Contacts of the helix formed by residues 441 - 448 (chain A) in PDB entry 5IKP
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 MET 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A THR* 3.6 15.3 - - + -
343A ALA* 3.8 17.4 - - + +
344A LEU* 4.2 14.1 - - + -
385A GLU* 3.1 24.5 + - - +
387A TRP* 3.6 30.7 - - + -
392A PHE* 4.0 22.2 - - + -
403A ILE* 5.0 0.2 - - + -
439A ILE* 3.7 30.5 - - + +
440A ASN* 1.3 70.0 - - - +
442A ALA* 1.3 58.9 + - - +
444A LEU* 3.4 27.9 + - + +
445A CYS* 3.0 32.1 + - - -
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Residues in contact with ALA 442 (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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340A THR* 3.4 14.2 - - + +
374A TYR* 4.0 14.4 - - - +
384A LEU* 3.8 35.2 - - + -
385A GLU 4.0 1.6 + - - +
440A ASN* 3.1 10.2 + - - +
441A MET* 1.3 76.8 - - - +
443A HIS* 1.3 63.4 + - - +
445A CYS* 3.3 14.7 + - - +
446A VAL* 3.4 19.4 + - - +
468A PHE* 4.1 7.5 - - + -
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Residues in contact with HIS 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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384A LEU* 5.7 1.6 - - + +
426A ARG 5.5 0.9 - - - -
427A ARG 3.7 20.9 + - - -
428A MET 4.3 1.0 + - - -
429A SER 2.8 24.0 + - - +
430A VAL* 4.1 13.0 - - + -
432A GLU* 4.6 4.9 - - + -
440A ASN* 3.0 43.2 + - - +
441A MET 3.3 0.2 - - - -
442A ALA* 1.3 71.8 - - - +
444A LEU* 1.3 60.7 + - - +
446A VAL* 3.1 7.0 + - - +
447A ILE* 3.0 33.5 + - - +
467A VAL 5.2 3.4 + - - -
468A PHE* 4.2 21.1 - + - -
471A PHE* 3.8 28.7 - + + -
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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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343A ALA* 3.5 24.9 - - + +
346A ILE* 3.4 20.7 - - + +
347A PRO* 3.9 12.8 - - + -
403A ILE* 4.0 28.7 - - + -
406A ILE* 4.4 19.1 - - + -
430A VAL* 4.0 22.1 - - + +
439A ILE* 5.2 0.9 - - + -
440A ASN 3.4 8.7 + - - +
441A MET* 3.4 32.3 + - + +
443A HIS* 1.3 77.2 - - - +
445A CYS* 1.3 56.1 + - - +
447A ILE* 4.5 2.9 - - + -
448A GLY* 3.1 22.8 + - - -
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Residues in contact with CYS 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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337A LEU* 5.0 3.6 - - + -
339A ASP 4.9 0.9 - - - -
340A THR* 4.1 6.7 - - - -
343A ALA* 3.5 30.5 - - - -
346A ILE* 3.8 8.3 - - - -
374A TYR* 3.6 42.0 - - + +
441A MET 3.0 24.3 + - - -
442A ALA 3.4 10.1 - - - +
443A HIS 3.2 0.4 - - - -
444A LEU* 1.3 76.5 - - - +
446A VAL* 1.3 57.8 + - - +
448A GLY 3.9 0.3 - - - -
449A SER* 3.0 34.8 + - - -
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Residues in contact with VAL 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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374A TYR* 4.2 3.1 - - + -
442A ALA 3.4 13.4 + - - +
443A HIS* 3.1 7.2 + - - +
445A CYS* 1.3 73.0 - - - +
447A ILE* 1.3 63.0 + - - +
448A GLY 3.1 1.3 - - - -
449A SER 3.1 12.0 + - - +
452A VAL* 3.8 24.2 - - + -
468A PHE* 4.1 32.5 - - + -
471A PHE* 4.1 31.4 - - + -
478A LYS* 2.9 39.9 + - - -
479A PHE* 4.3 8.3 - - + -
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Residues in contact with ILE 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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365A TRP* 3.2 17.8 - - + -
369A LYS* 3.6 15.5 - - - +
406A ILE* 3.6 30.7 - - + -
410A HIS* 3.5 53.4 - - + +
428A MET 4.2 0.4 - - - +
430A VAL* 3.5 29.6 - - + -
443A HIS 3.0 16.9 + - - +
444A LEU* 4.3 4.7 - - - +
446A VAL* 1.3 75.3 - - - +
448A GLY* 1.3 57.8 + - - +
449A SER 3.9 0.2 + - - -
471A PHE* 3.6 18.8 - - + -
478A LYS* 4.3 6.0 + - - +
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Residues in contact with GLY 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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346A ILE* 3.9 16.7 - - - +
365A TRP* 3.6 16.6 - - - -
368A THR* 3.7 2.8 - - - +
369A LYS* 3.3 20.8 + - - -
372A CYS* 3.4 13.3 - - - +
444A LEU 3.1 18.3 + - - -
445A CYS 3.9 0.7 - - - -
447A ILE* 1.3 78.3 - - - +
449A SER* 1.3 59.2 + - - +
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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