Contacts of the helix formed by residues 293 - 303 (chain Z) in PDB entry 5JPQ
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 GLN 293 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136Z GLY 4.7 16.8 - - - +
137Z LEU* 5.7 3.6 - - - +
140Z VAL* 4.8 12.8 - - + +
255Z SER 5.7 3.6 - - - +
289Z VAL* 4.0 15.7 - - + -
290Z GLY 3.2 10.9 + - - +
292Z ASN* 1.4 76.6 - - - +
294Z LEU* 1.3 64.6 + - - +
295Z PRO 3.5 1.8 - - - -
296Z LEU* 3.4 11.0 + - - +
297Z ALA* 3.1 22.4 + - - +
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Residues in contact with LEU 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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289Z VAL* 4.6 4.9 - - + +
290Z GLY 3.1 15.4 + - - +
291Z ARG* 3.6 12.9 + - - +
293Z GLN* 1.3 75.7 - - - +
295Z PRO* 1.4 57.9 - - - +
297Z ALA* 3.2 8.0 + - - +
298Z ILE* 2.8 31.5 + - - +
317Z GLN* 5.8 7.4 - - + -
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Residues in contact with PRO 295 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291Z ARG 4.5 3.4 - - - -
292Z ASN 5.2 3.1 - - - +
293Z GLN 3.5 0.8 - - - -
294Z LEU* 1.4 74.7 - - - +
296Z LEU* 1.3 57.3 + - - +
298Z ILE* 3.4 6.9 + - + +
299Z VAL* 2.9 30.3 + - - +
325Z LEU* 5.5 12.6 - - + -
85a LEU* 5.8 8.3 - - + -
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Residues in contact with LEU 296 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137Z LEU* 5.9 8.5 - - + +
140Z VAL* 5.8 6.1 - - + -
293Z GLN* 3.4 13.3 + - - +
294Z LEU 3.3 0.4 - - - -
295Z PRO* 1.3 74.8 - - - +
297Z ALA* 1.3 60.1 + - - +
299Z VAL* 3.3 4.7 + - - +
300Z TYR* 2.9 31.1 + - - +
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Residues in contact with ALA 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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140Z VAL* 5.7 8.6 - - + +
289Z VAL* 5.2 9.4 - - + -
293Z GLN 3.1 13.9 + - - +
294Z LEU* 3.6 11.4 - - - +
296Z LEU* 1.3 74.9 - - - +
298Z ILE* 1.4 61.4 + - - +
300Z TYR* 3.3 7.6 + - - +
301Z MET* 3.1 22.5 + - - +
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Residues in contact with ILE 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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294Z LEU 2.8 20.5 + - - +
295Z PRO* 3.8 7.2 - - + +
297Z ALA* 1.4 71.5 - - - +
299Z VAL* 1.3 63.7 + - - +
301Z MET* 3.2 8.1 + - - +
302Z VAL* 3.1 20.7 + - - +
325Z LEU* 6.4 2.2 - - + -
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Residues in contact with VAL 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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105Z TYR* 6.1 5.8 - - + -
295Z PRO 2.9 17.2 + - - +
296Z LEU* 4.0 4.7 - - - +
298Z ILE* 1.3 75.9 - - - +
300Z TYR* 1.3 63.1 + - - +
302Z VAL* 3.1 18.9 + - - +
303Z ILE* 3.1 15.8 + - - +
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Residues in contact with TYR 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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144Z PHE* 4.7 11.9 - - + -
177Z PRO* 3.5 31.2 - - + +
178Z ILE 5.0 1.4 - - - +
296Z LEU 2.9 18.2 + - - +
297Z ALA* 3.7 7.4 - - - +
299Z VAL* 1.3 75.3 - - - +
301Z MET* 1.4 59.4 + - - +
303Z ILE* 3.6 4.8 + - - +
304Z GLY* 3.3 15.9 + - - -
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Residues in contact with MET 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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178Z ILE 5.7 2.7 - - - -
179Z THR* 6.5 0.4 - - - +
180Z MET* 4.8 19.1 - - + +
297Z ALA 3.1 13.5 + - - +
298Z ILE* 3.7 8.1 - - - +
299Z VAL 3.2 0.2 - - - -
300Z TYR* 1.4 72.6 - - - +
302Z VAL* 1.3 65.9 - - - +
303Z ILE 3.2 0.2 - - - -
304Z GLY* 3.3 10.1 + - - +
309Z GLY* 5.5 5.6 - - - -
354Z ILE* 4.2 22.0 - - + +
355Z LYS 4.6 0.7 - - - -
356Z GLY* 3.4 15.4 + - - -
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Residues in contact with VAL 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 ILE 3.1 12.2 + - - +
299Z VAL* 3.1 12.9 + - - +
301Z MET* 1.3 74.9 - - - +
303Z ILE* 1.4 53.5 + - + +
329Z ILE* 5.6 10.1 - - + -
333Z PHE* 5.6 6.7 - - + -
335Z THR* 5.1 14.8 - - - -
354Z ILE* 5.0 5.7 - - + +
355Z LYS 4.4 4.3 - - - +
356Z GLY* 3.5 1.7 - - - -
357Z ILE* 2.8 37.5 + - - +
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Residues in contact with ILE 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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26Z LEU* 5.6 11.0 - - + -
176Z GLN* 3.4 18.3 - - - +
177Z PRO* 5.1 2.0 - - + -
299Z VAL 3.1 14.1 + - - +
300Z TYR* 3.6 6.3 + - - +
301Z MET 3.2 0.2 - - - -
302Z VAL* 1.4 75.7 - - + +
304Z GLY* 1.3 64.9 + - - +
357Z ILE* 4.6 5.6 - - - +
358Z GLY 5.1 0.8 + - - -
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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