Contacts of the helix formed by residues 418 - 428 (chain M) in PDB entry 5NSS
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 THR 418 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360M GLU 5.2 1.1 - - - -
361M TYR* 3.6 26.5 - - - -
362M MET 3.4 20.9 - - - -
417M SER* 1.3 75.5 - - - +
419M ALA* 1.3 56.1 + - - -
420M ILE 2.7 14.2 + - - -
421M ARG* 2.7 21.9 + - - +
422M ALA* 2.9 14.8 + - - -
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Residues in contact with ALA 419 (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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415M ALA* 4.6 12.3 - - + -
417M SER 3.1 3.0 + - - -
418M THR* 1.3 77.6 - - - +
420M ILE* 1.3 53.5 + - - +
422M ALA* 4.0 10.8 - - - -
423M LEU* 2.7 39.0 + - + +
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Residues in contact with ILE 420 (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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415M ALA* 3.2 33.7 - - - +
416M SER 3.3 16.8 - - - +
417M SER 3.8 2.0 + - - -
418M THR 2.7 5.9 + - - -
419M ALA* 1.3 73.7 - - - +
421M ARG* 1.3 56.9 + - - +
423M LEU* 3.9 1.9 - - - +
424M VAL* 2.9 27.2 + - - +
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Residues in contact with ARG 421 (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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416M SER 4.8 2.2 + - - +
418M THR 2.7 13.6 + - - +
420M ILE* 1.3 74.8 - - + +
422M ALA* 1.3 57.7 + - - +
424M VAL* 3.7 8.2 - - - +
425M LYS* 2.9 26.5 + - - +
461M TYR* 4.8 20.2 - - + +
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Residues in contact with ALA 422 (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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418M THR* 2.9 17.8 + - - +
419M ALA* 4.0 8.5 - - - -
421M ARG* 1.3 73.6 - - - +
423M LEU* 1.3 62.1 + - - +
425M LYS* 3.2 10.0 + - - +
426M LYS* 2.9 24.6 + - - +
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Residues in contact with LEU 423 (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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419M ALA* 2.7 26.0 + - + +
420M ILE* 3.9 2.0 - - - +
422M ALA* 1.3 75.6 - - - +
424M VAL* 1.3 59.7 + - - +
425M LYS 3.1 0.2 - - - -
426M LYS* 3.0 9.7 + - + +
427M LEU* 2.9 28.2 + - - +
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Residues in contact with VAL 424 (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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420M ILE 2.9 18.3 + - - +
421M ARG* 3.7 9.2 - - - +
422M ALA 3.4 0.2 - - - -
423M LEU* 1.3 75.2 - - - +
425M LYS* 1.3 56.0 + - - +
427M LEU* 3.6 6.9 + - - +
428M ILE* 2.9 28.9 + - - +
446M LEU* 6.6 0.2 - - + -
458M VAL 5.3 1.1 - - - +
461M TYR* 4.5 5.2 - - + -
462M ARG* 4.0 33.9 - - + +
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Residues in contact with LYS 425 (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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421M ARG 2.9 18.4 + - - +
422M ALA* 3.3 11.7 - - - +
423M LEU 3.1 0.4 - - - -
424M VAL* 1.3 75.5 - - - +
426M LYS* 1.3 58.0 + - - +
428M ILE* 3.7 7.3 - - - +
429M ALA* 2.9 25.9 + - - +
461M TYR 5.3 0.9 + - - -
462M ARG 5.6 0.2 - - - -
464M SER 5.4 0.2 - - - -
465M LEU* 3.7 31.0 - - + +
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Residues in contact with LYS 426 (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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422M ALA 2.9 11.3 + - - +
423M LEU* 3.0 12.7 + - - +
425M LYS* 1.3 76.3 - - - +
427M LEU* 1.3 60.0 + - - +
429M ALA* 2.9 20.7 + - - +
430M ALA* 2.9 17.3 + - - +
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Residues in contact with LEU 427 (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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423M LEU 2.9 15.8 + - - +
424M VAL* 4.0 6.5 - - - +
426M LYS* 1.3 76.2 - - - +
428M ILE* 1.3 56.6 + - - +
430M ALA 2.9 22.8 - - - +
431M GLU* 3.3 9.0 - - - +
445M MET* 6.5 0.9 - - + -
446M LEU* 6.0 7.2 - - + -
462M ARG* 6.3 1.3 - - + -
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Residues in contact with ILE 428 (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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424M VAL 2.9 16.5 + - - +
425M LYS* 3.7 7.4 - - - +
427M LEU* 1.3 75.0 - - - +
429M ALA* 1.3 64.2 + - - +
431M GLU* 4.3 10.4 + - - +
462M ARG* 3.2 29.4 - - + +
464M SER 4.5 2.2 - - - +
465M LEU 5.0 3.8 - - - +
466M SER 5.7 0.2 - - - -
467M ILE* 3.7 24.1 - - + +
468M PRO* 4.9 5.4 - - - +
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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