Contacts of the helix formed by residues 283 - 289 (chain A) in PDB entry 1JQP
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 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A PRO 3.2 6.9 + - - -
279A TYR 3.3 8.3 - - - -
281A ILE 3.0 1.0 - - - -
282A ALA* 1.3 79.9 - - - +
284A LYS* 1.3 59.2 + - - -
285A TYR 3.4 0.4 - - - -
286A ALA* 3.3 2.6 + - - +
287A GLN* 2.9 28.9 + - - +
317A SER* 4.0 0.7 - - - -
320A TYR* 3.3 33.4 - - - -
430A MET* 3.6 1.7 - - - +
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU* 3.0 22.7 + - - +
76A LYS* 4.2 13.5 + - - +
78A PHE* 3.4 34.4 - - + +
101A TRP* 5.2 4.0 - - - -
103A HIS* 3.7 14.6 + - - -
269A TYR* 3.6 14.4 - - + -
279A TYR* 3.0 10.1 + - + +
280A LEU* 3.7 35.6 + - + +
283A GLY* 1.3 69.9 - - - -
285A TYR* 1.3 57.5 + - - +
287A GLN* 3.3 0.7 + - - +
288A ASP* 2.9 55.1 + - - +
320A TYR* 3.7 23.2 + - + +
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Residues in contact with TYR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A GLU* 2.6 40.8 + - - -
263A VAL* 4.6 6.7 - - + -
266A CYS* 3.9 10.0 + - - +
267A SER* 3.1 39.5 - - - -
268A PRO* 3.8 5.4 - - + -
269A TYR* 3.6 14.1 - + + -
280A LEU 2.7 23.9 + - - +
281A ILE* 3.6 13.2 - - + +
283A GLY 3.4 0.4 - - - -
284A LYS* 1.3 72.7 - - - +
286A ALA* 1.3 58.6 + - - +
289A PHE* 2.9 58.8 + + + +
290A GLY 2.9 18.7 + - - -
291A VAL* 3.9 15.5 - - + -
314A ARG* 3.7 5.2 + - - -
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A LEU* 4.2 15.3 - - + -
281A ILE 2.9 12.3 + - - +
282A ALA 3.3 24.5 - - - +
283A GLY 3.3 0.4 + - - -
285A TYR* 1.3 74.8 - - - +
287A GLN* 1.3 63.4 + - - +
290A GLY* 3.1 28.2 + - - -
291A VAL* 4.4 6.7 - - + -
315A TYR 4.7 2.0 - - - +
316A TYR* 3.1 15.2 - - - -
317A SER* 3.3 16.6 - - - +
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Residues in contact with GLN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LYS* 2.7 35.1 + - - +
103A HIS* 5.1 1.4 - - + -
105A VAL 4.7 10.7 + - - +
283A GLY 2.9 16.9 + - - +
284A LYS 3.7 3.4 - - - +
286A ALA* 1.3 77.8 - - - +
288A ASP* 1.3 67.3 + - - +
316A TYR* 3.2 19.2 - - - +
317A SER 3.2 24.5 + - - +
318A SER* 3.2 27.5 + - - +
319A GLU* 4.4 1.2 + - - +
320A TYR* 3.3 19.5 + - + -
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Residues in contact with ASP 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 2.9 31.8 + - - +
103A HIS* 2.8 39.2 + - - -
107A GLY* 5.7 1.7 - - - -
110A TRP* 3.5 18.1 - - + -
269A TYR* 3.0 18.1 + - - +
284A LYS* 2.9 32.1 + - - +
287A GLN* 1.3 87.8 - - - +
289A PHE* 1.3 70.6 + - + +
316A TYR* 3.9 1.2 - - - -
320A TYR* 5.2 0.2 + - - -
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 4.0 32.9 + - + +
28A ILE* 4.4 9.0 - - + -
101A TRP* 5.7 3.1 - + - -
110A TRP* 3.6 27.6 - + - -
268A PRO* 4.9 10.8 - - + -
269A TYR* 3.6 27.1 - + - -
285A TYR* 2.9 48.5 + + + +
288A ASP* 1.3 79.3 - - + +
290A GLY* 1.3 56.7 + - - +
314A ARG* 2.7 36.4 + - - +
316A TYR* 3.5 9.4 + - - -
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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