Contacts of the helix formed by residues 491 - 499 (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 491 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489M SER 3.6 4.6 + - - -
490M LEU* 1.3 74.2 - - - +
492M GLU* 1.3 67.5 + - - +
493M HIS 4.3 0.2 - - - +
494M GLU* 3.5 17.0 - - - +
495M ARG* 3.9 8.8 + - - +
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Residues in contact with GLU 492 (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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491M SER* 1.3 78.6 + - - +
493M HIS* 1.3 87.5 + - + +
494M GLU 3.2 0.3 + - - -
495M ARG* 3.4 22.2 + - - +
496M ALA* 2.9 46.7 + - - +
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Residues in contact with HIS 493 (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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486M LEU* 3.3 5.5 - - + +
490M LEU* 3.6 34.7 - - + +
491M SER 3.4 1.0 - - - +
492M GLU* 1.3 95.5 + - + +
494M GLU* 1.3 56.2 + - - +
496M ALA* 3.7 7.9 - - + -
497M ALA* 2.8 35.3 + - - +
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Residues in contact with GLU 494 (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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295M LEU* 4.0 23.4 - - - +
296M GLN* 4.9 0.7 - - - -
299M ALA* 3.4 23.2 - - - +
482M MET* 4.1 20.6 - - + +
486M LEU* 3.7 13.1 - - + +
487M LEU 5.3 1.1 - - - +
488M ALA* 4.2 22.4 - - - +
490M LEU 2.9 26.2 + - - +
491M SER* 3.5 11.8 + - - +
492M GLU 3.1 0.2 - - - -
493M HIS* 1.3 78.3 - - - +
495M ARG* 1.3 59.8 + - - +
497M ALA* 3.2 3.1 + - - +
498M ILE* 2.9 33.9 + - + +
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Residues in contact with ARG 495 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302M ALA* 6.3 2.0 - - + -
491M SER 4.0 8.7 - - - +
492M GLU* 3.5 26.9 + - - +
494M GLU* 1.3 81.8 - - + +
496M ALA* 1.3 71.1 + - - +
498M ILE* 3.2 17.5 + - + +
499M LEU* 2.9 57.7 + - + +
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Residues in contact with ALA 496 (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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492M GLU* 2.9 39.9 + - - +
493M HIS* 3.8 11.0 - - + -
495M ARG* 1.3 89.0 - - - +
497M ALA* 1.3 56.3 + - - +
499M LEU* 3.4 1.6 - - - +
500M SER* 2.8 37.8 + - - +
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Residues in contact with ALA 497 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482M MET* 6.1 0.7 - - + -
485M ASN* 5.5 8.1 - - + +
486M LEU* 4.2 19.5 - - + -
493M HIS 2.8 22.8 + - - +
494M GLU 3.7 2.9 - - - +
496M ALA* 1.3 70.2 - - - +
498M ILE* 1.3 61.6 + - - +
499M LEU 3.2 0.4 - - - -
500M SER* 4.0 6.3 - - - +
501M VAL* 2.9 38.5 + - + +
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Residues in contact with ILE 498 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299M ALA* 3.9 33.0 - - + +
302M ALA* 4.0 21.3 - - + -
303M ASP* 4.6 6.3 - - + +
306M LEU* 3.4 28.5 - - + +
482M MET* 3.8 29.6 - - + -
485M ASN* 6.4 0.4 - - + -
494M GLU* 2.9 22.3 + - + +
495M ARG* 3.2 17.9 + - + +
497M ALA* 1.3 75.4 - - - +
499M LEU* 1.3 66.4 + - + +
501M VAL* 3.3 20.8 - - - +
502M PRO* 4.6 0.7 - - - +
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Residues in contact with LEU 499 (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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302M ALA* 5.4 5.8 - - + -
306M LEU* 3.8 24.7 - - + -
495M ARG* 2.9 48.4 + - + +
496M ALA 3.4 1.8 - - - +
498M ILE* 1.3 89.9 - - + +
500M SER* 1.3 63.4 + - - +
501M VAL 3.8 0.2 - - - -
502M PRO* 4.0 14.1 - - + +
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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