Contacts of the helix formed by residues 379 - 385 (chain M) in PDB entry 4K4I
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 HIS 379 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375M ILE* 3.1 36.7 + - + +
376M GLY 3.4 2.9 - - - -
377M LEU 3.1 0.6 - - - -
378M LYS* 1.3 96.7 + - + +
380M TYR* 1.3 65.5 + - - +
381M SER 3.1 2.9 - - - -
382M ASP* 2.9 16.1 + - - +
383M PHE* 2.9 51.6 + + + +
458M THR* 4.0 7.0 - - + +
459M ASP* 3.6 19.4 + - - -
476M VAL* 4.2 2.5 - - + -
486M HIS* 3.4 45.3 + + + +
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Residues in contact with TYR 380 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337M LEU* 2.9 56.1 + - + +
340M ASN* 3.5 35.7 + - + +
341M ILE* 3.9 19.3 - - + -
360M LEU* 3.8 31.4 - - + -
376M GLY 2.9 10.3 + - - +
377M LEU* 3.1 15.9 + - + +
378M LYS 3.4 1.2 + - - -
379M HIS* 1.3 78.2 - - - +
381M SER* 1.3 73.5 + - - +
383M PHE* 3.5 4.2 + - - +
384M LEU* 3.2 39.1 + - + +
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Residues in contact with SER 381 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379M HIS 3.1 0.4 - - - -
380M TYR* 1.3 88.3 - - - +
382M ASP* 1.3 70.2 + - - +
383M PHE 3.2 0.4 - - - -
384M LEU* 3.5 11.7 + - - +
385M GLU* 3.7 8.7 + - - +
485M ARG* 3.7 16.6 + - - -
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Residues in contact with ASP 382 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378M LYS 5.2 0.2 - - - +
379M HIS* 2.9 17.6 + - + +
381M SER* 1.3 80.4 - - - +
383M PHE* 1.3 68.4 + - + +
385M GLU* 3.3 20.6 + - - +
485M ARG* 3.3 34.8 + - + +
486M HIS* 3.1 51.5 + - + +
487M ARG* 4.0 6.8 + - - -
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Residues in contact with PHE 383 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340M ASN 5.7 4.7 - - - +
342M TRP* 4.4 19.1 - - + +
375M ILE* 4.5 2.7 - - + -
376M GLY* 4.4 15.7 - - - +
379M HIS* 2.9 40.5 + + + +
380M TYR* 4.0 4.7 - - - +
382M ASP* 1.3 79.5 - - - +
384M LEU* 1.3 59.6 + - - +
385M GLU 3.2 5.8 + - - +
426M GLY 4.8 7.1 - - - +
461M LEU* 4.9 2.0 - - + -
476M VAL* 3.7 36.3 - - + -
486M HIS 3.7 20.4 - - - -
487M ARG* 3.9 14.8 - - - -
488M ARG* 3.9 34.7 - - + +
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Residues in contact with LEU 384 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340M ASN* 3.6 49.4 - - + +
380M TYR* 3.2 33.8 + - + +
381M SER* 3.9 7.6 - - - +
382M ASP 3.3 0.4 - - - -
383M PHE* 1.3 76.6 - - - +
385M GLU* 1.3 60.8 + - + +
386M ARG* 4.0 4.0 + - - +
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Residues in contact with GLU 385 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381M SER 3.7 3.9 + - - +
382M ASP 3.3 13.8 + - - +
383M PHE 3.2 5.9 - - - +
384M LEU* 1.3 83.0 - - + +
386M ARG* 1.3 76.2 + - - +
387M MET* 4.0 1.2 + - - +
388M PRO* 4.8 2.1 - - - +
426M GLY 4.5 6.1 - - - +
485M ARG* 3.1 43.7 + - - +
487M ARG* 2.8 38.6 + - - +
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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