Contacts of the helix formed by residues 523 - 532 (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 ARG 523 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521M ARG 3.3 7.6 + - - +
522M GLY* 1.3 71.3 - - - -
524M HIS* 1.3 57.2 + - - +
525M HIS* 3.3 43.4 + - - +
526M LEU* 3.1 43.4 + - + +
527M GLU* 2.6 35.0 + - - +
320N LYS 5.1 4.0 + - - -
321N ASN* 4.4 15.8 + - - +
323N ILE* 3.6 35.2 - - + +
324N ARG* 3.7 34.7 - - - +
326N LEU* 6.3 0.2 - - - -
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Residues in contact with HIS 524 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452M SER* 5.0 4.4 + - - -
513M PHE* 4.1 30.1 - + - -
517M LEU* 6.2 2.5 - - + -
522M GLY 3.7 3.1 + - - -
523M ARG* 1.3 77.1 - - - +
525M HIS* 1.3 62.9 + - - +
527M GLU* 3.1 6.9 + - - +
528M GLU* 2.9 62.9 + - - +
531M TYR* 4.5 1.4 + - - -
239N LEU* 3.7 44.3 - - + +
240N GLN 5.7 1.5 + - - -
241N TYR* 5.2 11.5 - + - -
323N ILE* 3.8 7.0 - - + +
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Residues in contact with HIS 525 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523M ARG* 3.3 33.0 + - - +
524M HIS* 1.3 81.1 + - - +
526M LEU* 1.3 59.3 + - - +
528M GLU* 3.3 15.1 + - + +
529M ILE* 2.9 54.0 + - + +
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Residues in contact with LEU 526 (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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523M ARG* 3.1 50.8 + - + +
525M HIS* 1.3 78.3 - - - +
527M GLU* 1.3 60.5 + - + +
529M ILE* 3.3 22.7 + - + +
530M MET* 3.0 47.8 + - + +
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Residues in contact with GLU 527 (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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513M PHE* 5.4 5.2 - - + -
516M LEU* 5.6 6.0 - - + +
517M LEU* 5.9 0.7 - - + +
520M PHE* 3.6 25.4 - - + -
521M ARG 4.8 0.7 - - - +
522M GLY* 3.4 28.3 - - - +
523M ARG 2.6 23.5 + - - +
524M HIS* 3.1 7.2 + - - +
526M LEU* 1.3 79.4 - - - +
528M GLU* 1.3 57.4 + - - +
530M MET* 3.1 19.8 + - - +
531M TYR* 2.8 47.7 + - + -
544M PHE* 5.3 9.7 - - - -
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Residues in contact with GLU 528 (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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452M SER* 4.2 8.8 + - - -
453M SER* 5.4 2.1 + - - -
524M HIS* 2.9 46.5 + - + +
525M HIS* 3.3 15.0 + - + +
527M GLU* 1.3 71.7 - - - +
529M ILE* 1.3 60.4 - - - +
531M TYR* 3.5 31.9 + - + +
532M ASN* 2.7 51.8 + - - +
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Residues in contact with ILE 529 (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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525M HIS* 2.9 46.5 + - + +
526M LEU* 3.3 28.0 - - + +
528M GLU* 1.3 75.9 - - - +
530M MET* 1.3 78.1 + - + +
532M ASN* 4.9 0.7 - - - +
533M GLU* 3.0 26.8 - - - +
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Residues in contact with MET 530 (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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526M LEU* 3.0 40.1 + - + +
527M GLU* 3.1 26.0 + - - +
529M ILE* 1.3 94.0 - - + +
531M TYR* 1.3 59.5 + - + +
532M ASN 3.2 1.1 - - - -
533M GLU* 2.9 9.0 + - - +
534M ASN* 2.9 45.1 + - - +
540M LEU* 5.8 8.5 - - + -
543M LEU* 5.1 14.6 - - + -
544M PHE* 5.1 4.7 - - + -
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Residues in contact with TYR 531 (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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448M GLY* 5.7 4.8 - - - +
450M PRO* 5.1 16.6 - - + -
452M SER* 4.2 10.1 + - - -
457M THR* 4.4 30.3 - - + -
458M LEU 4.4 13.9 - - - +
513M PHE* 3.2 44.0 - + - -
524M HIS* 4.5 0.7 + - - -
527M GLU* 2.8 46.2 + - + -
528M GLU* 3.5 29.7 + - + +
530M MET* 1.3 71.8 - - + +
532M ASN* 1.3 65.6 + - - +
533M GLU 3.3 0.7 - - - -
534M ASN* 3.2 19.8 + - + +
535M THR* 4.8 3.1 + - - -
544M PHE* 5.9 2.5 - - + -
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Residues in contact with ASN 532 (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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457M THR* 5.1 7.4 - - - +
458M LEU 5.8 2.2 - - - -
528M GLU* 2.7 45.6 + - - +
529M ILE* 4.9 0.6 - - - +
530M MET 3.1 0.2 + - - -
531M TYR* 1.3 88.9 - - - +
533M GLU* 1.3 77.9 + - - +
534M ASN 3.9 0.4 - - - -
535M THR* 5.1 4.2 + - - -
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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