Contacts of the helix formed by residues 528 - 534 (chain M) in PDB entry 6QX2
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 MET 528 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482M ILE* 3.9 21.1 - - + -
485M PHE* 3.7 29.6 - - + -
487M THR* 3.9 13.0 - - - +
488M GLY 4.0 1.8 - - - +
489M ILE* 3.8 21.5 - - + -
493M PHE* 3.9 14.8 - - + -
523M PHE* 4.1 10.1 - - + -
524M PHE* 2.9 29.3 + - + +
527M PHE* 1.3 85.8 - - + +
529M ARG* 1.3 64.0 + - - +
530M PRO* 3.3 8.5 - - - -
531M LEU* 3.1 45.2 + - + +
532M ILE* 3.8 2.6 + - - +
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Residues in contact with ARG 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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524M PHE 3.1 6.6 + - - -
525M TYR* 3.4 57.6 + - + +
526M ARG* 3.9 9.2 - - - +
527M PHE 3.9 1.2 - - - +
528M MET* 1.3 75.5 - - - +
530M PRO* 1.4 65.5 - - + +
532M ILE* 3.0 22.7 + - + +
533M GLU* 3.1 30.5 + - - +
608M LEU* 4.2 12.6 - - + -
611M ALA* 4.4 12.1 - - - +
615M ASP* 3.2 26.7 + - - -
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Residues in contact with PRO 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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490M GLY 5.9 1.8 - - - +
493M PHE* 3.3 35.9 - - + -
495M LEU* 4.1 8.6 - - + +
527M PHE 5.6 0.2 - - - -
528M MET* 3.3 5.8 - - - -
529M ARG* 1.4 95.5 - - + +
531M LEU* 1.3 51.2 + - - +
533M GLU* 3.2 20.3 - - + +
534M ALA* 2.9 35.4 + - - +
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Residues in contact with LEU 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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485M PHE* 4.5 11.9 - - + -
487M THR* 4.4 7.0 - - + +
493M PHE* 3.4 20.3 - - + -
495M LEU* 4.3 8.1 - - + -
498M ALA* 4.9 8.7 - - + -
503M ILE* 3.8 16.4 - - + -
524M PHE* 5.3 4.5 - - + -
528M MET* 3.1 47.2 + - + +
530M PRO* 1.3 76.6 - - - +
532M ILE* 1.3 58.5 + - - +
534M ALA* 3.7 0.7 + - - +
535M GLY 3.5 2.9 + - - -
536M TYR* 3.1 66.6 + - + +
537M VAL* 4.0 11.6 + - + -
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Residues in contact with ILE 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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14L ILE* 3.6 21.1 - - + -
521M LEU* 4.6 1.8 - - + +
524M PHE* 3.8 13.5 - - + +
525M TYR* 3.6 39.3 - - + +
528M MET 4.5 1.3 - - - +
529M ARG* 3.0 10.6 + - + +
531M LEU* 1.3 72.1 - - - +
533M GLU* 1.3 63.2 + - - +
535M GLY* 3.0 19.9 + - - -
537M VAL* 3.9 26.7 - - + +
606M VAL* 3.6 31.0 - - + +
607M LYS* 5.2 0.5 - - - -
608M LEU* 4.0 27.2 + - + +
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Residues in contact with GLU 533 (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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529M ARG* 3.1 35.1 + - - +
530M PRO* 3.2 28.1 - - + +
532M ILE* 1.3 76.9 - - - +
534M ALA* 1.3 57.5 + - - +
535M GLY* 3.1 6.4 + - - -
608M LEU* 4.0 21.8 - - + +
611M ALA* 6.1 0.2 - - - +
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Residues in contact with ALA 534 (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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495M LEU* 3.6 33.9 - - + -
530M PRO 2.9 20.7 + - - +
531M LEU 3.9 2.5 - - - +
533M GLU* 1.3 71.9 - - - +
535M GLY* 1.3 59.7 + - - +
536M TYR* 3.5 23.6 - - + -
605M GLN* 4.8 0.9 + - - -
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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