Contacts of the helix formed by residues 415 - 420 (chain M) in PDB entry 5IIO
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 CYS 415 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413M VAL* 3.7 15.5 - - - -
414M ALA* 1.3 73.1 - - - +
416M GLY* 1.3 71.0 + - - +
418M TYR* 3.4 10.6 + - - +
419M ARG* 2.9 22.2 + - - -
428M VAL* 6.1 0.5 - - - -
429M ASP* 2.8 21.7 + - + +
431M LEU* 3.9 20.4 - - - -
503M LEU* 4.0 22.7 - - - -
506M PHE* 3.4 29.6 - - + +
507M THR* 3.8 7.9 - - - +
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Residues in contact with GLY 416 (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 CYS* 1.3 82.7 - - - +
417M SER* 1.3 62.1 + - - -
419M ARG* 3.1 6.9 + - - +
420M ARG* 3.1 22.9 + - - +
427M ASP* 5.7 3.8 - - - -
429M ASP* 4.9 7.0 - - - +
506M PHE 2.9 17.2 + - - -
507M THR* 3.5 9.3 - - - +
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Residues in contact with SER 417 (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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386M ARG* 3.8 10.6 + - - -
416M GLY* 1.3 68.8 - - - -
418M TYR* 1.3 67.7 + - - +
420M ARG* 3.1 25.9 + - - +
421M GLY 3.0 16.8 + - - -
422M LYS* 3.1 30.3 + - - +
425M CYS* 3.5 26.9 - - - +
426M GLY 4.2 2.8 + - - -
427M ASP* 4.7 3.4 + - - -
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Residues in contact with TYR 418 (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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389M ARG* 2.8 69.1 + - + +
392M ALA* 3.5 21.3 - - + -
393M THR* 2.7 46.7 + - - +
396M GLU* 5.6 2.1 - - + +
414M ALA* 3.5 34.5 - - + -
415M CYS 3.4 8.3 - - - +
417M SER* 1.3 82.2 + - - +
419M ARG* 1.3 61.1 + - - +
421M GLY 3.0 8.0 + - - -
425M CYS* 3.7 17.2 - - + +
427M ASP 5.5 3.5 + - - +
428M VAL* 5.8 3.4 - - + -
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Residues in contact with ARG 419 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389M ARG* 5.0 0.8 + - - +
413M VAL* 4.1 14.3 - - - +
414M ALA 3.5 21.8 - - - +
415M CYS* 2.9 19.6 + - - +
416M GLY 3.7 1.3 - - - +
418M TYR* 1.3 81.8 - - - +
420M ARG* 1.3 58.8 + - - +
421M GLY* 3.1 4.2 + - - -
503M LEU* 4.0 20.3 + - - +
507M THR* 2.8 42.5 + - + +
556M GLU* 2.8 41.2 + - - -
567M TYR* 4.5 3.0 + - - -
570M PRO* 3.3 28.5 - - + +
571M ALA 4.7 0.2 + - - -
573M ARG* 3.7 5.3 - - - +
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Residues in contact with ARG 420 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416M GLY* 3.1 17.6 + - - +
417M SER* 3.1 25.2 + - - +
419M ARG* 1.3 77.9 - - - +
421M GLY* 1.3 58.8 + - - +
422M LYS* 3.4 17.5 + - - +
507M THR* 2.9 36.4 + - + -
508M GLY 3.9 3.1 - - - -
509M SER* 3.6 27.6 - - - +
570M PRO 3.3 25.6 - - - +
571M ALA* 3.4 23.6 - - - +
573M ARG* 3.6 18.5 + - - -
574M ASP* 3.0 25.0 + - - +
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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