Contacts of the helix formed by residues 393 - 402 (chain A) in PDB entry 1W1J
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 SER 393 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A LEU* 5.7 0.9 - - - +
321A LEU* 5.2 3.1 - - - -
389A THR* 3.2 29.5 + - - +
390A PRO* 2.8 19.3 + - - -
391A GLU 3.2 2.6 + - - -
392A ASN* 1.3 86.8 + - - +
394A VAL* 1.3 62.2 + - - +
395A LEU* 2.8 23.2 + - - +
396A ARG* 3.2 12.2 + - - +
397A VAL* 3.2 21.7 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 3.6 15.5 - - - +
317A ASP* 3.3 37.7 - - + +
320A VAL* 3.9 33.2 - - + -
321A LEU* 4.7 10.2 - - + +
354A TYR* 3.9 10.1 - - - +
392A ASN 3.6 0.2 + - - -
393A SER* 1.3 69.6 + - - +
395A LEU* 1.3 56.7 + - - +
397A VAL* 3.2 6.2 + - + -
398A ARG* 2.7 53.0 + - + +
410A GLU* 4.6 4.9 - - - +
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Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 4.5 6.3 - - - +
279A TYR* 3.4 36.6 - - - +
280A LEU* 3.6 17.9 - - + +
354A TYR* 3.7 20.9 + - + -
384A TYR 3.2 15.0 - - - +
385A PHE 3.2 11.4 - - - +
386A PRO* 3.1 37.7 - - + -
389A THR* 4.1 8.7 - - + +
393A SER* 2.8 18.4 + - - +
394A VAL* 1.3 72.7 - - - +
396A ARG* 1.3 50.1 + - - +
398A ARG* 4.6 0.4 - - - +
399A ASP* 2.7 37.2 + - - +
402A MET* 5.2 3.4 - - + -
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Residues in contact with ARG 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PRO* 2.8 37.0 + - + +
387A GLU* 3.0 28.5 + - - +
389A THR* 2.9 26.3 + - - -
390A PRO 3.9 5.1 + - - -
391A GLU* 3.6 28.0 - - - +
393A SER* 3.2 14.7 + - - +
394A VAL 3.1 0.8 - - - -
395A LEU* 1.3 75.1 - - - +
397A VAL* 1.3 68.0 + - + +
399A ASP* 3.4 11.6 + - + +
400A LYS* 3.4 29.7 + - - +
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 5.5 5.2 - - + -
392A ASN 4.8 5.4 - - - +
393A SER 3.2 14.0 + - - +
394A VAL* 3.6 10.8 - - + +
396A ARG* 1.3 76.3 - - + +
398A ARG* 1.3 65.3 + - - +
400A LYS* 3.0 28.4 + - - +
401A THR* 3.2 7.4 + - - +
407A THR* 4.5 14.2 + - - +
409A ASP* 3.6 44.4 - - + +
410A GLU* 4.0 25.1 - - + +
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Residues in contact with ARG 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASP* 2.7 29.7 + - - +
187A TYR* 3.1 37.4 - - - +
310A THR* 3.8 19.2 + - - +
312A ARG* 3.1 30.7 - - - +
354A TYR* 4.2 20.1 - - + +
394A VAL* 2.7 32.5 + - + +
395A LEU 4.3 1.6 - - - +
397A VAL* 1.3 73.6 - - - +
399A ASP* 1.3 54.0 + - - +
401A THR* 2.6 32.2 + - - +
402A MET* 2.9 33.8 + - + +
410A GLU* 2.5 39.8 + - - +
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Residues in contact with ASP 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TYR* 2.9 29.5 + - - -
277A GLN* 5.0 1.6 + - - -
278A SER* 2.5 37.0 + - - +
386A PRO* 3.4 20.0 - - + +
395A LEU 2.7 23.5 + - - +
396A ARG* 3.8 6.1 - - - +
397A VAL 3.2 0.4 - - - -
398A ARG* 1.3 72.4 - - - +
400A LYS* 1.3 63.2 + - - +
402A MET* 4.7 0.6 - - - +
403A GLN* 3.2 20.3 + - - +
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Residues in contact with LYS 400 (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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396A ARG* 3.4 27.0 + - - +
397A VAL* 3.0 12.3 + - - +
399A ASP* 1.3 83.8 - - - +
401A THR* 1.3 61.9 + - - +
402A MET 3.3 0.2 - - - -
403A GLN* 3.2 17.2 + - - +
405A ILE* 3.0 47.7 + - + -
407A THR* 4.2 22.0 - - + -
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Residues in contact with THR 401 (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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168A VAL* 3.4 23.7 - - + +
169A PRO 4.2 7.2 + - - +
170A ASP* 4.7 8.3 + - - +
187A TYR* 3.9 28.5 - - + +
188A THR* 4.3 3.6 - - - +
397A VAL* 3.2 10.1 + - - +
398A ARG* 2.6 35.1 + - - +
400A LYS* 1.3 73.0 - - - +
402A MET* 1.3 57.8 + - + +
403A GLN 2.9 5.4 + - - -
404A GLY* 3.1 11.1 + - - -
405A ILE 3.9 7.0 + - - -
407A THR* 3.2 22.0 + - - -
410A GLU* 5.1 2.4 + - - +
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Residues in contact with MET 402 (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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187A TYR* 3.6 31.2 - - + +
188A THR* 3.5 6.6 - - - +
276A TYR* 3.3 20.2 + - - +
278A SER* 3.8 16.8 - - - -
279A TYR 4.8 1.3 - - - +
307A ASN* 3.4 18.2 - - - -
308A VAL 5.2 2.2 - - - +
309A PRO* 5.4 0.4 - - - -
310A THR* 5.8 1.3 - - - -
354A TYR* 4.4 13.9 - - + +
355A GLY* 2.5 43.3 - - - +
356A ALA* 4.2 0.9 - - + -
358A TYR* 2.6 33.6 + - - +
395A LEU* 5.2 2.5 - - + -
398A ARG* 2.9 29.3 + - + +
399A ASP 4.7 0.2 - - - +
401A THR* 1.3 76.5 - - + +
403A GLN* 1.3 55.0 + - - +
404A GLY 3.6 0.7 - - - -
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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