Contacts of the helix formed by residues 353 - 362 (chain A) in PDB entry 1JQI
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 PRO 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A CYS* 4.4 14.4 - - + -
351A GLU 4.7 1.3 - - - +
352A MET* 1.3 91.1 - - + +
354A ALA* 1.3 65.0 + - - +
355A GLU 3.3 3.1 - - - -
356A ARG* 3.1 37.1 + - + +
357A TYR* 3.0 51.1 + - + +
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Residues in contact with ALA 354 (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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265A CYS* 4.8 4.0 - - - -
336A SER 4.6 1.7 - - - +
339A ALA* 4.7 7.4 - - + +
340A ILE* 3.8 26.3 - - + +
343A LEU* 3.8 27.4 - - + -
347A GLY* 4.2 6.5 - - - +
352A MET* 3.3 2.9 - - + -
353A PRO* 1.3 80.5 - - - +
355A GLU* 1.3 62.5 + - - +
357A TYR* 3.2 17.2 + - + +
358A TYR* 3.1 21.5 + - - +
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Residues in contact with GLU 355 (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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37A ASP* 4.7 0.3 - - - +
340A ILE* 4.0 10.3 - - - -
347A GLY 3.7 14.1 + - - +
348A TYR 4.6 3.1 - - - +
349A VAL 3.8 25.8 + - - +
350A THR* 4.0 22.9 - - + +
352A MET 4.1 6.3 + - - +
354A ALA* 1.3 76.0 - - - +
356A ARG* 1.3 72.8 + - - +
358A TYR* 3.3 3.2 + - - +
359A ARG* 2.8 66.6 + - - +
607B LEU* 3.4 32.5 - - + +
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Residues in contact with ARG 356 (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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30A VAL 5.2 2.6 + - - -
33A ALA* 3.4 39.4 + - - +
34A ALA* 3.9 17.8 - - - +
37A ASP* 3.8 20.8 + - - +
84A GLY 4.2 7.9 + - - -
85A CYS* 4.9 5.1 - - - +
86A ALA 5.5 0.8 - - - +
353A PRO* 3.1 35.8 + - + +
355A GLU* 1.3 83.0 - - - +
357A TYR* 1.3 78.1 + - - +
359A ARG* 3.2 29.0 + - - +
360A ASP* 2.8 55.0 + - - +
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Residues in contact with TYR 357 (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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83A ARG 4.9 5.9 + - - -
258A ILE* 3.6 16.9 - - + +
261A ALA* 3.5 43.2 + - + +
262A SER* 3.4 31.6 - - - +
265A CYS* 4.2 8.7 - - + +
336A SER* 3.9 3.6 - - - -
339A ALA* 5.6 0.7 - - + -
353A PRO* 3.0 47.1 + - + +
354A ALA* 3.2 15.2 + - + +
356A ARG* 1.3 100.9 + - - +
358A TYR* 1.3 57.8 + - - +
360A ASP* 3.4 4.0 + - - +
361A ALA* 2.9 32.7 + - - +
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Residues in contact with TYR 358 (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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333A THR* 4.2 7.0 + - + -
336A SER* 3.6 21.5 - - - +
337A HIS* 3.5 42.7 - + + -
340A ILE* 3.6 25.4 - - + -
354A ALA 3.1 6.1 + - - +
355A GLU 3.4 8.3 - - - +
356A ARG 3.2 0.2 - - - -
357A TYR* 1.3 77.5 - - - +
359A ARG* 1.3 63.5 + - + +
361A ALA* 3.9 2.1 - - - +
362A ARG* 3.4 21.0 + - - +
607B LEU* 4.3 13.5 - - + -
733B THR* 3.7 9.0 - - - +
758B TYR* 3.1 55.7 + + - -
759B ARG* 5.9 0.4 - - + -
762B ARG* 3.7 26.7 - - + +
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Residues in contact with ARG 359 (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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37A ASP* 2.7 36.6 + - - -
207A LEU* 2.8 63.0 + - + +
208A GLY* 4.0 2.7 - - - -
210A ARG* 3.2 23.1 - - - +
355A GLU* 2.8 48.8 + - - +
356A ARG* 3.4 14.3 - - - +
358A TYR* 1.3 77.9 - - + +
360A ASP* 1.3 58.4 + - - +
361A ALA 3.6 0.2 + - - -
362A ARG* 3.6 7.6 + - - +
607B LEU* 3.6 22.9 - - + -
748B TYR* 2.7 31.3 + - - -
758B TYR* 6.0 0.4 - - - -
759B ARG* 4.7 3.1 - - + +
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Residues in contact with ASP 360 (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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37A ASP* 4.9 2.8 - - - +
86A ALA* 3.5 33.4 + - + +
87A SER* 5.1 1.1 + - - -
208A GLY* 3.5 3.6 - - - -
209A ILE* 2.8 28.7 + - + +
258A ILE* 3.9 11.4 - - + +
356A ARG* 2.8 48.9 + - - +
357A TYR* 4.0 6.6 - - - +
359A ARG* 1.3 70.8 - - - +
361A ALA* 1.3 65.6 + - - +
363A ILE* 3.2 24.4 - - - +
364A THR* 4.2 0.3 - - - +
748B TYR* 3.9 4.0 - - - -
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Residues in contact with ALA 361 (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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258A ILE* 3.9 14.3 - - + +
332A ALA* 3.8 26.5 - - + +
333A THR* 3.9 8.2 + - - +
336A SER* 3.7 17.5 - - - +
357A TYR 2.9 19.5 + - - +
358A TYR 3.9 2.2 - - - +
360A ASP* 1.3 78.1 - - - +
362A ARG* 1.3 62.5 + - - +
364A THR* 2.7 27.6 + - - -
365A GLU 4.1 0.9 + - - -
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Residues in contact with ARG 362 (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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207A LEU* 4.5 3.6 - - + -
333A THR* 4.0 6.0 + - - -
358A TYR 3.4 10.5 + - - +
359A ARG 3.8 11.2 - - - +
360A ASP 3.3 1.0 - - - -
361A ALA* 1.3 78.5 - - - +
363A ILE* 1.3 59.3 + - - +
364A THR 3.5 0.2 + - - -
365A GLU* 3.4 19.5 + - - +
366A ILE* 3.7 11.5 - - - +
737B HIS* 2.8 51.7 + - - -
740B ILE* 3.5 21.9 - - + +
741B GLN* 2.9 42.2 + - - +
748B TYR* 3.9 14.4 - - + -
758B TYR* 3.7 33.6 - - + +
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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