Contacts of the helix formed by residues 408 - 417 (chain c) in PDB entry 5M32
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 ASP 408 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392c ALA* 3.4 10.2 - - - +
395c PHE* 3.7 21.4 - - + -
396c ALA* 3.7 8.3 - - - +
401c ARG* 2.7 27.1 + - - +
404c ALA* 3.4 12.7 - - - +
405c THR* 2.8 41.8 + - - +
407c LYS* 1.3 73.6 - - + +
409c PHE* 1.3 66.9 + - - -
411c GLU* 3.6 10.1 - - - +
412c ALA* 2.9 27.7 + - - +
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Residues in contact with PHE 409 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355c PHE* 4.0 22.0 - + - -
362c MET* 3.5 34.1 - - + -
364c VAL* 4.2 9.0 - - + -
368c ILE* 3.5 31.4 - - + -
370c PHE* 5.1 0.2 - + - -
373c LEU* 3.6 32.7 - - + +
388c VAL* 4.8 8.1 - - + +
392c ALA* 3.5 22.7 - - + -
404c ALA* 4.0 17.3 - - + -
405c THR 3.3 17.9 - - - -
406c GLU* 3.0 6.9 + - - +
408c ASP* 1.3 83.1 + - - +
410c LEU* 1.3 58.9 + - + +
412c ALA* 2.9 4.7 + - - +
413c VAL* 2.9 28.8 + - - +
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Residues in contact with LEU 410 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D MET* 4.2 20.6 - - + +
207D GLU* 5.7 3.1 - - + -
368c ILE* 5.9 0.4 - - + -
372c LEU* 3.7 27.8 - - + -
373c LEU* 4.0 12.1 - - + -
376c LEU* 5.5 4.0 - - + -
406c GLU* 2.6 47.2 + - + +
407c LYS* 4.1 7.6 - - + -
409c PHE* 1.3 70.6 - - + +
411c GLU* 1.3 63.9 + - - +
413c VAL* 3.5 13.3 - - + +
414c ASN* 3.3 20.6 + - - +
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Residues in contact with GLU 411 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395c PHE* 3.6 28.8 - - + +
407c LYS* 2.7 30.9 + - - +
408c ASP* 3.7 13.7 - - - +
409c PHE 3.2 0.4 - - - -
410c LEU* 1.3 76.3 - - - +
412c ALA* 1.3 62.3 + - - +
414c ASN* 3.5 9.8 - - + +
415c LYS* 3.4 19.9 + - - +
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Residues in contact with ALA 412 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388c VAL* 4.0 12.3 - - + +
391c GLU* 4.3 6.3 - - + -
392c ALA* 3.7 27.6 - - + +
395c PHE* 3.7 10.5 - - + -
408c ASP 2.9 18.9 + - - +
409c PHE* 2.9 6.2 + - - +
411c GLU* 1.3 75.1 - - - +
413c VAL* 1.3 57.5 + - - +
414c ASN 3.1 1.6 - - - -
415c LYS* 2.7 20.9 + - - +
416c VAL* 2.8 20.6 + - - +
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Residues in contact with VAL 413 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373c LEU* 4.8 12.1 - - + +
376c LEU* 4.2 25.8 - - + +
377c CYS* 4.0 24.0 - - + +
388c VAL* 4.8 11.1 - - + +
409c PHE 2.9 15.1 + - - +
410c LEU* 3.5 20.6 - - + +
412c ALA* 1.3 72.5 - - - +
414c ASN* 1.3 66.6 + - + +
416c VAL* 4.3 7.2 - - - -
417c ILE* 3.3 40.4 - - + +
418c LYS* 3.8 1.7 + - - +
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Residues in contact with ASN 414 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410c LEU 3.3 11.3 + - - +
411c GLU* 3.5 14.3 - - - +
412c ALA 3.1 0.2 - - - -
413c VAL* 1.3 83.7 - - + +
415c LYS* 1.3 57.4 + - - +
418c LYS* 3.3 36.0 - - - +
419c SER* 3.6 5.9 + - - -
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Residues in contact with LYS 415 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391c GLU* 3.2 41.9 + - - +
395c PHE* 4.0 14.1 - - + -
411c GLU 3.4 12.8 + - - +
412c ALA* 2.7 20.0 + - - +
414c ASN* 1.3 73.3 - - - +
416c VAL* 1.3 61.6 + - + +
417c ILE 3.6 0.4 - - - -
419c SER* 2.3 30.3 + - - +
420c TYR* 2.7 41.9 + - - -
349d ARG* 3.3 20.9 - - - +
351d ILE* 5.6 1.1 - - - +
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Residues in contact with VAL 416 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384c GLU* 3.7 10.0 - - + +
387c SER* 3.8 19.1 - - - +
388c VAL* 3.7 37.7 - - + +
391c GLU* 4.0 13.5 - - + +
412c ALA 2.8 22.9 + - - +
413c VAL* 4.6 0.9 - - - -
415c LYS* 1.3 89.5 - - + +
417c ILE* 1.3 67.6 + - + +
420c TYR* 3.6 38.7 - - + +
344d PRO* 6.6 0.2 - - + -
349d ARG* 6.3 0.2 - - - -
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Residues in contact with ILE 417 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376c LEU 4.7 5.4 - - - +
377c CYS* 4.0 23.6 - - + +
380c SER* 3.9 24.5 - - - -
384c GLU* 3.8 16.2 - - - +
388c VAL* 5.3 0.9 - - + -
413c VAL* 3.3 35.2 + - + +
416c VAL* 1.3 89.0 - - + +
418c LYS* 1.3 69.1 + - + +
420c TYR 4.2 0.7 - - - -
421c ALA* 3.3 22.9 + - - +
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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