Contacts of the strand formed by residues 428 - 433 (chain M) in PDB entry 4K4I
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 VAL 428 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387M MET* 3.7 26.7 - - + -
392M ALA* 4.1 20.4 - - + +
395M ILE* 4.1 29.6 - - + -
396M GLU 4.8 0.7 - - - +
414M ALA* 4.3 15.9 - - + -
418M TYR* 6.1 3.1 - - + -
427M ASP* 1.3 81.6 - - - +
429M ASP* 1.3 60.5 + - - +
430M VAL* 4.1 21.3 - - + -
488M ARG 3.1 6.8 + - - +
489M LEU* 3.3 8.4 - - + +
490M ASP 2.8 31.4 + - - -
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Residues in contact with ASP 429 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413M VAL 3.8 0.2 - - - +
414M ALA* 3.3 3.3 - - - -
415M CYS* 2.9 43.6 + - + +
416M GLY* 4.3 9.5 - - - +
427M ASP* 2.8 6.1 - - - +
428M VAL* 1.3 73.3 - - - +
430M VAL* 1.3 59.9 + - - +
431M LEU 3.9 0.6 + - - -
490M ASP* 2.9 32.6 - - + +
492M ILE* 4.5 11.4 - - + -
506M PHE* 4.7 12.3 - - + +
601M 1RY 5.4 4.1 - - - +
604M CA 2.3 31.0 - - - -
605M CA 2.4 17.7 - - - -
6O C 5.4 1.5 - - - +
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Residues in contact with VAL 430 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396M GLU* 4.2 19.5 - - + -
399M VAL* 3.9 43.3 - - + -
412M CYS* 4.2 12.1 - - + -
413M VAL 3.7 9.4 - - - +
414M ALA* 4.7 0.9 - - - -
428M VAL* 4.1 18.8 - - + -
429M ASP* 1.3 72.3 - - - +
431M LEU* 1.3 63.5 + - - +
432M ILE* 4.2 13.0 - - + +
489M LEU* 4.1 5.2 - - + -
490M ASP 2.8 14.3 + - - +
491M ILE* 3.3 6.1 - - + +
492M ILE* 2.9 28.8 + - - +
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Residues in contact with LEU 431 (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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411M LEU 3.8 1.0 - - - +
412M CYS* 3.4 2.3 - - - -
413M VAL* 2.9 40.8 + - + +
415M CYS* 3.9 11.0 - - - -
429M ASP 3.9 1.0 + - - -
430M VAL* 1.3 71.8 - - - +
432M ILE* 1.3 61.3 + - - +
492M ILE* 3.4 31.6 - - + +
494M VAL* 3.9 15.3 - - + -
499M PHE* 3.7 29.2 - - + -
502M ALA* 3.7 21.1 - - + +
503M LEU* 3.5 40.6 - - + +
506M PHE* 4.4 5.4 - - + -
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Residues in contact with ILE 432 (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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399M VAL* 4.2 12.1 - - + -
403M ALA* 4.6 2.2 - - + -
410M LEU* 4.1 26.0 - - + -
411M LEU 3.2 7.4 - - - +
412M CYS* 3.8 22.9 - - + -
430M VAL* 4.2 3.1 - - + -
431M LEU* 1.3 82.1 - - - +
433M THR* 1.3 65.2 + - - +
443M ILE* 4.7 6.3 - - + -
447M LEU* 3.4 32.8 - - + -
491M ILE* 3.9 18.2 - - + -
492M ILE 2.7 11.6 + - - +
493M VAL* 3.3 16.6 - - + +
494M VAL* 2.9 28.2 + - - +
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Residues in contact with THR 433 (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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410M LEU* 3.4 12.9 - - - +
411M LEU* 2.9 37.8 + - + +
432M ILE* 1.3 73.5 - - - +
434M HIS* 1.4 65.3 + - - +
440M HIS* 4.4 3.4 - - - -
494M VAL* 2.7 25.8 + - - -
496M TYR* 3.1 32.4 + - + -
499M PHE* 3.5 45.8 - - + -
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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