Contacts of the helix formed by residues 530 - 543 (chain M) in PDB entry 6M6A
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 PRO 530 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528M PHE 3.5 8.1 - - - +
529M THR* 1.3 87.3 - - + +
531M PRO* 1.4 62.8 - - + +
532M LYS* 3.5 1.8 - - + +
533M GLU* 3.0 40.8 + - + +
534M GLU* 2.6 31.6 + - - +
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Residues in contact with PRO 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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529M THR 3.7 1.1 - - - +
530M PRO* 1.4 82.9 - - + +
532M LYS* 1.3 66.7 + - + +
534M GLU* 3.2 19.9 - - - +
535M GLU* 2.8 36.5 + - - +
2N C 6.0 2.0 - - - +
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Residues in contact with LYS 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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530M PRO* 3.5 1.1 - - + -
531M PRO* 1.3 80.0 - - + +
533M GLU* 1.3 79.1 + - + +
535M GLU* 3.5 4.8 + - - +
536M ALA* 2.9 33.9 + - + +
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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 THR* 4.5 4.9 - - + +
530M PRO* 3.0 41.2 + - + +
532M LYS* 1.3 97.6 + - + +
534M GLU* 1.3 58.7 + - - +
536M ALA* 3.5 8.0 - - + +
537M ILE* 2.9 40.6 + - + +
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Residues in contact with GLU 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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525M LEU* 3.6 22.5 - - + +
526M SER 2.9 23.6 - - - +
527M ARG 4.6 0.2 - - - +
529M THR* 3.0 25.0 - - - +
530M PRO 2.6 20.3 + - - +
531M PRO* 3.0 22.2 + - - +
533M GLU* 1.3 73.4 - - - +
535M GLU* 1.3 65.2 + - - +
537M ILE* 3.3 5.0 + - - +
538M LEU* 2.9 33.9 + - + +
554M ARG* 3.0 30.2 + - - -
558M GLU* 5.3 3.3 - - - +
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Residues in contact with GLU 535 (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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531M PRO* 2.8 31.1 + - - +
532M LYS* 4.4 3.7 - - - +
534M GLU* 1.3 80.5 - - - +
536M ALA* 1.3 60.0 + - - +
537M ILE 3.3 0.2 - - - -
538M LEU* 3.6 19.5 - - + +
539M LYS* 2.8 30.5 + - - +
558M GLU* 4.6 10.0 - - - +
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Residues in contact with ALA 536 (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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532M LYS* 2.9 27.1 + - - +
533M GLU* 3.5 11.9 - - + +
534M GLU 3.2 0.2 - - - -
535M GLU* 1.3 77.5 - - - +
537M ILE* 1.3 58.3 + - + +
539M LYS* 3.5 18.0 + - - +
540M GLY* 2.9 24.9 + - - -
546M VAL* 5.3 0.2 - - - +
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Residues in contact with ILE 537 (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 ALA* 3.8 32.5 - - + -
524M VAL 3.3 23.6 - - - +
525M LEU* 4.4 19.7 - - + -
529M THR* 4.1 9.4 - - + -
533M GLU* 2.9 25.6 + - + +
534M GLU* 3.7 3.8 - - - +
536M ALA* 1.3 73.7 - - + +
538M LEU* 1.3 60.6 + - - +
540M GLY 4.2 0.2 - - - +
541M LEU* 2.9 30.9 + - + +
546M VAL* 4.1 9.9 - - + +
549M VAL* 4.4 13.7 - - + -
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Residues in contact with LEU 538 (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 LEU* 3.7 21.5 - - + -
534M GLU* 2.9 24.6 + - + +
535M GLU* 3.6 27.6 - - + +
536M ALA 3.3 0.2 - - - -
537M ILE* 1.3 76.5 - - - +
539M LYS* 1.3 56.3 + - - +
541M LEU* 4.0 2.4 - - - +
542M ALA* 2.9 29.5 + - - +
558M GLU* 3.8 26.9 - - + +
559M ASP 3.3 29.3 - - - +
560M VAL* 3.8 20.0 - - + -
561M ARG 4.9 3.8 + - - +
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Residues in contact with LYS 539 (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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535M GLU 2.8 17.7 + - - +
536M ALA* 3.8 17.9 + - - +
538M LEU* 1.3 76.0 - - - +
540M GLY* 1.3 54.2 + - - +
542M ALA* 3.2 8.4 - - + +
543M GLU* 2.4 54.5 + - + +
545M THR* 5.7 3.0 + - - +
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Residues in contact with GLY 540 (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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536M ALA 2.9 18.0 + - - -
537M ILE 3.2 1.7 + - - -
539M LYS* 1.3 79.9 - - - +
541M LEU* 1.3 54.6 + - - +
543M GLU* 3.0 3.7 + - - -
544M GLY 2.6 29.1 + - - -
545M THR* 2.7 29.2 + - - -
546M VAL* 3.5 11.9 - - - -
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Residues in contact with LEU 541 (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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493M GLN* 2.4 46.4 + - + +
494M VAL 5.3 0.2 - - - +
537M ILE 2.9 15.3 + - - +
538M LEU* 4.4 2.9 - - - +
540M GLY* 1.3 74.7 - - - +
542M ALA* 1.3 61.2 + - - +
544M GLY 3.4 0.9 + - - -
546M VAL* 3.3 46.1 - - + +
547M ASP 4.0 9.0 - - - +
549M VAL* 3.9 37.7 - - + +
560M VAL* 5.2 8.3 - - + -
561M ARG 3.1 20.4 - - - +
562M PHE* 3.9 21.3 - - + -
563M ARG 3.7 1.6 + - - -
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Residues in contact with ALA 542 (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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538M LEU 2.9 23.0 + - - +
539M LYS* 3.3 11.4 - - + +
541M LEU* 1.3 77.7 - - - +
543M GLU* 1.3 55.6 + - + +
561M ARG* 2.4 66.3 + - + +
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Residues in contact with GLU 543 (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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539M LYS* 2.4 48.4 + - + +
540M GLY* 3.0 6.0 + - - +
542M ALA* 1.3 73.6 - - + +
544M GLY* 1.3 61.2 + - - +
545M THR* 3.4 19.7 + - + +
561M ARG* 4.6 3.6 - - - +
563M ARG* 4.7 3.9 - - - +
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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