Contacts of the helix formed by residues 399 - 411 (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 ASP 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LYS* 4.1 5.2 + - - -
112A GLU* 4.6 1.8 - - - +
139A HIS* 4.3 3.6 + - - -
266A LYS* 4.4 14.9 - - + +
303A ARG* 5.1 2.3 + - - -
307A TYR* 2.7 33.3 + - - -
397A ASP 2.8 4.8 + - - +
398A GLN* 1.3 75.3 - - - +
400A TRP* 1.3 61.3 + - - +
401A ALA 3.3 13.2 + - - -
402A LEU* 3.1 29.2 + - + +
403A ASN* 2.6 35.3 + - - +
521A FAD 2.9 20.7 + - + +
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Residues in contact with TRP 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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53A TRP* 3.5 22.1 - + + +
54A MET* 5.8 1.7 - - + +
111A ILE* 3.9 13.2 - - + -
112A GLU* 3.5 40.5 + - + +
113A PRO* 3.5 33.7 - - + -
310A ALA* 3.7 28.9 - - + -
313A GLU 3.9 4.3 - - - -
314A PRO* 3.9 8.5 - - + -
316A PHE* 3.7 31.6 - - + -
317A ASP* 2.8 34.7 + - + +
388A GLN* 5.8 2.1 - - - -
392A GLU* 5.4 7.4 - - - -
398A GLN* 3.5 15.4 + - - +
399A ASP* 1.3 74.0 + - - +
401A ALA* 1.3 75.3 + - + +
403A ASN* 4.2 2.3 - - - +
404A ALA* 3.3 24.4 + - - +
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Residues in contact with ALA 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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111A ILE* 4.4 4.9 - - + -
112A GLU* 4.9 0.4 + - + -
306A TYR* 3.9 14.4 - - - +
307A TYR* 4.3 11.0 - - + -
310A ALA* 3.8 22.2 - - + -
316A PHE* 3.2 14.3 - - - -
399A ASP* 3.2 10.0 + - - +
400A TRP* 1.3 86.2 - - + +
402A LEU* 1.3 67.6 + - + +
405A GLY* 3.0 24.9 + - - -
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Residues in contact with LEU 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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303A ARG* 3.8 25.6 - - + +
306A TYR* 4.2 9.9 - - + -
307A TYR* 3.6 27.1 - - + -
399A ASP* 3.1 27.4 + - + +
401A ALA* 1.3 78.6 - - - +
403A ASN* 1.3 66.2 + - - +
406A ASN* 2.7 36.1 + - - +
521A FAD 3.3 69.5 - - + +
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Residues in contact with ASN 403 (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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388A GLN* 3.1 37.3 + - + +
391A PHE* 3.5 7.8 - - - +
392A GLU* 3.9 17.4 + - - +
395A LEU* 4.7 1.6 - - - -
398A GLN* 4.6 4.4 + - - +
399A ASP 2.6 24.4 + - - +
400A TRP* 4.2 2.9 - - - +
402A LEU* 1.3 74.3 - - - +
404A ALA* 1.3 61.3 + - - +
407A TRP* 2.9 54.4 + - - -
521A FAD 3.3 30.3 + - - +
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Residues in contact with ALA 404 (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* 3.6 30.3 - - + +
317A ASP* 3.9 7.6 - - + -
384A TRP* 4.2 1.9 - - + -
388A GLN* 3.3 24.6 + - - +
400A TRP 3.3 17.6 + - - +
403A ASN* 1.3 78.8 - - - +
405A GLY* 1.3 63.1 + - - +
407A TRP* 3.4 4.8 + - - +
408A MET* 3.1 28.5 + - - +
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Residues in contact with GLY 405 (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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306A TYR* 3.5 33.9 - - - -
316A PHE* 3.4 13.4 - - - -
401A ALA 3.0 14.3 + - - -
404A ALA* 1.3 77.4 - - - +
406A ASN* 1.3 56.2 + - - +
408A MET* 3.2 9.8 + - - +
409A TRP* 3.0 22.9 + - - +
