Contacts of the helix formed by residues 403 - 407 (chain A) in PDB entry 3MPM
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 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A ASN* 5.2 2.2 - - - +
366A ARG* 3.4 28.5 - - - +
388A LEU* 5.4 3.4 - - + -
389A ILE 3.4 26.5 - - - +
390A GLU* 4.2 7.4 - - + -
391A ASP* 5.7 0.4 - - - +
402A PHE* 1.4 100.1 - - + +
404A ILE* 1.3 64.6 + - - +
405A LYS 3.1 4.1 + - - +
406A TRP* 3.3 31.6 + - + +
407A THR* 3.0 16.2 + - - -
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Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A PHE* 2.9 33.3 + - + +
403A PRO* 1.3 72.4 - - - +
405A LYS* 1.3 58.7 + - - +
406A TRP 3.0 5.9 + - - -
407A THR* 3.0 30.0 + - + +
412A ILE* 4.6 11.9 - - + +
446A ASN* 3.7 39.5 - - + +
449A VAL* 4.7 9.9 - - + +
450A ILE* 3.8 36.1 - - + -
453A LEU* 5.6 0.5 - - - +
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Residues in contact with LYS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A PRO 3.1 2.2 - - - -
404A ILE* 1.3 75.9 - - - +
406A TRP* 1.3 73.1 + - + +
407A THR 3.5 0.4 - - - -
424A TRP* 4.9 1.1 + - - -
428A ILE* 3.5 14.7 - - - +
439A ILE* 4.0 25.1 - - + +
440A PRO* 3.0 34.0 + - + +
441A TYR* 3.0 41.7 + - + -
442A PRO* 4.8 0.8 - - - +
443A GLY 4.9 1.0 - - - +
444A MET 2.8 30.1 + - - +
445A THR 4.6 0.2 - - - -
446A ASN* 4.0 19.0 + - - +
449A VAL* 3.7 24.7 - - + -
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Residues in contact with TRP 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LEU 3.6 14.4 - - - +
366A ARG* 3.2 40.2 - - + +
391A ASP* 5.4 5.2 - - - -
403A PRO* 3.3 30.7 + - + +
404A ILE 3.2 1.0 - - - -
405A LYS* 1.3 91.8 - - + +
407A THR* 1.3 59.0 + - - +
408A ALA 3.8 0.2 + - - -
424A TRP* 3.5 9.6 - - - -
425A SER* 2.6 40.3 + - - +
428A ILE* 3.5 27.9 - - + +
429A LEU 4.3 0.4 - - - -
432A GLU* 2.9 43.1 + - - -
439A ILE* 4.1 14.4 - - + -
440A PRO* 3.7 24.7 - - + -
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Residues in contact with THR 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LEU* 5.7 3.7 - - + +
402A PHE* 6.1 0.2 - - - -
403A PRO 3.0 17.8 + - - -
404A ILE* 3.0 20.8 + - + +
405A LYS 3.5 0.8 - - - -
406A TRP* 1.3 77.4 - - - +
408A ALA* 1.3 65.2 + - - +
409A PRO 3.9 0.2 - - - -
411A ALA* 3.6 25.4 - - + -
412A ILE* 3.4 33.9 - - + +
417A PHE* 4.3 15.8 - - + -
424A TRP* 3.7 8.3 + - - -
425A SER* 4.9 0.4 - - - -
453A LEU* 4.4 4.9 - - - +
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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