Contacts of the helix formed by residues 476 - 486 (chain M) in PDB entry 6CET
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 SER 476 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454M ASP* 5.2 5.2 - - - -
470M LEU* 5.7 5.9 - - - +
473M SER* 4.7 3.7 + - - -
474M GLY 3.7 5.7 + - - -
475M ASP* 1.3 66.0 - - - +
477M PRO* 1.4 66.3 - - - +
478M LEU* 3.0 11.0 + - - -
479M ASN* 2.8 28.4 + - - +
480M GLN* 2.3 33.3 + - - +
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Residues in contact with PRO 477 (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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430M PHE 5.4 0.7 - - - +
431M THR* 4.8 11.9 - - + -
454M ASP* 3.8 38.8 - - + +
455M ASP* 4.1 9.4 - - + +
475M ASP* 3.5 12.8 - - + +
476M SER* 1.4 87.1 - - - +
478M LEU* 1.3 53.9 + - - +
480M GLN* 3.7 12.6 - - + +
481M ARG* 2.4 62.6 + - - +
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Residues in contact with LEU 478 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296M GLN* 5.8 0.7 - - - +
300M GLN* 4.2 23.1 - - + +
303M ASP* 5.5 5.9 - - - +
308M GLN* 5.3 11.4 - - + +
430M PHE* 3.7 32.1 + - + +
470M LEU* 5.6 5.4 - - + -
473M SER* 3.3 35.2 - - - +
475M ASP 3.3 12.8 + - - +
476M SER* 3.0 4.1 + - - +
477M PRO* 1.3 76.2 - - - +
479M ASN* 1.3 86.5 + - + +
481M ARG* 3.4 12.0 + - - +
482M MET* 3.0 25.2 + - - +
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Residues in contact with ASN 479 (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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470M LEU* 3.4 43.9 - - - +
476M SER* 2.8 34.1 + - - +
478M LEU* 1.3 88.2 - - + +
480M GLN* 1.3 58.5 + - - +
482M MET* 4.1 8.5 - - + +
483M THR* 2.5 46.5 + - + +
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Residues in contact with GLN 480 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454M ASP* 5.0 13.0 + - + +
456M MET* 3.4 30.0 + - + +
458M LEU* 5.3 11.7 - - + +
476M SER* 2.3 46.3 + - - +
477M PRO* 3.6 15.6 - - + +
479M ASN* 1.3 83.4 + - - +
481M ARG* 1.3 56.8 + - - +
483M THR* 3.1 6.3 + - - -
484M GLU* 2.9 37.1 + - + +
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Residues in contact with ARG 481 (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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303M ASP* 6.1 2.5 - - - +
308M GLN* 5.5 0.8 - - - +
431M THR* 3.4 9.1 - - - +
432M ALA* 3.0 57.7 + - + +
437M ARG* 2.7 47.3 + - - +
455M ASP* 4.0 12.5 + - - +
456M MET* 3.6 34.2 - - + +
477M PRO* 2.4 60.0 + - - +
478M LEU* 3.8 7.2 - - - +
480M GLN* 1.3 73.0 - - - +
482M MET* 1.3 59.0 + - - +
485M ASN* 2.8 14.0 + - - +
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Residues in contact with MET 482 (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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299M ALA* 4.9 15.0 - - + +
300M GLN* 5.9 3.1 - - + +
303M ASP* 5.0 15.7 - - + +
478M LEU 3.0 17.2 + - - +
479M ASN* 3.5 8.7 + - + +
480M GLN 3.3 0.2 - - - -
481M ARG* 1.3 77.7 - - - +
483M THR* 1.3 59.0 + - + +
485M ASN* 3.1 22.2 + - + +
486M LEU* 2.9 38.7 + - + +
488M ALA* 6.2 4.3 - - + -
494M GLU* 4.1 23.6 - - + +
497M ALA* 6.1 0.4 - - + -
498M ILE* 3.8 36.1 - - + +
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Residues in contact with THR 483 (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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479M ASN* 2.5 32.7 + - + +
480M GLN* 3.1 10.6 + - - -
482M MET* 1.3 75.8 - - + +
484M GLU* 1.3 61.2 + - - +
486M LEU* 3.1 25.6 + - - +
487M LEU* 3.9 8.4 + - - +
488M ALA* 5.4 8.3 - - + +
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Residues in contact with GLU 484 (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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437M ARG* 3.4 16.2 + - - +
440M SER* 4.5 4.7 + - - -
447M PHE* 4.3 11.2 - - - +
449M SER* 2.9 37.9 + - - +
456M MET* 4.3 14.4 - - + +
458M LEU* 3.4 23.9 - - + +
480M GLN* 2.9 25.0 + - + +
481M ARG* 4.5 0.9 - - - -
483M THR* 1.3 74.5 + - - +
485M ASN* 1.3 65.3 + - - +
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Residues in contact with ASN 485 (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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303M ASP* 5.3 4.3 - - - +
437M ARG* 3.1 30.8 + - - +
481M ARG* 2.8 24.7 + - - +
482M MET* 3.1 24.4 + - + +
483M THR 3.8 0.2 - - - -
484M GLU* 1.3 78.6 - - - +
486M LEU* 1.3 69.0 - - + +
497M ALA* 5.5 9.0 - - + +
498M ILE* 6.4 0.9 - - + -
501M VAL* 3.4 30.6 - - + +
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Residues in contact with LEU 486 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482M MET* 2.9 27.3 + - + +
483M THR* 3.1 14.9 + - - +
485M ASN* 1.3 85.4 - - + +
487M LEU* 1.3 77.9 + - + +
488M ALA* 3.7 2.1 + - - +
490M LEU* 3.7 30.3 - - + -
493M HIS* 3.3 37.2 - - + +
494M GLU* 3.7 10.3 - - + +
497M ALA* 4.2 11.2 - - + -
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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