Contacts of the helix formed by residues 383 - 395 (chain A) in PDB entry 3CVW
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 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A MET* 5.5 2.3 - - - +
330A TRP* 3.6 37.0 + - - +
331A GLN 4.8 1.0 + - - -
375A LEU* 4.0 2.8 - - - +
382A ILE* 1.3 80.0 - - - +
384A TRP* 1.3 67.0 + - - +
385A GLU* 3.1 27.1 + - - +
386A GLU* 3.3 28.0 + - - +
387A GLY 3.9 2.8 + - - -
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Residues in contact with TRP 384 (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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316A PHE 3.9 4.9 - - - -
317A ASP* 3.2 37.5 - - - -
318A ARG* 3.8 15.5 - - - -
319A MET* 4.0 5.4 - - + +
325A CYS* 3.6 26.6 - - - -
330A TRP* 4.0 15.6 - - - +
376A THR* 3.8 15.1 - - + +
382A ILE 3.6 1.6 + - - -
383A SER* 1.3 72.4 + - - +
385A GLU* 1.3 65.9 - - + +
386A GLU 3.2 0.4 - - - -
387A GLY 3.5 1.5 + - - -
388A GLN* 2.9 44.6 + - - +
404A ALA 4.2 9.6 - - - -
407A TRP* 3.7 43.4 - - + +
408A MET* 3.7 18.8 - - + -
411A SER* 3.4 20.9 - - - -
413A SER* 3.3 15.1 + - - -
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Residues in contact with GLU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASP 3.8 16.2 - - - +
318A ARG* 3.4 12.9 - - - +
319A MET* 2.6 38.2 + - - +
320A LEU* 4.6 0.7 + - - +
383A SER* 3.1 15.0 + - - +
384A TRP* 1.3 88.8 - - + +
386A GLU* 1.3 64.8 + - + +
388A GLN* 3.3 21.7 + - - +
389A ARG* 3.5 34.9 + - - +
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Residues in contact with GLU 386 (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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332A GLU* 5.0 10.0 - - - +
337A LEU* 3.3 40.0 - - + +
375A LEU* 5.1 0.2 - - + -
382A ILE* 3.9 15.0 - - + -
383A SER* 3.3 20.2 + - - +
384A TRP 3.2 0.4 - - - -
385A GLU* 1.3 77.1 - - + +
387A GLY* 1.3 64.4 + - - +
389A ARG* 2.9 50.3 + - - +
390A VAL* 3.4 17.5 + - - +
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Residues in contact with GLY 387 (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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340A TRP* 3.7 12.3 - - - -
375A LEU* 3.7 20.9 - - - +
383A SER 3.9 0.2 + - - -
384A TRP 3.5 3.0 + - - -
385A GLU 3.5 0.2 - - - -
386A GLU* 1.3 76.3 - - - +
388A GLN* 1.3 59.1 + - - +
390A VAL* 3.4 0.6 + - - +
391A PHE* 3.0 26.9 + - - -
407A TRP* 3.3 30.8 - - - -
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Residues in contact with GLN 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASP* 3.1 36.3 + - - +
384A TRP* 2.9 41.5 + - - +
385A GLU* 3.3 12.8 + - - +
386A GLU 3.1 0.2 - - - -
387A GLY* 1.3 77.9 - - - +
389A ARG* 1.3 55.0 + - + +
391A PHE 3.5 0.2 + - - -
392A GLU* 2.7 45.9 + - - +
400A TRP* 5.8 1.7 - - - -
403A ASN* 3.1 21.6 + - - +
404A ALA* 3.3 20.4 - - - +
407A TRP* 3.8 13.0 - - + +
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Residues in contact with ARG 389 (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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55A GLN* 4.3 19.7 - - + +
385A GLU* 3.5 29.5 + - - +
386A GLU* 2.9 35.3 + - - +
388A GLN* 1.3 77.6 - - + +
