Contacts of the helix formed by residues 357 - 365 (chain A) in PDB entry 1QM4
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 ARG 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLU* 3.1 45.6 + - - +
130A ASP* 2.8 32.5 + - - -
326A ALA* 3.5 21.5 - - + +
327A GLU* 3.5 38.1 + - - +
328A PRO* 4.1 0.2 - - - +
355A ASP* 2.9 35.7 + - - +
356A LEU* 1.3 76.7 - - - +
358A PRO* 1.3 72.1 - - + +
359A GLY 3.3 0.2 - - - -
360A VAL* 3.1 11.6 + - + +
361A ILE* 2.9 19.9 + - - +
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Residues in contact with PRO 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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131A VAL* 5.3 2.9 - - + -
132A GLY 5.0 6.7 - - - +
133A ALA* 4.1 18.4 - - + +
289A THR 6.0 1.8 - - - +
291A VAL* 4.0 22.0 - - + -
294A SER* 5.3 5.0 - - - -
321A TYR* 3.8 19.5 - - + -
326A ALA* 3.1 22.9 - - + +
356A LEU 3.5 0.6 - - - -
357A ARG* 1.3 81.7 - - + +
359A GLY* 1.3 62.3 + - - +
361A ILE* 3.1 18.9 + - + +
362A VAL* 3.1 22.1 + - - +
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Residues in contact with GLY 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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129A GLU* 3.9 22.4 + - - -
131A VAL* 4.0 20.3 - - - +
357A ARG 3.3 1.2 - - - -
358A PRO* 1.3 75.8 - - - +
360A VAL* 1.3 65.4 + - - +
362A VAL* 3.6 10.9 + - - +
363A ARG* 3.2 22.0 + - - +
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Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 3.6 15.5 - - + +
355A ASP* 3.0 50.7 - - + +
357A ARG* 3.1 27.5 + - + +
359A GLY* 1.3 73.1 - - - +
361A ILE* 1.3 61.4 + - - +
363A ARG* 3.2 23.9 + - - +
364A ASP* 2.8 46.3 + - - +
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Residues in contact with ILE 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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294A SER* 3.7 25.4 - - - +
295A ALA* 4.2 8.3 - - + +
298A ALA* 3.3 24.9 - - + -
301A TRP* 6.0 3.8 - - + -
321A TYR* 3.4 10.8 - - - +
355A ASP 4.3 1.6 - - - +
356A LEU* 3.3 36.6 - - + +
357A ARG 2.9 15.0 + - - +
358A PRO* 3.1 11.0 + - + +
360A VAL* 1.3 75.4 - - - +
362A VAL* 1.3 63.7 + - - +
364A ASP* 4.9 2.7 - - - -
365A LEU* 2.9 42.8 + - + +
367A LEU* 4.0 8.1 - - + -
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A TYR* 4.0 41.1 - - + +
289A THR* 5.8 1.8 - - + -
294A SER* 4.6 4.3 - - - +
358A PRO* 3.1 19.3 + - + +
359A GLY* 4.0 10.3 - - - +
361A ILE* 1.3 74.7 - - - +
363A ARG* 1.3 64.2 + - + +
366A ASP* 3.1 3.6 + - - -
367A LEU* 2.9 46.9 + - + -
368A LYS* 4.4 20.0 - - + +
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Residues in contact with ARG 363 (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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129A GLU* 2.8 50.5 + - - +
359A GLY 3.2 18.4 + - - +
360A VAL* 3.6 19.0 - - - +
362A VAL* 1.3 82.6 - - + +
364A ASP* 1.3 80.0 + - - +
366A ASP* 3.5 9.6 + - - +
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Residues in contact with ASP 364 (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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301A TRP* 4.2 28.0 - - + -
355A ASP* 5.2 4.7 + - - +
360A VAL* 2.8 34.8 + - - +
361A ILE* 4.1 2.7 - - - +
363A ARG* 1.3 95.3 + - - +
365A LEU* 1.3 64.0 + - - +
366A ASP* 3.3 3.0 + - - +
387A PRO* 5.3 0.9 - - - +
392A LYS* 4.7 9.0 + - - -
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Residues in contact with LEU 365 (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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297A TYR* 4.5 2.0 - - + -
298A ALA* 4.1 16.4 - - - +
301A TRP* 3.7 51.6 - - + -
361A ILE* 2.9 39.2 + - + +
364A ASP* 1.3 78.1 - - + +
366A ASP* 1.3 71.3 + - - +
367A LEU* 3.3 23.0 + - + +
387A PRO* 3.1 31.9 - - + +
388A TRP* 4.2 23.3 - - + -
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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