Contacts of the helix formed by residues 287 - 301 (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 ASP 287 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286Z LYS* 1.3 76.8 - - - +
288Z VAL* 1.4 56.9 + - - +
289Z VAL* 4.1 3.6 - - + +
290Z VAL* 3.4 27.1 - - + +
291Z GLN* 2.6 37.4 + - - +
835Z GLU 5.9 2.0 - - - +
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Residues in contact with VAL 288 (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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286Z LYS 3.4 4.3 + - - -
287Z ASP* 1.4 70.0 - - - +
289Z VAL* 1.3 50.7 - - - +
291Z GLN* 3.0 8.1 + - - +
292Z LYS* 2.2 38.0 + - - +
331Z LEU* 4.1 13.0 - - + +
332Z ALA 5.1 2.8 + - - +
333Z LEU* 5.9 8.1 - - + +
335Z ARG* 5.9 4.0 - - + -
835Z GLU 6.1 0.4 - - - +
836Z GLU 4.2 15.5 - - - +
837Z LEU* 5.1 2.2 - - + -
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Residues in contact with VAL 289 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287Z ASP* 3.1 2.8 - - + +
288Z VAL* 1.3 75.2 - - - +
290Z VAL* 1.3 64.5 + - - +
291Z GLN 3.1 1.1 - - - -
292Z LYS* 3.5 11.3 - - + +
293Z GLN* 3.2 19.2 + - - +
834Z ASP 3.9 14.1 - - - +
835Z GLU* 4.3 14.1 + - - +
837Z LEU* 3.7 24.2 - - + -
890Z VAL* 4.4 3.9 - - - +
899Z ILE* 4.9 15.9 - - + +
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Residues in contact with VAL 290 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285Z CYS* 4.0 14.5 - - + +
286Z LYS 4.9 0.2 - - - +
287Z ASP* 3.4 27.5 + - + +
289Z VAL* 1.3 77.1 - - - +
291Z GLN* 1.3 57.1 + - - +
293Z GLN* 3.6 5.5 + - - +
294Z MET* 3.0 21.5 + - - +
890Z VAL* 3.7 23.8 - - + +
891Z THR* 5.6 2.6 - - - -
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Residues in contact with GLN 291 (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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282Z PHE* 6.3 0.4 - - - -
285Z CYS* 4.1 17.2 - - + +
286Z LYS 4.9 1.1 - - - -
287Z ASP 2.6 23.7 + - - +
288Z VAL 3.1 4.9 - - - +
290Z VAL* 1.3 71.4 - - - +
292Z LYS* 1.3 52.6 + - - +
293Z GLN 3.1 1.3 - - - -
294Z MET* 3.3 11.0 - - + -
295Z ALA* 2.1 41.7 + - - +
329Z ASN 4.7 4.7 - - - +
331Z LEU* 3.3 24.5 - - + -
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Residues in contact with LYS 292 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288Z VAL 2.2 27.6 + - - +
289Z VAL* 3.5 15.7 - - + +
291Z GLN* 1.3 68.4 - - - +
293Z GLN* 1.3 56.3 + - - +
295Z ALA* 3.2 10.2 - - - +
296Z PHE* 2.9 27.9 + - - +
331Z LEU* 5.4 0.9 - - - -
332Z ALA 5.6 2.0 - - - +
336Z GLU* 4.9 16.8 - - + -
339Z ILE* 6.5 1.1 - - + -
340Z MET* 5.4 7.2 - - + +
837Z LEU* 5.2 7.2 - - + -
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Residues in contact with GLN 293 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289Z VAL 3.2 12.6 + - - +
290Z VAL 3.6 8.5 - - - +
291Z GLN 3.1 0.2 - - - -
292Z LYS* 1.3 75.8 - - - +
294Z MET* 1.3 50.8 + - - +
296Z PHE* 3.3 7.5 + - - +
297Z MET* 2.6 35.8 + - - +
890Z VAL* 4.7 13.0 - - + +
891Z THR* 4.8 15.5 - - - +
899Z ILE* 6.1 3.4 - - + -
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Residues in contact with MET 294 (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 5.9 0.2 - - - +
