Contacts of the helix formed by residues 408 - 416 (chain A) in PDB entry 5I74
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 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A SER* 4.4 5.2 - - - +
228A ALA* 3.9 7.9 - - + +
229A GLU* 3.6 46.4 - - + +
232A TYR* 3.6 36.3 - - + -
233A THR* 4.9 0.4 - - - +
404A SER* 3.0 25.7 + - - +
406A LEU 3.4 0.2 - - - -
407A PHE* 1.3 81.3 - - - +
409A THR* 1.3 65.0 + - - +
410A TYR 3.5 0.2 - - - -
411A ALA 3.9 0.2 - - - -
412A GLU* 2.7 41.8 + - - +
566A PHE* 4.4 9.2 - - + -
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Residues in contact with THR 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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383A LEU* 4.1 22.0 - - + -
386A MET* 4.3 10.8 - - + +
390A ARG* 5.7 1.0 + - - +
397A VAL* 3.7 42.4 + - + +
400A ASP* 5.8 3.1 - - - +
404A SER 3.1 8.5 + - - -
405A LEU* 3.4 16.0 - - + +
408A ILE* 1.3 81.6 - - - +
410A TYR* 1.3 64.8 + - - +
412A GLU* 3.7 6.5 - - - +
413A ALA* 2.9 21.9 + - + +
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Residues in contact with TYR 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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295A LEU* 3.9 16.0 - - + +
378A VAL* 3.3 22.4 + - + +
379A ILE* 3.6 32.5 - - + -
382A VAL* 3.2 44.1 - - + +
383A LEU* 4.2 11.0 - - + -
405A LEU* 2.8 21.5 + - + +
406A LEU* 3.5 13.2 - - + +
409A THR* 1.3 74.8 - - - +
411A ALA* 1.3 57.2 + - - +
413A ALA* 3.1 7.8 + - - +
414A ILE* 2.9 49.7 + - + +
417A MET* 6.2 0.2 - - + -
427A PHE* 3.5 33.9 - + - -
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Residues in contact with ALA 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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186A TYR* 5.0 1.1 - - + -
197A TRP* 3.2 31.5 + - + +
228A ALA* 5.3 0.7 - - + -
406A LEU 3.3 7.6 + - - +
407A PHE* 3.3 28.9 - - - +
408A ILE 3.4 0.8 + - - +
409A THR 3.2 0.8 - - - -
410A TYR* 1.3 78.8 - - - +
412A GLU* 1.3 56.8 + - - +
414A ILE* 2.9 27.3 + - - +
415A ALA 2.9 12.1 + - - -
427A PHE* 5.8 0.4 - - - -
428A PHE* 4.6 11.9 - - + -
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Residues in contact with GLU 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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197A TRP* 4.3 7.4 - - + +
212A TYR* 5.7 8.6 - - - -
226A SER* 3.3 33.6 + - - -
227A PRO* 3.9 13.1 - - + +
228A ALA* 3.6 17.6 - - + +
386A MET* 3.5 21.6 - - + +
390A ARG* 5.1 6.1 + - - -
408A ILE* 2.7 25.8 + - - +
409A THR* 3.7 4.8 - - - +
411A ALA* 1.3 73.1 - - - +
413A ALA* 1.3 59.5 + - - +
414A ILE 3.5 0.3 + - - -
415A ALA* 3.5 9.2 + - + +
416A ASN* 3.0 28.9 + - - +
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Residues in contact with ALA 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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382A VAL* 3.6 26.9 - - + +
383A LEU* 6.3 0.7 - - + -
385A TYR* 4.1 10.3 - - + -
386A MET* 3.6 26.2 - - + +
409A THR* 2.9 13.8 + - + +
410A TYR* 3.4 9.9 - - - +
411A ALA 3.1 0.2 - - - -
412A GLU* 1.3 75.9 - - - +
414A ILE* 1.3 63.4 + - - +
416A ASN* 3.8 5.2 + - - +
417A MET* 3.3 23.1 - - - +
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Residues in contact with ILE 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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195A LEU* 5.4 1.3 - - + -
197A TRP* 5.5 2.0 - - + +
295A LEU* 5.4 1.8 - - + -
382A VAL* 5.6 0.4 - - + -
410A TYR* 2.9 46.2 + - + +
411A ALA* 2.9 13.5 + - - +
413A ALA* 1.3 75.2 - - + +
415A ALA* 1.3 64.1 + - - +
416A ASN 3.1 3.3 + - - -
417A MET* 3.1 28.5 + - + +
420A SER* 3.4 19.1 - - - +
423A PHE* 3.8 27.1 - - + +
424A ALA* 3.7 30.5 - - + +
427A PHE* 3.9 17.0 - - + -
428A PHE* 5.8 1.3 - - + -
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Residues in contact with ALA 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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195A LEU* 5.0 4.1 - - + +
197A TRP* 3.4 29.6 - - + +
198A THR* 3.3 34.1 + - + +
411A ALA 2.9 6.5 + - - +
412A GLU* 3.5 7.6 + - + +
413A ALA 3.4 0.4 - - - -
414A ILE* 1.3 76.9 - - - +
416A ASN* 1.3 62.9 + - - +
417A MET 3.3 1.3 + - - +
420A SER* 4.2 16.1 + - - -
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Residues in contact with ASN 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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198A THR* 5.6 5.5 - - - +
212A TYR* 4.8 19.8 - - - +
385A TYR* 4.0 20.4 + - - +
389A MET* 3.7 25.1 - - + +
412A GLU* 3.0 27.3 + - - +
413A ALA 4.2 4.3 - - - +
414A ILE 3.1 1.8 + - - -
415A ALA* 1.3 79.7 + - - +
417A MET* 1.3 60.2 + - - +
418A PRO* 4.4 1.7 - - - +
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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