Contacts of the helix formed by residues 295 - 307 (chain Z) in PDB entry 5WTI
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 295 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294Z ARG* 1.3 77.5 - - - +
296Z TRP* 1.3 61.1 + - - +
297Z ARG 3.5 1.6 - - - -
298Z GLU* 3.7 6.8 + - - +
299Z ILE* 3.0 31.4 + - - +
322Z TYR* 3.7 35.6 - - - -
329Z GLU 4.6 0.2 + - - -
331Z GLY 4.7 3.2 - - - +
336Z TYR* 3.4 8.0 + - - -
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Residues in contact with TRP 296 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293Z LEU* 3.4 29.2 - - + +
294Z ARG 3.0 6.4 + - - +
295Z GLY* 1.3 74.5 - - - +
297Z ARG* 1.3 63.6 + - + +
299Z ILE* 3.0 2.5 + - - +
300Z ILE* 2.8 73.8 + - + +
303Z TRP* 4.4 11.9 - + - -
336Z TYR* 3.2 33.1 + + - +
339Z LEU* 4.6 10.1 - - + -
351Z HIS 5.3 0.4 - - - -
352Z PRO 3.4 27.5 + - - -
355Z PRO* 3.5 38.4 - - + -
356Z TYR* 4.2 20.9 - + + +
1047Z LEU* 4.0 23.2 - - + +
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Residues in contact with ARG 297 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294Z ARG 4.9 0.2 + - - -
295Z GLY 3.5 0.2 - - - -
296Z TRP* 1.3 82.6 - - + +
298Z GLU* 1.3 70.0 + - + +
300Z ILE* 3.7 8.4 - - - +
301Z GLN* 2.4 51.4 + - - +
356Z TYR* 5.4 9.3 + - - -
1047Z LEU* 3.2 38.3 - - + +
1050Z GLU* 3.2 28.1 + - - -
1051Z LEU* 5.3 4.3 - - + -
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Residues in contact with GLU 298 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294Z ARG 5.0 1.7 - - - +
295Z GLY* 4.3 6.6 - - - +
296Z TRP 3.2 0.4 - - - -
297Z ARG* 1.3 94.1 + - + +
299Z ILE* 1.3 64.7 + - - +
301Z GLN* 3.8 14.8 - - - +
302Z LYS* 3.6 17.0 + - - +
322Z TYR* 2.2 48.9 + - + -
326Z HIS* 4.6 2.1 - - - -
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Residues in contact with ILE 299 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295Z GLY* 3.0 21.9 + - - +
296Z TRP 3.0 3.4 + - - +
298Z GLU* 1.3 79.3 - - - +
300Z ILE* 1.3 59.5 + - + +
302Z LYS* 2.9 28.1 - - - +
303Z TRP* 3.1 32.7 + - + +
318Z VAL* 4.2 11.0 - - + +
319Z PHE* 3.6 31.6 - - + +
322Z TYR* 4.0 28.3 - - + -
336Z TYR* 3.8 34.8 - - + -
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Residues in contact with ILE 300 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296Z TRP* 2.8 69.0 + - + +
297Z ARG* 3.7 9.2 - - - +
299Z ILE* 1.3 71.3 - - - +
301Z GLN* 1.3 58.5 + - - +
302Z LYS 3.1 1.6 - - - -
303Z TRP* 2.6 32.4 + - + +
304Z LEU* 2.5 53.2 + - + +
351Z HIS* 6.1 4.7 - - + +
352Z PRO* 4.9 6.5 - - + +
1051Z LEU* 3.9 23.6 - - + -
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Residues in contact with GLN 301 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297Z ARG* 2.4 51.7 + - - +
298Z GLU* 3.8 11.2 - - - +
300Z ILE* 1.3 76.2 - - - +
302Z LYS* 1.3 69.8 + - - +
304Z LEU* 3.8 14.1 + - + +
305Z LYS* 3.1 29.3 + - - +
1050Z GLU 5.7 1.5 + - - +
1051Z LEU* 3.7 26.9 - - + +
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Residues in contact with LYS 302 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298Z GLU 3.6 16.3 + - - +
299Z ILE* 2.9 13.4 + - - +
301Z GLN* 1.3 82.7 + - - +
303Z TRP* 1.3 62.5 + - + +
305Z LYS* 3.1 36.8 + - + +
306Z MET* 3.4 14.9 - - - +
318Z VAL* 3.7 29.6 - - + -
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Residues in contact with TRP 303 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296Z TRP* 4.4 16.4 - + - -
299Z ILE* 3.1 23.5 + - + +
300Z ILE* 2.6 39.5 + - + +
302Z LYS* 1.3 74.6 - - - +
304Z LEU* 1.3 56.3 + - - -
306Z MET* 3.0 15.2 + - - -
307Z ASP* 2.7 40.0 + - + +
315Z TYR* 3.1 62.8 + + + -
316Z LEU* 4.5 2.0 - - - -
318Z VAL* 3.8 11.9 - - + +
319Z PHE* 5.3 1.8 - - + -
336Z TYR* 3.8 37.0 - + + -
339Z LEU* 4.0 22.4 - - + -
340Z SER* 4.2 7.2 - - - -
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Residues in contact with LEU 304 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Z ILE* 2.5 56.3 + - + +
301Z GLN* 3.8 11.2 - - - +
302Z LYS 3.3 0.4 - - - -
303Z TRP* 1.3 73.5 - - - +
305Z LYS* 1.3 57.4 + - + +
307Z ASP* 2.8 23.3 - - - +
351Z HIS* 6.2 4.5 - - + +
352Z PRO* 4.3 18.6 - - + -
1051Z LEU* 4.0 32.8 - - + +
1052Z LYS* 4.3 27.4 - - + +
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Residues in contact with LYS 305 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301Z GLN* 3.1 18.6 + - - +
302Z LYS* 3.1 32.3 - - - +
304Z LEU* 1.3 75.8 - - + +
306Z MET* 1.3 57.6 + - - +
307Z ASP* 3.7 0.7 - - - -
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Residues in contact with MET 306 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302Z LYS* 3.4 19.1 - - - +
303Z TRP* 3.0 23.4 + - - -
305Z LYS* 1.3 78.1 - - + +
307Z ASP* 1.3 50.0 - - - +
308Z GLU* 3.2 8.2 + - - -
309Z ASN 4.4 1.2 + - - -
310Z GLU* 4.4 11.1 - - + +
314Z LYS* 4.1 15.3 - - + +
315Z TYR* 2.2 74.4 + - + +
318Z VAL* 4.1 12.3 - - + -
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Residues in contact with ASP 307 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303Z TRP* 2.7 22.0 + - + +
304Z LEU* 2.8 26.2 - - - +
305Z LYS 3.7 0.7 - - - -
306Z MET* 1.3 69.2 - - - +
308Z GLU* 1.3 64.8 + - - +
315Z TYR* 3.2 19.7 + - + -
351Z HIS* 4.0 25.9 + - + -
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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