281Z ILE* 3.9 20.8 - - + +
282Z PHE* 4.9 2.7 - - - +
285Z CYS* 3.8 16.8 - - + -
290Z VAL 3.0 9.5 + - - +
291Z GLN* 2.8 22.6 + - + +
293Z GLN* 1.3 69.1 - - - +
295Z ALA* 1.3 56.8 + - - +
297Z MET* 3.2 9.1 - - - +
298Z LEU* 2.4 40.1 + - - +
891Z THR* 5.9 1.0 - - - -
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Residues in contact with ALA 295 (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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291Z GLN 2.1 30.3 + - - +
292Z LYS* 3.2 13.0 - - - +
294Z MET* 1.3 68.1 - - - +
296Z PHE* 1.3 51.7 + - - +
298Z LEU* 3.2 6.1 + - - +
299Z GLY* 2.5 33.6 + - - -
321Z MET 5.9 1.6 - - - +
330Z PHE 5.2 4.9 - - - +
331Z LEU* 5.2 0.7 - - + -
332Z ALA* 4.5 24.2 - - + +
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Residues in contact with PHE 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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292Z LYS 2.9 16.3 + - - +
293Z GLN* 3.6 8.5 - - - +
295Z ALA* 1.3 71.5 - - - +
297Z MET* 1.3 53.4 + - - +
299Z GLY* 4.0 2.9 - - - +
300Z ARG* 2.3 40.9 + - - +
340Z MET* 5.9 7.3 - - + +
785Z ARG* 5.6 10.5 - - + -
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Residues in contact with MET 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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269Z ALA* 6.0 5.8 - - + -
281Z ILE* 5.5 5.8 - - + -
293Z GLN 2.6 21.9 + - - +
294Z MET* 3.2 12.1 - - + +
296Z PHE* 1.3 74.0 - - - +
298Z LEU* 1.3 61.5 + - - +
300Z ARG* 3.5 11.9 + - - +
301Z HIS* 3.5 10.6 + - - +
785Z ARG 5.6 5.6 - - - +
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Residues in contact with LEU 298 (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* 5.5 0.9 - - - +
278Z VAL* 4.1 33.4 - - + +
294Z MET 2.4 30.1 + - - +
295Z ALA* 3.6 6.1 - - - +
297Z MET* 1.3 67.7 - - - +
299Z GLY* 1.3 50.4 + - - +
301Z HIS* 2.7 34.1 + - - +
312Z GLU* 4.6 3.0 - - - +
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Residues in contact with GLY 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 ALA 2.5 20.0 + - - -
296Z PHE* 3.2 5.8 - - - -
298Z LEU* 1.3 68.7 - - - +
300Z ARG* 1.3 64.3 + - - +
301Z HIS 3.0 9.2 - - - +
309Z GLU* 2.9 24.3 + - - -
312Z GLU* 3.8 18.9 - - - +
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Residues in contact with ARG 300 (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 PHE* 2.3 31.7 + - + +
297Z MET* 3.8 8.3 - - - +
298Z LEU 3.4 0.2 - - - -
299Z GLY* 1.3 67.6 - - - +
301Z HIS* 1.3 56.8 + - - +
309Z GLU 4.2 7.0 + - - +
785Z ARG* 5.2 6.7 - - + +
787Z LEU* 2.8 37.9 - - + +
788Z MET 4.1 15.1 - - - +
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Residues in contact with HIS 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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273Z ASN 5.9 0.9 - - - +
274Z ASP 3.4 26.7 - - - +
275Z MET* 3.7 18.3 - - + +
297Z MET 3.5 7.8 + - - +
298Z LEU* 2.7 25.6 + - - +
299Z GLY 3.0 14.3 - - - +
300Z ARG* 1.3 76.9 - - - +
309Z GLU 4.0 7.9 - - - -
310Z ASP* 6.0 0.4 - - - -
311Z VAL* 2.8 36.7 - - + +
312Z GLU 3.9 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