Contacts of the helix formed by residues 356 - 365 (chain A) in PDB entry 5A19
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 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLU* 3.5 37.9 + - - +
129A ASP* 2.9 38.3 + - - +
325A SER* 3.5 21.1 - - - +
326A HIS* 3.5 36.2 + - - +
354A ASP* 2.7 37.2 + - - +
355A LEU* 1.3 79.6 - - - +
357A PRO* 1.4 74.5 - - + +
359A VAL* 3.1 17.5 + - + +
360A ILE* 3.0 20.9 + - - +
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Residues in contact with PRO 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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130A ILE* 3.6 23.1 - - + +
131A GLY 4.1 2.2 - - - +
132A ALA* 4.0 20.4 - - - +
287A TYR* 3.8 22.0 - - + +
288A THR* 4.8 4.3 - - - -
290A VAL* 4.2 14.1 - - + -
293A SER* 4.7 3.1 + - - +
320A TYR* 4.4 8.3 - - + -
325A SER 3.3 16.2 - - - +
355A LEU 3.8 3.1 - - - +
356A ARG* 1.4 85.6 - - + +
358A GLY* 1.3 57.0 + - - +
360A ILE* 3.9 11.2 - - + +
361A VAL* 3.0 31.2 + - - +
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Residues in contact with GLY 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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127A GLU 3.5 15.2 - - - +
128A GLU* 3.4 29.0 + - - -
130A ILE* 3.6 11.4 - - - +
287A TYR* 4.6 0.7 - - - -
356A ARG 3.3 1.4 - - - -
357A PRO* 1.3 78.1 - - - +
359A VAL* 1.3 58.4 + - - +
361A VAL* 3.2 21.1 - - - +
362A ARG* 4.0 11.1 + - - +
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 3.6 32.8 - - + +
354A ASP* 3.4 44.9 - - + +
356A ARG* 3.1 12.4 + - - +
358A GLY* 1.3 76.6 - - - +
360A ILE* 1.3 65.8 + - - +
361A VAL 3.1 1.8 - - - -
362A ARG* 3.0 25.9 + - - +
363A ASP* 3.0 38.2 + - - +
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Residues in contact with ILE 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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290A VAL* 5.7 0.4 - - + -
293A SER* 3.6 22.4 - - - +
294A ALA* 4.3 6.3 - - + +
297A ALA* 3.9 23.6 - - + -
300A TRP* 6.0 2.9 - - + -
320A TYR* 4.2 7.4 - - + +
354A ASP 4.1 11.0 + - - +
355A LEU* 3.5 28.7 - - + +
356A ARG 3.0 16.7 + - - +
357A PRO* 3.9 8.3 - - + +
359A VAL* 1.3 76.3 - - - +
361A VAL* 1.3 58.3 + - - +
363A ASP* 4.4 7.6 - - - +
364A LEU* 2.8 56.5 + - + +
366A LEU* 3.9 10.1 - - + -
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 3.5 41.3 - - + +
357A PRO 3.0 17.1 + - - +
358A GLY* 3.2 26.7 - - - +
360A ILE* 1.3 77.1 - - - +
362A ARG* 1.3 61.2 + - + +
365A ASP* 3.0 24.3 + - - -
366A LEU* 3.1 21.5 + - + +
367A LYS* 3.7 33.8 + - + +
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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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128A GLU* 2.9 42.3 + - - +
358A GLY 4.0 14.4 + - - +
359A VAL* 3.0 28.2 + - - +
361A VAL* 1.3 76.0 - - + +
363A ASP* 1.3 71.8 + - - +
364A LEU 3.4 0.9 + - - -
365A ASP* 3.5 11.0 + - - +
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Residues in contact with ASP 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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300A TRP* 3.7 37.7 - - + -
354A ASP 4.7 6.9 + - - +
359A VAL* 3.0 35.0 + - - +
360A ILE* 3.9 5.9 + - - +
362A ARG* 1.3 84.0 + - - +
364A LEU* 1.3 65.5 + - + +
365A ASP* 5.3 0.5 - - - +
386A PRO* 4.5 5.0 - - - +
391A LYS* 5.2 5.3 + - - -
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Residues in contact with LEU 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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296A TYR* 4.1 15.0 - - + -
297A ALA* 3.9 25.6 - - + +
300A TRP* 3.8 31.9 - - + -
360A ILE* 2.8 40.9 + - + +
363A ASP* 1.3 79.8 - - + +
365A ASP* 1.3 70.4 + - - +
366A LEU* 3.3 21.0 + - + +
386A PRO* 3.4 24.9 - - + +
387A TRP* 4.1 25.6 - - + +
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Residues in contact with ASP 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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361A VAL 3.0 10.5 + - - -
362A ARG 3.5 9.1 + - - +
363A ASP 5.3 0.7 - - - +
364A LEU* 1.3 80.1 - - - +
366A LEU* 1.3 57.9 + - - +
367A LYS* 3.3 5.5 + - - +
368A LYS* 3.2 60.4 + - - +
370A ILE* 5.1 4.2 - - - +
386A PRO* 4.6 9.6 - - + -
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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