Contacts of the helix formed by residues 456 - 466 (chain A) in PDB entry 3MK2
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 THR 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ALA* 3.3 11.7 - - + -
102A GLY 3.5 31.6 - - - +
103A VAL* 3.6 6.3 - - - +
104A LYS* 3.6 34.3 - - + +
454A GLU* 3.5 15.2 - - - +
455A GLN* 1.3 74.0 - - - +
457A PHE* 1.3 66.9 + - - +
458A ILE 3.1 1.4 + - - -
459A ALA* 3.1 13.0 + - - +
460A HIS* 3.1 18.8 + - - -
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Residues in contact with PHE 457 (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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448A LEU* 3.2 27.8 - - + -
449A VAL* 3.9 6.3 - - + -
450A HIS* 5.2 0.9 - + - -
453A GLN* 3.1 51.4 - - + -
454A GLU* 3.0 16.8 + - + +
456A THR* 1.3 81.9 + - - +
458A ILE* 1.3 59.4 + - + +
460A HIS* 4.4 10.3 - - + -
461A VAL* 2.8 55.9 + - + +
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Residues in contact with ILE 458 (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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38A ILE* 3.7 21.3 - - + -
80A SER* 3.9 18.8 - - - +
99A TYR* 3.6 22.7 - - + +
353A LEU* 3.7 20.4 - - + -
355A THR* 3.8 24.7 - - + +
439A VAL* 4.0 27.8 - - + -
454A GLU 5.5 0.2 - - - +
455A GLN* 3.4 20.2 - - + +
456A THR 3.1 0.4 - - - -
457A PHE* 1.3 81.3 - - + +
459A ALA* 1.3 63.6 + - - +
461A VAL* 3.4 2.9 - - - +
462A MET* 3.1 29.4 + - - +
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Residues in contact with ALA 459 (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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98A ALA 3.6 1.6 - - - +
99A TYR 3.4 19.7 + - - +
100A LEU 3.8 1.3 - - - -
101A CYS 3.9 0.4 - - - -
102A GLY* 3.3 36.1 - - - +
132A VAL* 3.3 28.4 - - + +
135A ARG* 5.1 1.1 - - - +
456A THR 3.1 2.6 + - - -
458A ILE* 1.3 78.7 - - - +
460A HIS* 1.3 59.4 + - + +
462A MET* 3.3 4.9 + - - +
463A ALA* 3.0 24.9 + - - +
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Residues in contact with HIS 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A CYS 5.4 1.8 - - - -
102A GLY* 2.8 33.6 + - - -
103A VAL* 6.0 0.7 - - + -
135A ARG* 5.8 4.4 + - - +
456A THR* 3.1 28.4 + - - +
457A PHE* 3.2 15.9 + - + +
459A ALA* 1.3 77.7 - - - +
461A VAL* 1.3 57.3 + - - +
463A ALA* 3.3 2.0 + - - +
464A PHE* 2.8 31.1 + - - +
470A PRO* 5.1 9.8 - - + +
471A TYR* 2.7 39.3 + + + +
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Residues in contact with VAL 461 (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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351A LEU* 4.4 5.8 - - + -
353A LEU* 3.9 23.8 - - + -
445A GLN* 3.9 10.3 - - + +
448A LEU* 3.7 36.6 - - + -
449A VAL* 3.9 15.5 - - + -
457A PHE* 2.8 41.4 + - + +
458A ILE* 3.4 8.5 - - - +
460A HIS* 1.3 73.1 - - - +
462A MET* 1.3 60.6 + - + +
464A PHE* 3.6 4.6 - - - +
465A ALA* 2.8 32.6 + - - +
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Residues in contact with MET 462 (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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36A LEU* 3.4 36.8 - - + +
37A ILE 3.7 31.6 - - - +
38A ILE* 3.8 19.7 - - + -
99A TYR 5.0 1.3 - - - +
100A LEU* 6.3 0.2 - - - -
132A VAL* 4.3 9.6 - - + -
307A PHE* 3.7 25.8 - - + -
351A LEU* 4.1 9.0 - - + +
353A LEU* 4.1 22.4 - - + -
458A ILE* 3.1 22.9 - - - +
459A ALA* 3.3 9.8 + - - +
460A HIS 3.2 0.4 - - - -
461A VAL* 1.3 75.5 - - + +
463A ALA* 1.3 65.3 + - - +
465A ALA 3.4 0.7 + - - -
466A ALA 3.2 17.3 + - - -
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Residues in contact with ALA 463 (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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132A VAL* 4.0 9.8 - - + +
135A ARG* 3.8 13.7 - - - +
459A ALA 3.0 15.8 + - - +
460A HIS* 3.7 4.5 - - - +
462A MET* 1.3 75.5 - - - +
464A PHE* 1.3 62.5 + - - +
466A ALA 3.4 0.5 + - - -
467A CYS 3.0 3.3 + - - -
468A LEU* 2.8 38.4 + - + +
469A GLU 3.8 22.9 - - - +
471A TYR* 3.9 10.5 - - + -
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Residues in contact with PHE 464 (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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445A GLN* 3.7 15.0 - - + -
448A LEU* 3.5 33.7 - - + -
460A HIS 2.8 18.3 + - - +
461A VAL* 3.6 6.5 - - - +
463A ALA* 1.3 78.7 - - - +
465A ALA* 1.3 67.2 - - - +
467A CYS* 3.0 14.2 + - - -
471A TYR* 3.5 34.7 - + + -
474A CYS* 3.7 32.3 - - + +
476A LEU* 3.7 26.0 - - + +
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Residues in contact with ALA 465 (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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32A ALA* 3.3 13.3 - - - +
33A ALA* 2.7 32.3 + - + -
351A LEU* 3.4 25.8 - - + -
444A PRO 3.7 13.9 - - - +
445A GLN* 3.7 18.2 - - + -
461A VAL 2.8 21.5 + - - +
462A MET 3.8 2.5 - - - +
464A PHE* 1.3 73.7 - - - +
466A ALA* 1.3 54.4 + - - +
467A CYS 3.6 0.2 + - - -
476A LEU* 3.7 1.1 - - - +
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Residues in contact with ALA 466 (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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32A ALA* 5.0 1.1 - - - -
33A ALA 3.4 19.1 - - - +
36A LEU* 3.6 34.1 - - + -
141A LYS* 4.0 14.6 + - - -
462A MET 3.2 6.9 + - - +
465A ALA* 1.3 75.9 - - - +
467A CYS* 1.3 70.0 + - - +
468A LEU* 3.2 20.2 + - + +
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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