390A VAL* 1.3 60.7 + - + +
392A GLU* 3.2 14.3 + - - +
393A GLN* 2.9 32.4 + - - +
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 5.5 3.1 - - + -
340A TRP* 3.6 29.8 - - + -
341A THR* 3.8 36.6 - - + +
354A MET* 3.9 10.5 - - + -
386A GLU 3.4 16.1 + - - +
387A GLY 3.6 6.3 - - - +
388A GLN 3.4 0.2 - - - -
389A ARG* 1.3 78.3 - - + +
391A PHE* 1.3 63.7 + - + +
393A GLN* 3.4 7.6 + - - +
394A LEU* 3.1 43.5 + - + +
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Residues in contact with PHE 391 (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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340A TRP* 3.8 17.0 - + - -
357A LEU* 3.7 20.9 - - + -
363A ILE* 4.2 11.2 - - + -
368A ARG* 3.9 20.2 - - + -
371A VAL* 3.9 22.2 - - + -
387A GLY 3.0 20.9 + - - +
388A GLN 3.7 1.3 - - - +
390A VAL* 1.3 75.8 - - + +
392A GLU* 1.3 59.5 + - - +
394A LEU* 4.6 2.0 - - - +
395A LEU* 2.9 62.4 + - + +
403A ASN* 3.5 14.1 - - - +
407A TRP* 3.5 25.8 - + - +
521A FAD 3.7 27.6 - + + -
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Residues in contact with GLU 392 (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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53A TRP 4.0 4.8 - - - +
54A MET* 3.2 17.0 - - + -
55A GLN* 2.9 40.4 + - + +
60A ARG* 2.7 32.9 + - - -
388A GLN* 2.7 38.7 + - - +
389A ARG* 3.2 16.2 + - - +
391A PHE* 1.3 71.5 - - - +
393A GLN* 1.3 52.2 + - - +
398A GLN* 3.4 32.5 - - + +
400A TRP* 5.4 7.1 - - - -
403A ASN* 3.9 3.4 + - - +
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Residues in contact with GLN 393 (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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55A GLN* 3.7 33.1 + - + +
56A VAL 4.4 2.7 - - - -
57A GLY* 2.9 43.1 + - - +
60A ARG* 3.3 9.7 + - - +
211A ARG* 6.0 0.3 + - - -
214A GLU* 5.1 7.1 - - - +
341A THR* 6.1 2.0 - - - +
358A ARG* 4.2 15.9 + - - +
389A ARG 2.9 16.5 + - - +
390A VAL* 3.7 8.1 + - - +
391A PHE 3.2 0.2 - - - -
392A GLU* 1.3 77.6 - - - +
394A LEU* 1.3 75.0 + - + +
395A LEU 3.6 0.2 - - - -
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Residues in contact with LEU 394 (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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57A GLY* 5.4 2.5 - - - -
59A ASN* 4.7 10.3 + - - +
60A ARG* 5.6 0.7 + - - -
341A THR 4.8 3.1 - - - +
354A MET* 5.0 1.3 - - + +
357A LEU* 3.6 35.1 - - + +
358A ARG* 3.8 62.1 - - + +
361A GLY* 3.3 20.8 - - - -
390A VAL* 3.1 34.9 + - + +
393A GLN* 1.3 91.5 - - + +
395A LEU* 1.3 63.6 + - - +
396A LEU 3.7 0.2 + - - -
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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
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60A ARG* 2.9 31.2 + - - +
357A LEU* 3.7 22.7 - - + -
361A GLY 3.5 7.6 - - - +
362A TRP* 4.7 1.1 - - - -
363A ILE* 4.6 3.6 - - + -
368A ARG* 3.5 36.3 - - - +
391A PHE* 2.9 47.6 + - + +
394A LEU* 1.3 77.1 - - - +
396A LEU* 1.3 59.2 + - - +
397A ASP* 3.3 18.2 - - - +
398A GLN* 3.8 10.0 + - - +
403A ASN* 4.3 1.3 - - - +
521A FAD 3.8 18.6 - - - +
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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