Contacts of the strand formed by residues 486 - 493 (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 HIS 486 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379M HIS* 3.4 30.3 + + + +
382M ASP* 3.1 39.2 + - + +
383M PHE* 3.7 5.4 - - + -
458M THR* 3.4 44.2 + - + +
476M VAL* 3.9 9.9 - - + -
477M CYS 3.4 4.9 - - - -
478M ARG* 3.4 40.6 + - + -
484M ARG 5.2 0.8 + - - -
485M ARG* 1.3 73.2 - - - +
487M ARG* 1.3 67.1 + - - +
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Residues in contact with ARG 487 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382M ASP 4.0 4.7 + - - -
383M PHE* 3.9 7.0 - - - -
385M GLU* 2.8 51.6 + - - +
387M MET* 3.5 42.0 - - + +
388M PRO* 4.1 2.6 - - - +
391M GLU* 2.6 44.7 + - - +
395M ILE* 4.0 10.5 - - + -
476M VAL* 3.2 5.0 - - - -
477M CYS* 2.8 47.9 + - - +
478M ARG* 5.9 0.2 - - - -
479M LEU 6.2 0.2 - - - +
485M ARG* 3.7 26.0 - - - +
486M HIS* 1.3 81.8 - - - +
488M ARG* 1.3 63.9 + - - +
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Residues in contact with ARG 488 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342M TRP* 3.4 37.0 - - + +
383M PHE* 3.9 30.3 - - + -
387M MET* 5.3 0.2 - - - +
426M GLY 5.0 3.9 + - - +
427M ASP* 3.4 25.5 + - + +
428M VAL* 3.1 25.6 + - - +
461M LEU* 3.3 18.6 - - - +
474M LEU* 3.7 4.8 - - - +
475M GLY 2.8 24.8 + - - +
477M CYS* 5.3 0.2 - - - -
487M ARG* 1.3 76.2 - - - +
489M LEU* 1.3 80.7 + - - +
490M ASP* 2.5 34.6 + - - -
6O C 3.0 24.2 + - - -
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Residues in contact with LEU 489 (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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395M ILE* 4.1 7.9 - - + -
399M VAL* 4.1 11.9 - - + -
428M VAL* 3.3 17.7 - - + +
430M VAL* 4.1 16.8 - - + -
456M PHE* 4.1 16.2 - - + -
457M LEU* 4.1 14.1 - - + -
473M TYR* 4.1 4.3 - - + -
474M LEU* 3.9 0.2 - - - -
475M GLY 2.9 23.6 + - - +
476M VAL 4.9 0.2 - - - +
477M CYS* 4.1 22.7 - - + +
487M ARG 3.5 0.4 + - - -
488M ARG* 1.3 96.6 + - - +
490M ASP* 1.3 79.8 + - - +
491M ILE* 3.8 25.6 - - + -
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Residues in contact with ASP 490 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427M ASP* 5.5 0.7 - - - -
428M VAL 2.8 6.6 + - - +
429M ASP* 2.9 30.3 - - + +
430M VAL 2.8 24.2 + - - -
472M LYS* 5.2 0.9 - - + -
473M TYR 3.2 6.7 - - - +
474M LEU* 3.3 23.7 - - + +
488M ARG* 2.5 43.6 + - - -
489M LEU* 1.3 80.8 - - - +
491M ILE* 1.3 63.0 + - - +
492M ILE* 4.5 9.9 - - + -
604M CA 3.9 4.3 - - - -
6O C 4.0 17.3 + - - +
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Residues in contact with ILE 491 (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* 4.0 15.3 - - + -
430M VAL* 3.3 5.6 - - + +
432M ILE* 3.9 26.5 - - + -
444M PHE* 4.0 7.3 - - + -
447M LEU* 4.1 8.1 - - + -
448M LEU* 4.1 17.5 - - + -
451M LEU* 4.0 24.0 - - + -
457M LEU* 5.3 0.2 - - + -
471M GLN 3.9 0.5 - - - +
472M LYS* 3.4 2.8 - - - -
473M TYR* 2.7 48.5 + - + +
489M LEU* 3.8 26.7 - - + -
490M ASP* 1.3 79.4 - - - +
492M ILE* 1.3 66.8 + - - +
493M VAL* 4.6 6.3 - - + -
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Residues in contact with ILE 492 (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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429M ASP* 4.5 9.9 - - + -
430M VAL 2.9 27.1 + - - +
431M LEU* 3.4 20.4 - - + +
432M ILE* 2.7 33.8 + - - +
470M GLN* 4.1 7.2 - - + +
471M GLN 3.3 11.4 - - - +
472M LYS* 3.9 22.7 - - + -
490M ASP* 4.5 7.0 - - + -
491M ILE* 1.3 79.1 - - - +
493M VAL* 1.3 60.4 + - - +
494M VAL* 3.9 12.8 - - + -
506M PHE* 4.0 41.5 - - + -
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Residues in contact with VAL 493 (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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432M ILE* 3.3 26.5 - - + +
440M HIS* 3.7 40.7 - - + +
443M ILE* 5.2 2.5 - - + -
444M PHE* 3.7 41.1 - - + +
447M LEU* 5.5 0.4 - - + -
469M GLN 4.1 1.2 - - - +
470M GLN* 3.4 4.7 - - - -
471M GLN* 2.8 47.1 + - - +
491M ILE* 4.6 6.7 - - + -
492M ILE* 1.3 74.1 - - - +
494M VAL* 1.3 64.5 + - - +
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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
------------------------------------------------------------
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