Contacts of the helix formed by residues 382 - 388 (chain A) in PDB entry 5IY8
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 ARG 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A VAL 3.4 1.8 + - - -
381A PRO* 1.3 71.0 - - - +
383A SER* 1.3 57.9 + - - +
385A ALA* 3.2 2.6 + - - +
386A ALA* 2.9 28.4 + - + +
413A TYR* 4.0 37.5 - - + +
476A ILE* 3.9 22.3 - - + +
477A LEU 3.5 12.0 + - - +
478A PRO* 5.8 3.2 - - + +
2K ASN* 3.6 13.6 - - - +
4K PRO* 6.1 3.6 - - - +
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A PRO* 4.2 4.2 - - - +
382A ARG* 1.3 73.4 - - - +
384A ILE* 1.3 64.4 + - - +
386A ALA* 3.4 6.9 + - - +
387A ASN* 3.1 27.2 + - - +
480A SER* 4.6 2.3 + - - -
1059B ILE* 4.9 9.5 - - - +
1K MET 6.3 0.2 - - - -
2K ASN* 3.0 32.3 + - - +
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Residues in contact with ILE 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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363A ALA* 3.9 23.1 - - + -
365A THR* 3.5 32.1 - - + -
380A VAL* 4.0 15.5 - - + -
381A PRO* 3.1 22.5 + - + +
383A SER* 1.3 79.3 + - - +
385A ALA* 1.3 63.3 + - - +
387A ASN* 4.0 0.6 - - - +
388A MET* 3.3 24.8 + - - +
450A MET* 3.8 5.9 - - + +
482A PHE* 4.6 3.6 - - + -
503A LEU* 5.4 1.3 - - + -
1059B ILE* 4.7 6.1 - - + -
1060B HIS 3.8 20.2 - - - +
1061B SER* 4.0 20.0 - - - +
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Residues in contact with ALA 385 (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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380A VAL* 4.4 2.8 - - + +
381A PRO 3.0 11.1 + - - +
382A ARG 3.5 9.0 - - - +
384A ILE* 1.3 78.5 - - - +
386A ALA* 1.3 60.2 + - - +
388A MET 3.5 6.4 - - - +
413A TYR* 3.6 7.9 - - + -
449A HIS* 3.9 1.0 - - - +
450A MET* 3.3 47.4 + - + +
476A ILE* 3.4 33.4 - - + -
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Residues in contact with ALA 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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382A ARG* 2.9 16.9 + - + +
383A SER* 3.7 8.3 - - - +
385A ALA* 1.3 74.6 - - - +
387A ASN* 1.3 61.7 + - - +
410A ASN* 5.7 0.2 - - - +
413A TYR* 4.0 18.5 - - + -
417A LYS* 3.7 3.1 - - - -
449A HIS* 2.4 47.9 + - + +
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Residues in contact with ASN 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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383A SER 3.1 16.9 + - - +
384A ILE 3.4 2.6 + - - +
386A ALA* 1.3 78.4 - - - +
388A MET* 1.3 61.7 + - - +
389A THR 3.9 0.3 + - - -
417A LYS* 3.1 30.8 + - - +
1061B SER* 3.0 42.0 + - - +
1062B ARG* 4.0 7.7 - - - +
1063B ALA* 3.7 14.3 - - - +
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Residues in contact with MET 388 (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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361A PHE* 3.4 39.5 - - + +
362A SER* 4.4 1.3 - - - +
363A ALA* 4.3 13.2 - - - -
384A ILE* 3.3 18.2 + - - +
385A ALA 3.5 1.8 - - - +
386A ALA 3.4 0.8 - - - -
387A ASN* 1.3 86.4 - - + +
389A THR* 1.3 61.4 + - - +
449A HIS* 4.9 0.2 - - - -
450A MET* 3.1 43.6 + - + +
503A LEU* 4.9 6.5 - - + -
505A LEU* 3.8 27.4 - - + +
1061B SER* 4.3 18.6 - - - -
1062B ARG 4.2 18.6 - - - +
1063B ALA* 4.6 3.8 - - - +
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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