Contacts of the helix formed by residues 401 - 411 (chain A) in PDB entry 1CWS
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 ILE 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A LEU* 4.2 14.1 - - + -
389A GLN 3.8 17.7 - - - +
390A THR* 4.5 0.2 - - + -
391A VAL* 4.0 6.3 - - - -
400A TYR* 1.3 75.9 - - - +
402A SER* 1.3 62.2 + - - +
405A THR* 4.1 12.6 - - + -
406A MET* 4.1 32.1 - - + +
409A LEU* 4.9 2.0 - - + -
470A ILE* 4.3 25.8 - - + -
506A TYR* 3.4 39.0 - - + -
507A ILE 2.9 14.3 + - - +
508A LEU* 3.7 7.6 - - + -
509A LYS* 2.9 26.5 + - - +
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Residues in contact with SER 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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389A GLN 5.2 0.4 + - - -
391A VAL* 4.1 22.3 - - - +
401A ILE* 1.3 76.5 - - - +
403A PRO* 1.3 77.7 - - - +
404A GLU* 3.4 11.0 + - - +
405A THR* 2.9 34.1 + - - -
406A MET 3.1 8.1 + - - -
508A LEU* 3.9 5.1 - - - +
509A LYS* 4.9 2.0 - - - -
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Residues in contact with PRO 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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402A SER* 1.3 88.1 - - - +
404A GLU* 1.3 56.1 + - - +
406A MET* 2.9 18.2 + - - +
407A VAL* 2.9 13.5 + - - +
508A LEU* 3.9 7.8 - - + -
509A LYS* 4.3 18.2 - - + +
514A GLU* 4.5 12.3 - - + +
515A PHE* 3.7 36.3 - - + +
518A GLN* 4.3 23.8 - - - +
519A HIS* 4.3 13.7 - - + +
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Residues in contact with GLU 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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402A SER* 3.1 10.0 + - - +
403A PRO* 1.3 81.5 - - - +
405A THR* 1.3 57.6 + - - +
407A VAL* 3.3 6.4 + - + +
408A ALA* 3.0 25.6 + - - +
518A GLN* 6.0 0.2 - - - +
519A HIS* 4.6 15.2 + - + +
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Residues in contact with THR 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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388A LEU* 4.0 42.6 - - + -
389A GLN* 4.1 17.5 + - - +
401A ILE* 4.1 15.3 - - + -
402A SER* 2.9 21.1 + - - -
404A GLU* 1.3 76.7 - - - +
406A MET* 1.3 66.1 + - - +
408A ALA* 3.1 7.5 + - - +
409A LEU* 3.1 21.7 + - - +
414A PHE* 5.1 5.8 - - + -
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Residues in contact with MET 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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401A ILE* 4.1 10.2 - - + +
402A SER 3.1 7.3 + - - +
403A PRO 2.9 12.0 + - - +
405A THR* 1.3 78.4 - - - +
407A VAL* 1.3 62.5 + - - +
409A LEU* 3.3 9.9 + - + -
410A LEU* 3.0 29.9 + - + +
421A PHE* 3.9 19.3 - - + -
423A ILE* 3.3 42.6 - - + -
437A ILE* 4.6 9.9 - - + -
470A ILE* 4.4 21.3 - - + -
508A LEU* 4.2 11.9 - - + -
515A PHE* 3.8 22.2 - - + -
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Residues in contact with VAL 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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403A PRO 2.9 14.0 + - - +
404A GLU* 3.7 9.0 - - + +
406A MET* 1.3 75.8 - - - +
408A ALA* 1.3 64.1 + - - +
410A LEU* 4.3 5.6 - - - +
411A THR* 2.9 42.8 + - + +
515A PHE* 4.0 12.6 - - + -
519A HIS* 3.6 43.1 - - + +
522A PHE* 4.0 20.4 - - + -
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Residues in contact with ALA 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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404A GLU 3.0 13.5 + - - +
405A THR* 3.1 13.2 + - - +
407A VAL* 1.3 77.7 - - - +
409A LEU* 1.3 61.2 + - - +
411A THR* 3.3 8.9 + - - -
413A LYS* 2.8 46.3 + - + +
414A PHE* 3.9 17.9 - - + -
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Residues in contact with LEU 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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388A LEU* 3.9 28.7 - - + -
401A ILE* 4.9 2.0 - - + -
405A THR 3.1 15.6 + - - +
406A MET* 3.6 16.4 - - + +
408A ALA* 1.3 78.3 - - - +
410A LEU* 1.3 61.6 + - - +
412A GLY* 3.1 13.2 + - - -
413A LYS 4.8 0.4 - - - +
414A PHE* 4.0 24.7 - - + +
418A VAL* 4.3 20.6 - - + -
421A PHE* 3.6 44.7 - - + -
468A ILE* 5.0 2.5 - - + -
470A ILE* 4.1 25.8 - - + -
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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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406A MET* 3.0 37.8 + - + +
407A VAL* 3.2 5.6 + - - +
409A LEU* 1.3 78.1 - - - +
411A THR* 1.3 59.6 + - - +
412A GLY 3.2 1.1 + - - -
421A PHE* 4.1 15.5 - - + -
423A ILE* 4.2 2.5 - - + -
437A ILE* 3.8 24.2 - - + -
438A LYS* 3.6 24.2 - - + +
439A THR* 3.9 15.5 - - + +
515A PHE* 4.6 4.0 - - + -
522A PHE* 4.1 30.3 - - + +
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Residues in contact with THR 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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407A VAL* 2.9 37.5 + - + +
408A ALA* 3.3 8.5 + - - -
410A LEU* 1.3 76.0 - - - +
412A GLY* 1.3 59.8 + - - +
413A LYS* 3.5 26.5 + - - +
522A PHE* 3.9 20.6 - - + -
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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