Contacts of the helix formed by residues 442 - 449 (chain A) in PDB entry 2KFZ
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 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A VAL* 4.2 3.6 - - + -
418A GLY 3.0 9.8 + - - -
419A GLN* 2.6 29.9 + - - +
440A PHE 4.1 0.2 - - - -
441A ASP* 1.3 71.6 - - - +
443A MET* 1.3 60.3 + - - +
445A GLU* 3.6 22.0 - - - +
446A SER* 3.1 21.0 + - - -
461A LEU* 3.7 3.4 - - - +
505A THR* 3.5 36.4 + - + +
508A LEU* 4.1 10.1 - - + +
509A HIS* 3.9 13.0 - - + +
512A MET* 3.3 14.7 - - - +
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Residues in contact with MET 443 (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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419A GLN* 3.3 20.5 + - - +
420A ASN* 4.0 22.2 - - - +
441A ASP* 3.1 16.4 + - - +
442A THR* 1.3 77.1 - - - +
444A LEU* 1.3 85.0 + - + +
446A SER* 3.6 3.8 + - - -
447A TYR* 3.1 24.5 + - - +
456A HIS* 3.5 26.2 - - + +
461A LEU* 4.5 0.4 - - - -
661A GLN* 4.5 10.8 - - + +
662A ALA* 3.9 23.8 - - + +
1005B A 3.6 38.8 - - - +
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Residues in contact with LEU 444 (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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441A ASP* 3.0 22.5 + - + +
443A MET* 1.3 93.4 - - + +
445A GLU* 1.3 63.7 + - - +
447A TYR* 3.7 7.2 - - + -
448A ILE* 3.0 29.8 + - - +
526A PHE* 3.9 12.7 - - + -
530A GLU* 4.0 17.0 - - + +
531A MET* 4.1 4.7 - - - -
534A VAL* 3.4 33.0 - - + -
661A GLN* 3.9 44.4 - - + +
662A ALA* 4.3 5.2 - - + -
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Residues in contact with GLU 445 (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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440A PHE* 3.5 15.5 - - - +
441A ASP 2.9 12.0 + - - +
442A THR* 3.6 13.1 - - - +
443A MET 3.4 0.2 - - - -
444A LEU* 1.3 76.1 - - - +
446A SER* 1.3 65.0 + - - +
448A ILE* 3.9 1.9 - - - +
449A LEU* 3.0 28.6 + - - +
509A HIS* 2.8 47.2 + - - -
512A MET* 3.4 35.9 - - + +
513A TRP* 4.3 6.7 - - - +
516A LEU* 3.8 14.9 - - + +
526A PHE* 3.5 23.1 - - + -
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Residues in contact with SER 446 (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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442A THR 3.1 14.1 + - - -
443A MET 3.6 4.5 - - - -
445A GLU* 1.3 81.6 - - - +
447A TYR* 1.3 61.6 + - - +
449A LEU* 3.3 6.4 + - - +
450A ASN* 3.2 23.9 + - - +
453A ALA* 5.7 1.2 - - - +
456A HIS* 2.7 27.0 - - - -
461A LEU* 3.2 28.7 - - - +
464A ARG* 4.1 4.0 + - - -
465A TRP* 4.7 3.3 + - - -
512A MET* 3.7 13.6 - - - -
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Residues in contact with TYR 447 (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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443A MET 3.1 18.3 + - - +
444A LEU* 3.7 11.4 - - + +
445A GLU 3.3 0.2 - - - -
446A SER* 1.3 77.4 - - - +
448A ILE* 1.3 63.7 + - + +
451A SER* 3.1 40.0 + - - -
456A HIS* 3.6 24.0 - + - +
530A GLU* 4.7 1.3 - - - -
661A GLN 3.3 24.8 + - - -
662A ALA* 3.5 30.1 - - + -
663A VAL 3.6 2.4 + - - -
664A THR* 2.5 45.6 + - - -
667A GLY* 3.2 12.4 - - - -
668A ARG 4.4 0.5 + - - -
821A ARG* 3.2 29.8 - - - -
857A LYS* 4.9 0.7 - - - -
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Residues in contact with ILE 448 (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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444A LEU 3.0 19.4 + - - +
445A GLU 4.0 2.7 - - - +
447A TYR* 1.3 78.4 - - + +
449A LEU* 1.3 66.2 + - - +
450A ASN* 3.5 0.7 + - - -
451A SER 5.1 0.2 + - - -
516A LEU* 3.9 10.8 - - + -
522A PRO* 3.2 50.4 - - + +
525A VAL* 3.7 12.8 - - + -
526A PHE* 4.0 11.7 - - + -
530A GLU* 3.5 33.0 - - + -
821A ARG* 3.6 23.8 - - + +
822A ARG* 5.4 8.5 + - - +
824A TYR* 5.5 1.2 - - - -
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Residues in contact with LEU 449 (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 GLU 3.0 17.3 + - - +
446A SER* 3.3 6.0 + - - +
448A ILE* 1.3 78.9 - - - +
450A ASN* 1.3 63.6 + - + +
465A TRP* 3.5 37.5 - - + -
512A MET* 3.9 25.4 - - + +
515A ASP* 4.3 9.6 - - + +
516A LEU* 3.4 43.5 - - + +
522A PRO* 5.6 3.7 - - + +
824A TYR* 3.4 19.4 + - - -
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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