Contacts of the helix formed by residues 408 - 415 (chain A) in PDB entry 2HK5
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 ALA 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A TRP 4.0 0.4 + - - -
407A THR* 1.3 75.6 - - - +
409A PRO* 1.3 75.7 - - + +
410A GLU* 3.3 28.3 - - - +
411A ALA* 3.0 5.8 + - + +
412A ILE* 2.9 19.2 + - - +
421A SER* 3.6 23.2 + - - -
424A TRP* 3.7 25.1 - - + +
484A ARG* 4.0 1.1 - - - +
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Residues in contact with PRO 409 (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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407A THR 3.4 2.9 - - - +
408A ALA* 1.3 86.0 - - + +
410A GLU* 1.3 62.7 + - - +
412A ILE* 3.2 11.4 + - + +
413A ASN* 2.8 44.1 + - - +
424A TRP* 3.6 42.8 - - + -
453A LEU* 4.4 18.4 - - + -
454A GLU* 6.5 1.6 - - + -
458A ARG* 5.8 0.9 - - - +
479A ASN* 5.8 7.6 - - - +
484A ARG* 5.0 0.7 - - - +
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Residues in contact with GLU 410 (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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408A ALA* 3.5 14.8 - - - +
409A PRO* 1.3 77.0 - - - +
411A ALA* 1.3 61.1 + - - +
413A ASN* 4.5 1.6 - - - +
414A PHE* 3.0 40.7 + - + +
416A SER* 3.4 32.1 + - - +
418A THR* 4.7 1.4 + - - -
421A SER* 3.6 10.6 + - - -
479A ASN 4.4 2.5 - - - +
481A PRO* 3.8 24.9 - - + +
484A ARG* 2.8 46.8 + - - -
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Residues in contact with ALA 411 (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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402A PHE* 5.0 3.7 - - - -
407A THR* 3.8 16.8 - - + -
408A ALA* 3.0 18.0 + - + +
410A GLU* 1.3 79.7 - - - +
412A ILE* 1.3 65.7 + - - +
415A GLY* 3.0 20.6 + - - -
416A SER 3.7 22.4 - - - +
417A PHE* 3.8 26.8 - - + -
421A SER* 4.4 2.5 - - - -
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Residues in contact with ILE 412 (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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402A PHE* 5.1 8.7 - - + +
404A ILE* 3.6 37.9 - - + +
407A THR* 3.3 37.9 - - + +
408A ALA 2.9 13.3 + - - +
409A PRO* 3.5 9.9 - - + +
411A ALA* 1.3 80.2 - - - +
413A ASN* 1.3 72.1 + - - +
415A GLY 4.4 1.2 + - - -
450A ILE* 4.2 25.1 - - + -
453A LEU* 6.1 3.4 - - + -
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Residues in contact with ASN 413 (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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398A GLU* 4.9 5.4 - - - +
409A PRO* 2.8 32.3 + - - +
410A GLU* 5.0 0.2 - - - +
412A ILE* 1.3 85.2 - - - +
414A PHE* 1.3 93.2 + - + +
450A ILE* 4.5 14.0 - - - +
454A GLU* 4.5 17.0 + - - +
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Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A THR* 4.4 11.1 - - - +
396A ALA 4.7 0.9 - - - +
398A GLU* 4.5 16.8 - - - +
410A GLU* 3.0 21.3 + - + +
413A ASN* 1.3 103.9 - - + +
415A GLY* 1.3 64.6 + - - +
416A SER* 3.4 13.5 + - - +
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Residues in contact with GLY 415 (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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394A TYR 3.3 3.5 - - - +
395A THR* 3.3 3.2 - - - -
396A ALA* 2.9 43.8 + - - -
397A ARG 5.7 0.4 - - - -
398A GLU* 5.0 1.7 + - - -
402A PHE* 6.0 0.2 - - - -
411A ALA 3.0 19.0 + - - -
412A ILE 4.4 1.4 + - - -
413A ASN 3.9 0.8 - - - -
414A PHE* 1.3 78.1 - - - +
416A SER* 1.3 57.8 + - - +
417A PHE* 3.2 13.0 + - - -
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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