LEU* 3.5 3.5 + - - -
287C LYS* 2.8 46.7 + - - +
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Residues in contact with ASP 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C PRO 3.1 17.7 + - - +
281C PRO* 3.6 4.7 - - + +
283C SER* 1.3 75.7 + - - +
285C LEU* 1.3 58.2 + - - +
287C LYS* 3.2 15.7 + - - +
288C GLY* 2.9 24.6 + - - -
298C PHE* 4.5 5.9 - - - -
306C HIS* 2.3 33.8 + - + +
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C PHE* 4.2 8.3 - - + -
245C LEU* 3.9 16.4 - - + -
281C PRO 3.4 5.1 + - - +
282C LEU* 3.4 6.7 + - + +
284C ASP* 1.3 74.0 - - - +
286C LEU* 1.3 60.8 - - - +
288C GLY* 3.1 3.5 + - - -
289C MET* 2.8 48.2 + - + +
298C PHE* 3.8 22.9 - - + -
303C ILE* 3.9 17.9 - - + -
306C HIS* 3.4 34.7 + - + +
308C TRP* 3.5 35.4 - - + -
309C PHE* 4.9 2.2 - - + +
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C GLY 3.5 25.8 - - - +
245C LEU* 3.7 21.8 - - + -
246C TYR* 3.6 40.6 - - + +
249C THR* 4.9 1.6 - - - +
250C THR* 6.3 0.4 - - - -
272C TYR* 4.5 0.9 - - - -
274C ILE* 4.3 9.0 - - + -
278C CYS* 4.5 15.3 - - - -
282C LEU* 3.0 35.9 + - + +
283C SER* 3.8 6.5 - - - +
285C LEU* 1.3 72.7 - - - +
287C LYS* 1.3 55.5 + - - +
289C MET* 2.9 8.2 + - + +
290C LEU* 2.7 45.4 + - + +
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Residues in contact with LYS 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C TYR* 3.4 17.3 + - + +
274C ILE* 3.8 15.8 - - + +
283C SER* 2.8 45.1 + - - +
284C ASP* 3.4 14.5 - - - +
286C LEU* 1.3 72.4 - - - +
288C GLY* 1.3 61.4 + - - +
290C LEU 3.5 1.9 + - - -
291C GLU* 3.2 31.9 + - - +
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Residues in contact with GLY 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C ASP 2.9 14.1 + - - -
285C LEU 3.1 4.7 + - - -
286C LEU 3.1 0.2 - - - -
287C LYS* 1.3 77.4 - - - +
289C MET* 1.3 60.4 + - - +
290C LEU 3.3 0.4 + - - -
291C GLU* 3.7 10.3 - - - +
297C ARG* 3.4 9.4 - - - -
298C PHE* 3.1 47.7 + - - -
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Residues in contact with MET 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C PHE* 3.6 22.4 - - + -
238C ILE* 4.4 10.5 - - + +
239C TRP* 3.8 14.4 + - - -
241C ALA* 4.5 2.0 - - - -
242C GLY* 3.9 31.0 - - - -
245C LEU* 3.3 34.8 - - + -
285C LEU* 2.8 35.4 + - + +
286C LEU* 2.9 8.3 + - + +
288C GLY* 1.3 78.1 - - - +
290C LEU* 1.3 58.8 + - - +
291C GLU 3.4 1.1 - - - -
297C ARG* 3.4 24.1 + - - +
298C PHE* 4.3 1.1 - - + +
303C ILE* 3.7 29.2 - - + -
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Residues in contact with LEU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C TRP* 3.3 52.1 - - + +
242C GLY* 4.1 9.2 - - - +
243C VAL* 3.8 18.8 - - + +
246C TYR* 4.1 22.2 - - + -
254C PRO* 4.1 14.6 - - + -
255C PHE* 5.4 0.9 - - + -
270C GLY 5.5 0.3 - - - +
272C TYR* 3.6 46.3 + - + +
286C LEU* 2.7 21.5 + - + +
287C LYS 3.7 3.8 - - - -
289C MET* 1.3 82.6 - - - +
291C GLU* 1.3 63.3 + - - -
292C TYR* 3.5 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
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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