Contacts of the helix formed by residues 524 - 534 (chain M) in PDB entry 2JA7
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 VAL 524 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472M LEU* 5.4 8.0 - - + +
473M SER* 5.0 6.9 + - - +
475M THR* 4.8 13.2 - - + -
476M SER* 5.2 6.7 - - - +
522M GLY* 5.0 2.7 - - - +
523M ILE* 1.3 83.9 - - - +
525M GLN* 1.3 109.3 + - + +
527M THR* 3.4 8.3 + - - -
528M LEU* 3.1 13.8 + - + -
650M GLN* 5.9 0.8 - - - +
750M GLY 6.0 0.2 - - - +
751M SER* 4.3 12.1 - - - +
835N GLN* 3.6 4.4 - - - +
836N GLU* 4.5 12.6 - - + +
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Residues in contact with GLN 525 (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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472M LEU* 4.9 1.3 - - + -
524M VAL* 1.3 106.4 - - + +
526M ASP* 1.3 73.6 + - - +
528M LEU* 2.6 16.2 + - - +
529M CYS* 2.8 10.9 + - - +
751M SER* 4.1 13.2 + - - -
752M LYS* 4.6 9.7 - - - +
835N GLN* 3.2 30.6 - - + +
836N GLU* 2.9 49.3 + - + +
837N ASP 4.7 0.2 + - - -
1013N ASN* 4.8 1.0 - - - +
1015N HIS* 3.4 42.2 - - + +
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Residues in contact with ASP 526 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525M GLN* 1.3 74.2 - - - +
527M THR* 1.3 61.0 + - - +
528M LEU 2.7 1.0 + - - -
529M CYS* 4.5 0.9 - - - -
530M GLY* 2.5 33.1 + - - -
654M ASN* 4.0 8.3 - - - +
657M LEU* 3.6 21.0 - - + +
829N CYS* 3.6 21.3 - - - +
830N TYR 3.7 19.1 - - - +
832N GLY* 3.8 8.1 - - - -
834N ASN* 4.0 2.4 - - - +
835N GLN* 3.4 19.9 - - - +
1013N ASN* 2.6 31.7 + - - -
1015N HIS* 3.4 5.8 + - - -
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Residues in contact with THR 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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472M LEU* 5.1 2.3 - - - +
523M ILE* 3.5 21.2 - - + +
524M VAL 3.6 4.1 + - - -
525M GLN 3.4 0.2 - - - -
526M ASP* 1.3 75.7 - - - +
528M LEU* 1.3 57.5 + - - +
531M ILE* 2.9 29.6 + - - +
649M ILE* 4.4 5.4 - - + -
650M GLN* 3.3 48.8 + - + +
653M VAL* 3.4 15.6 - - + +
654M ASN* 3.0 20.1 + - - +
835N GLN* 3.6 10.2 + - - -
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Residues in contact with LEU 528 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523M ILE* 3.5 30.2 - - - +
524M VAL* 3.1 10.7 + - + -
525M GLN 2.6 14.5 + - - +
527M THR* 1.3 68.5 - - - +
529M CYS* 1.3 70.4 + - - +
530M GLY 3.0 0.9 - - - -
531M ILE* 2.8 36.6 + - + +
532M ARG* 3.2 2.9 + - - +
618M GLU* 4.2 3.6 - - - -
619M LYS* 3.7 32.1 - - + +
622M VAL* 4.6 5.6 - - + -
623M GLY* 6.2 0.2 - - - -
749M ALA* 3.8 15.5 - - + +
750M GLY 3.8 6.3 - - - +
751M SER* 3.7 30.1 - - - +
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Residues in contact with CYS 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 GLN 2.8 9.8 + - - +
526M ASP* 3.7 3.1 - - - +
528M LEU* 1.3 75.6 - - - +
530M GLY* 1.3 62.9 + - - +
532M ARG* 3.4 13.0 + - - +
533M LYS* 3.5 19.0 + - - +
657M LEU* 5.3 2.7 - - + -
662M PHE* 3.8 45.3 - - - -
745M GLN* 5.5 2.2 - - - -
746M MET* 4.3 10.5 - - - -
749M ALA* 3.8 14.4 - - - -
751M SER* 3.8 3.3 - - - +
829N CYS* 6.1 0.2 - - - -
1015N HIS* 3.5 28.7 - - + +
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Residues in contact with GLY 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 ASP 2.5 19.6 + - - -
529M CYS* 1.3 70.2 - - - +
531M ILE* 1.3 61.4 + - - -
532M ARG 2.9 5.2 + - - -
533M LYS* 3.1 5.3 + - - +
534M LEU* 2.9 26.0 + - - +
653M VAL* 3.5 14.4 - - - -
656M TRP* 4.0 5.4 - - - -
657M LEU* 3.9 21.2 - - - +
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Residues in contact with ILE 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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523M ILE* 4.9 1.3 - - + -
527M THR 2.9 18.5 + - - +
528M LEU* 2.8 37.8 + - + +
530M GLY* 1.3 70.7 - - - +
532M ARG* 1.3 58.4 + - - +
534M LEU* 4.2 4.9 - - + +
535M THR* 2.9 21.7 + - - -
578M LEU* 3.7 30.9 - - + +
617M VAL* 3.4 33.8 - - + +
622M VAL* 4.0 17.5 - - + -
629M LEU* 6.5 0.2 - - + -
649M ILE* 4.0 17.7 - - + -
653M VAL* 3.3 17.1 - - + +
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Residues in contact with ARG 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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528M LEU 3.2 4.6 + - - +
529M CYS* 3.7 11.6 + - - +
530M GLY 3.0 0.8 - - - -
531M ILE* 1.3 80.0 - - - +
533M LYS* 1.3 84.1 + - - +
535M THR* 2.7 32.7 + - - -
536M LEU* 3.4 25.4 + - + +
616M VAL* 3.7 17.6 - - + +
617M VAL 3.3 16.2 - - - +
618M GLU* 4.4 8.3 - - + -
739M ASP* 4.7 4.2 + - - +
745M GLN* 3.7 33.0 + - - +
748M MET* 3.5 37.7 - - - +
749M ALA* 4.0 24.8 - - + +
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Residues in contact with LYS 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 CYS* 3.5 14.3 + - - +
530M GLY* 3.1 6.9 + - - +
532M ARG* 1.3 97.8 - - - +
534M LEU* 1.3 55.2 + - - +
535M THR 2.6 12.1 + - - -
536M LEU* 3.4 24.4 + - + +
539M THR* 3.6 14.9 + - - +
656M TRP* 3.9 15.0 - - + -
657M LEU* 5.9 2.7 - - + -
660M ASN* 3.8 23.5 - - - +
661M GLY 4.7 1.0 + - - +
662M PHE* 4.1 25.5 - - + -
745M GLN* 3.2 28.8 + - - +
1082N MET* 6.2 0.8 - - - +
1083N ALA* 4.8 9.3 - - - +
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Residues in contact with LEU 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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530M GLY 2.9 20.6 + - - +
531M ILE* 4.4 2.9 - - - +
533M LYS* 1.3 72.2 - - - +
535M THR* 1.3 50.9 - - - +
539M THR* 3.7 5.1 - - + +
541M ILE* 3.7 15.9 - - + -
549M MET* 4.6 2.0 - - - -
574M GLY* 2.7 41.0 - - - -
577M ILE* 5.0 1.3 - - + -
578M LEU* 3.8 33.4 - - + +
652M VAL* 4.6 7.2 - - + -
653M VAL* 4.2 26.0 - - + -
656M TRP* 3.2 57.2 - - + +
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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