Contacts of the helix formed by residues 403 - 416 (chain A) in PDB entry 5IWI
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 THR 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A SER* 3.6 8.3 - - - -
402A ASP* 1.3 95.1 + - - +
404A ASP* 1.3 62.4 + - - +
405A LYS* 3.3 11.5 + - - +
406A VAL* 3.0 26.7 + - + +
407A ALA* 3.0 19.9 + - - +
434C THR* 4.0 6.7 - - - +
436C LEU* 3.7 26.9 - - + -
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Residues in contact with ASP 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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403A THR* 1.3 74.2 - - - +
405A LYS* 1.3 65.0 + - - +
407A ALA* 3.8 6.3 - - - -
408A MET* 2.7 41.7 + - - +
423A GLN* 4.9 2.6 + - - -
426A LEU* 3.9 11.7 - - + -
431C ARG* 2.5 38.1 + - + +
434C THR* 4.2 14.6 + - + +
437C GLU* 6.4 2.2 - - + -
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Residues in contact with LYS 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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403A THR* 3.2 9.4 - - - +
404A ASP* 1.3 84.9 + - - +
406A VAL* 1.3 63.3 + - + +
408A MET* 3.5 8.3 - - - +
409A GLU* 3.1 23.6 + - - +
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Residues in contact with VAL 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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400A GLU* 6.3 0.2 - - + -
401A SER* 3.8 21.1 - - - +
402A ASP* 3.4 22.0 - - - +
403A THR* 3.0 19.8 + - + +
405A LYS* 1.3 78.0 - - + +
407A ALA* 1.3 62.2 + - - +
409A GLU* 3.3 7.0 + - - +
410A SER* 3.0 33.5 + - - +
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Residues in contact with ALA 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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397A THR* 4.6 1.1 - - - +
398A ILE* 4.5 10.3 - - + +
401A SER* 3.4 20.9 - - - +
403A THR 3.0 14.1 + - - +
404A ASP* 3.2 12.3 + - - +
406A VAL* 1.3 77.3 - - - +
408A MET* 1.3 56.9 + - - +
410A SER* 3.3 2.1 + - - -
411A LEU* 2.9 37.6 + - - +
426A LEU* 4.1 15.7 - - + -
434C THR* 4.1 11.2 - - + -
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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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404A ASP* 2.7 30.1 + - + +
405A LYS* 3.5 8.7 - - + +
407A ALA* 1.3 72.8 - - - +
409A GLU* 1.3 62.6 + - - +
411A LEU* 3.5 2.6 + - - +
412A GLN* 3.1 43.1 + - - +
419A GLU* 3.5 44.6 - - + +
422A ALA* 3.9 8.5 - - + +
423A GLN* 3.3 43.1 - - + +
426A LEU* 3.6 18.8 - - + +
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Residues in contact with GLU 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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405A LYS 3.1 14.0 + - - +
406A VAL* 3.7 6.5 - - - +
408A MET* 1.3 79.4 - - - +
410A SER* 1.3 65.5 + - - +
412A GLN* 3.5 12.3 + - - +
413A GLN* 3.2 37.9 + - + +
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Residues in contact with SER 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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397A THR* 3.5 23.3 - - - -
400A GLU* 4.3 10.4 + - - -
401A SER* 4.5 1.1 + - - -
406A VAL* 3.0 25.5 + - - +
407A ALA* 3.8 2.0 - - - -
409A GLU* 1.3 73.4 - - - +
411A LEU* 1.3 60.9 + - - +
413A GLN* 4.2 2.9 - - - +
414A ARG* 2.9 45.4 + - - +
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Residues in contact with LEU 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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394A ILE* 4.0 36.1 - - + +
397A THR* 3.8 24.0 - - + -
398A ILE* 4.4 7.0 - - + -
407A ALA 2.9 26.4 + - - +
408A MET 3.8 3.8 - - - +
410A SER* 1.3 76.2 - - - +
412A GLN* 1.3 58.0 + - - +
415A PHE* 3.0 39.2 + - + +
417A LEU* 3.6 9.9 - - + +
422A ALA* 4.1 22.0 - - + +
425A ILE* 4.5 11.2 - - + -
426A LEU* 4.1 30.3 - - + -
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Residues in contact with GLN 412 (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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408A MET* 3.1 48.1 + - - +
409A GLU* 3.8 13.0 - - - +
410A SER 3.3 0.4 - - - -
411A LEU* 1.3 76.2 - - - +
413A GLN* 1.3 59.2 + - - +
416A LYS* 3.0 24.6 + - - -
417A LEU* 3.1 30.9 + - - +
418A SER* 3.7 9.7 - - - +
419A GLU* 3.7 25.8 + - - +
422A ALA* 3.8 4.7 - - + -
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Residues in contact with GLN 413 (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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409A GLU* 3.2 31.2 + - + +
410A SER* 4.2 2.7 - - - +
412A GLN* 1.3 80.7 - - - +
414A ARG* 1.3 66.1 + - - +
415A PHE 3.5 0.3 + - - -
416A LYS* 3.9 8.0 + - - +
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Residues in contact with ARG 414 (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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393A GLU* 3.7 23.6 + - - +
396A SER* 5.8 0.4 + - - -
397A THR* 2.8 39.3 + - - +
400A GLU* 3.3 30.2 + - - -
410A SER* 2.9 24.3 + - - +
413A GLN* 1.3 78.8 - - - +
415A PHE* 1.3 76.9 + - + +
416A LYS* 3.9 3.1 + - - +
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Residues in contact with PHE 415 (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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386A ILE* 4.1 28.7 - - + +
390A HIS* 3.9 27.4 - + + -
393A GLU* 3.6 39.9 - - + -
394A ILE* 3.7 28.9 - - + -
397A THR* 4.0 9.6 - - - -
411A LEU* 3.0 29.3 + - + +
414A ARG* 1.3 99.0 - - + +
416A LYS* 1.3 75.0 + - - +
417A LEU* 3.4 20.3 + - + +
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Residues in contact with LYS 416 (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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386A ILE* 5.0 3.7 - - + +
412A GLN 3.0 11.1 + - - -
413A GLN 3.9 7.0 + - - +
414A ARG 3.6 3.2 - - - +
415A PHE* 1.3 81.8 - - - +
417A LEU* 1.3 62.4 + - - +
421A GLN* 4.2 3.1 - - - +
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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