Contacts of the helix formed by residues 276 - 285 (chain Z) in PDB entry 5GJQ
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 GLU 276 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274Z ASP* 4.3 5.8 - - + +
275Z MET* 1.3 76.4 - - - +
277Z LEU* 1.3 56.6 + - - +
278Z VAL 3.2 3.8 + - - -
279Z GLU* 4.0 10.4 + - - +
280Z ASP* 4.5 2.9 + - - +
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Residues in contact with LEU 277 (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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265Z ALA 4.2 1.3 - - - +
268Z LEU* 4.1 7.9 - - + +
269Z ALA* 3.2 46.6 - - + +
274Z ASP* 5.6 1.7 - - + +
275Z MET* 2.7 6.4 + - - +
276Z GLU* 1.3 74.4 - - - +
278Z VAL* 1.3 60.5 + - - +
279Z GLU 3.5 1.1 - - - -
280Z ASP* 3.4 17.0 - - + +
281Z ILE* 3.3 17.3 + - - +
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Residues in contact with VAL 278 (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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275Z MET* 2.4 35.6 + - + +
276Z GLU 3.1 0.2 - - - -
277Z LEU* 1.3 70.5 - - - +
279Z GLU* 1.3 62.0 + - - +
281Z ILE* 3.5 5.7 + - - +
282Z PHE* 3.0 24.6 + - - +
294Z MET* 5.9 0.2 - - - +
298Z LEU* 4.1 32.9 - - + +
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Residues in contact with GLU 279 (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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276Z GLU 4.0 8.1 + - - +
278Z VAL* 1.3 74.8 - - - +
280Z ASP* 1.3 56.7 + - - +
282Z PHE* 2.7 14.3 + - + -
283Z THR* 2.4 39.9 + - - -
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Residues in contact with ASP 280 (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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249Z LEU 6.1 0.9 - - - +
261Z ARG* 2.7 27.8 + - + +
265Z ALA* 3.8 24.7 - - + +
276Z GLU 4.5 1.4 + - - +
277Z LEU* 3.4 25.6 + - + +
278Z VAL 3.3 0.2 - - - -
279Z GLU* 1.3 79.1 - - - +
281Z ILE* 1.3 57.2 + - - +
283Z THR* 3.7 6.9 + - - -
284Z SER 3.4 8.0 + - - -
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Residues in contact with ILE 281 (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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261Z ARG 4.4 3.1 - - - -
262Z PHE* 5.8 1.8 - - - +
265Z ALA* 6.0 0.6 - - - -
266Z LEU* 5.7 7.4 - - + +
269Z ALA* 5.2 8.1 - - + -
277Z LEU 3.3 9.3 + - - +
278Z VAL* 3.9 6.7 - - - +
279Z GLU 3.0 0.4 - - - -
280Z ASP* 1.3 76.2 - - - +
282Z PHE* 1.3 60.2 + - - +
283Z THR 3.1 0.3 + - - -
284Z SER* 3.1 1.2 + - - -
285Z CYS* 2.4 42.1 + - + +
294Z MET* 3.9 22.9 - - + +
297Z MET* 5.5 5.6 - - + -
298Z LEU 6.3 0.2 - - - +
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Residues in contact with PHE 282 (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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278Z VAL 3.0 15.8 + - - +
279Z GLU* 2.7 18.7 + - + +
281Z ILE* 1.3 71.0 - - - +
283Z THR* 1.3 62.6 - - - +
285Z CYS* 2.8 24.9 - - - +
291Z GLN* 6.3 0.4 - - - -
294Z MET* 4.9 4.1 - - - +
328Z SER 4.9 1.2 - - - +
329Z ASN* 4.4 30.7 - - + +
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Residues in contact with THR 283 (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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260Z SER 4.3 11.1 - - - +
261Z ARG 4.8 2.5 - - - -
279Z GLU* 2.4 32.8 + - - -
280Z ASP* 3.8 8.3 - - - -
282Z PHE* 1.3 70.5 - - - +
284Z SER* 1.3 61.6 + - - +
285Z CYS 4.7 0.3 - - - +
286Z LYS* 5.3 2.4 - - - +
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Residues in contact with SER 284 (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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259Z PHE* 4.2 5.6 - - - -
260Z SER 3.7 9.6 + - - +
261Z ARG 3.0 41.5 - - - -
262Z PHE* 3.4 16.8 - - - -
280Z ASP 3.4 2.3 + - - -
281Z ILE* 3.1 2.5 + - - -
283Z THR* 1.3 81.5 - - - +
285Z CYS* 1.3 60.5 + - - +
286Z LYS* 2.9 16.8 + - - +
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Residues in contact with CYS 285 (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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262Z PHE* 5.2 2.2 - - + +
281Z ILE* 2.4 33.3 + - + +
282Z PHE* 2.8 21.4 - - - +
284Z SER* 1.3 64.5 - - - +
286Z LYS* 1.3 59.7 + - - +
287Z ASP 4.5 1.8 - - - -
290Z VAL* 4.0 19.3 - - + +
291Z GLN* 4.1 10.3 - - + +
294Z MET* 3.8 26.5 - - + -
328Z SER 4.4 3.3 - - - +
329Z ASN* 4.8 2.1 - - - +
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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