Contacts of the helix formed by residues 574 - 579 (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 GLY 574 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534M LEU* 2.7 37.9 - - - +
535M THR* 4.1 2.7 + - - -
539M THR* 3.1 16.2 + - - +
540M PHE* 4.9 0.2 - - - +
541M ILE* 4.6 3.4 - - - -
573M SER* 1.3 72.0 - - - +
575M LYS* 1.3 66.5 + - - +
576M GLN 2.7 1.9 + - - -
577M ILE* 2.7 15.9 + - - +
578M LEU* 3.1 13.9 + - - -
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Residues in contact with LYS 575 (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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534M LEU 3.8 1.0 + - - -
535M THR* 3.4 46.4 + - + +
536M LEU 4.6 0.2 - - - -
537M ARG* 4.4 7.7 - - - +
573M SER* 5.2 0.7 - - - -
574M GLY* 1.3 71.7 - - - +
576M GLN* 1.3 60.7 + - - +
578M LEU* 4.1 2.9 - - - -
579M SER* 2.7 33.6 + - - -
602M ASP* 2.6 40.1 + - - -
612M ILE* 3.6 42.2 - - + +
614M PHE* 3.8 4.8 - - - +
615M GLY 2.9 19.0 - - - +
119T GLY 4.2 10.3 - - - +
120T GLY* 3.9 22.9 - - - +
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Residues in contact with GLN 576 (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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561M PRO* 5.0 12.1 + - + +
562M THR 2.9 29.3 + - - -
564M ALA* 3.3 19.0 + - - +
572M TRP* 3.0 23.5 - - + +
573M SER* 2.9 42.6 + - - +
574M GLY 2.7 3.8 + - - -
575M LYS* 1.3 79.0 - - - +
577M ILE* 1.3 64.0 + - + +
579M SER* 3.5 12.1 - - - -
580M VAL* 4.1 5.5 - - - +
611M GLN* 4.6 4.3 - - - +
612M ILE 5.8 1.1 - - - -
98T TYR 5.4 1.0 + - - -
119T GLY* 3.9 15.4 + - - +
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Residues in contact with ILE 577 (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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534M LEU* 5.0 2.9 - - + -
541M ILE* 4.2 8.1 - - + -
546M VAL* 4.2 18.6 - - + +
549M MET* 3.0 58.1 - - + -
550M LEU* 4.9 4.5 - - + +
561M PRO* 5.4 3.1 - - + -
572M TRP* 4.2 22.0 - - + -
573M SER 3.8 9.6 - - - +
574M GLY 2.7 15.3 + - - +
576M GLN* 1.3 72.9 - - + +
578M LEU* 1.3 58.0 + - + +
579M SER 2.7 5.4 - - - -
580M VAL* 2.5 46.6 + - + +
581M ALA 4.0 0.2 + - - -
652M VAL* 4.1 12.7 - - + +
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Residues in contact with LEU 578 (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 ILE* 3.7 42.0 - - + +
534M LEU* 3.8 17.5 - - + -
535M THR* 4.2 7.4 - - - +
574M GLY 3.1 10.2 + - - +
575M LYS* 4.1 2.5 - - - +
577M ILE* 1.3 83.4 - - - +
579M SER* 1.3 61.1 + - - +
581M ALA* 3.3 16.7 + - + +
582M ILE* 4.1 7.5 + - + +
612M ILE* 3.5 25.1 - - + -
617M VAL* 4.1 10.1 - - + -
649M ILE* 4.3 19.1 - - + +
652M VAL* 4.7 8.5 - - + -
653M VAL* 4.2 13.7 - - + -
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Residues in contact with SER 579 (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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575M LYS 2.7 21.1 + - - -
576M GLN* 3.5 9.4 - - - -
577M ILE 2.6 4.2 + - - -
578M LEU* 1.3 72.5 - - - +
580M VAL* 1.3 52.7 + - - -
581M ALA 2.6 17.2 + - - -
582M ILE* 2.7 32.8 + - - +
610M GLY 3.9 5.5 - - - +
611M GLN* 3.7 21.5 + - - -
612M ILE* 3.0 33.1 + - - +
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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