415A PHE* 4.1 2.9 - - - -
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Residues in contact with ASN 406 (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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306A TYR* 3.2 21.1 + - - -
369A HIS* 5.7 0.3 + - - -
402A LEU 2.7 27.8 + - - +
405A GLY* 1.3 72.6 - - - +
407A TRP* 1.3 60.3 + - - +
409A TRP* 3.3 6.6 + - + +
410A LEU* 3.1 35.1 + - + +
521A FAD 3.3 83.8 + - + +
8C 64T 4.6 5.5 + - - +
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Residues in contact with TRP 407 (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 20.0 - + - -
372A ALA* 3.5 39.0 - - + -
375A LEU* 3.7 19.7 - - + -
376A THR* 4.0 4.9 - - + -
384A TRP* 3.7 40.4 - - + +
387A GLY* 3.3 25.7 + - - -
388A GLN* 3.8 8.0 - - + +
391A PHE* 3.5 27.5 - + - -
403A ASN* 2.9 49.6 + - - +
404A ALA* 3.6 5.4 - - - +
405A GLY 3.3 0.2 - - - -
406A ASN* 1.3 76.0 - - - +
408A MET* 1.3 53.1 + - - +
410A LEU* 3.6 1.1 + - - -
411A SER* 2.7 37.6 + - - -
521A FAD 3.5 17.6 - - + +
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Residues in contact with MET 408 (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* 3.4 54.5 - - + +
322A ASN* 3.7 20.9 - - - +
324A TYR* 4.9 1.3 - - + -
325A CYS* 3.8 16.6 - - - -
384A TRP* 3.7 23.3 - - + -
404A ALA 3.1 16.8 + - - +
405A GLY* 3.2 7.6 + - - +
407A TRP* 1.3 73.9 - - - +
409A TRP* 1.3 64.4 + - - +
411A SER* 3.4 5.6 - - - -
412A ALA 3.1 1.2 + - - -
413A SER* 2.7 32.8 + - - -
414A ALA* 3.2 28.2 + - + +
415A PHE* 4.3 5.6 - - + -
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Residues in contact with TRP 409 (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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302A TRP* 3.7 26.7 - + - -
305A PHE* 5.3 0.7 - + - -
306A TYR* 3.2 23.6 - - - +
369A HIS* 4.6 1.8 - + - -
405A GLY 3.0 12.8 + - - +
406A ASN* 3.4 11.9 - - - +
407A TRP 3.3 0.4 - - - -
408A MET* 1.3 78.2 - - - +
410A LEU* 1.3 77.0 + - + +
412A ALA 3.1 13.2 + - - -
414A ALA 3.7 8.0 + - - -
415A PHE* 3.6 32.8 - - + -
416A PHE* 3.2 53.7 - + + +
7C G 4.8 0.7 - - - -
8C 64T 3.2 38.1 - - + -
9C 5PY 3.2 35.4 - - + +
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Residues in contact with LEU 410 (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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369A HIS* 3.5 67.5 - - + +
372A ALA* 3.8 27.4 - - + -
373A CYS* 4.3 6.8 - - + +
376A THR* 3.9 3.5 + - - -
377A ARG* 2.7 38.0 + - - +
406A ASN* 3.1 20.4 + - + +
407A TRP* 4.3 2.2 - - + +
409A TRP* 1.3 86.7 - - + +
411A SER* 1.3 53.7 + - - +
412A ALA 3.2 4.7 - - - -
423A TYR* 3.7 16.8 - - + -
521A FAD 3.7 6.7 - - + -
8C 64T 5.5 0.2 - - - +
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Residues in contact with SER 411 (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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328A ILE* 4.2 0.7 - - - +
330A TRP* 4.0 9.6 - - - -
376A THR* 3.6 32.3 + - - -
377A ARG* 3.8 9.1 - - - +
384A TRP* 3.4 12.9 - - - -
407A TRP 2.7 22.5 + - - -
408A MET* 3.4 4.7 - - - -
410A LEU* 1.3 75.4 - - - +
412A ALA* 1.3 67.9 + - - +
413A SER* 2.9 24.8 + - - -
494A MET* 3.6 12.6 - - - +
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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