Contacts of the helix formed by residues 463 - 469 (chain D) in PDB entry 2IHU
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 ASP 463 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C ARG* 3.1 13.6 + - - +
462D GLY* 1.3 71.3 - - - -
464D GLY* 1.3 67.2 + - - +
466D PHE* 4.6 0.2 - - - -
467D HIS* 3.1 20.4 + - - +
487D VAL* 4.2 3.1 - - - +
488D VAL 3.2 5.0 + - - +
489D ASN* 3.1 26.4 - - + +
490D ASN 3.1 13.2 + - - -
491D ASP* 3.3 9.3 + - - -
492D THR 3.1 19.8 + - - -
514D PHE* 3.6 9.7 - - - -
519D PHE* 3.6 24.9 - - + -
600D TP9 3.3 0.2 + - - -
601D MG 2.4 26.5 - - - -
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Residues in contact with GLY 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ARG* 3.8 6.7 + - - +
438D PHE* 4.0 7.9 - - - -
463D ASP* 1.3 76.7 - - - +
465D GLY* 1.3 59.8 + - - +
468D SER* 3.4 19.2 + - - -
493D ASN* 3.2 26.0 - - - -
514D PHE* 3.8 14.4 - - - -
600D TP9 2.7 17.7 + - - -
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Residues in contact with GLY 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D ASP* 4.0 7.4 - - - -
438D PHE* 3.6 30.0 - - - -
439D GLY* 3.2 15.7 - - - -
464D GLY* 1.3 68.9 - - - +
466D PHE* 1.3 63.2 + - - +
468D SER* 2.7 21.3 + - - -
600D TP9 2.7 20.4 + - - -
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Residues in contact with PHE 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D ASP* 4.4 5.2 + - - -
439D GLY* 5.2 0.9 - - - -
442D ILE* 3.6 38.1 - - + +
459D LEU* 4.4 2.0 - - + -
461D ALA* 3.8 25.4 - - + +
462D GLY 2.8 26.1 + - - +
463D ASP 4.3 0.9 - - - +
465D GLY* 1.3 70.3 - - - +
467D HIS* 1.3 58.5 + - - +
469D ASN* 3.1 6.6 + - - +
470D SER* 3.0 37.2 + - - -
473D LEU* 3.8 14.6 - - + -
485D THR* 3.7 16.4 - - + -
487D VAL* 4.0 11.7 - - + -
519D PHE* 3.7 28.5 - + - -
522D LEU* 4.5 0.2 - - + -
554D LEU* 3.5 28.3 - - + -
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Residues in contact with HIS 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ARG* 3.3 30.1 - - - +
471C SER* 2.6 64.3 + - - -
474C GLU* 4.5 0.2 - - + -
526C ASN* 2.9 27.8 + - - -
463D ASP 3.1 21.0 + - - +
466D PHE* 1.3 73.4 - - - +
468D SER* 1.3 61.3 + - - +
469D ASN 3.0 3.2 + - - -
470D SER* 2.9 29.1 + - - -
517D VAL* 4.0 14.4 - - + +
519D PHE* 4.0 11.0 - + + -
522D LEU* 3.7 28.5 - - + +
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Residues in contact with SER 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ARG* 3.3 28.9 + - - +
56C HIS* 3.7 14.1 - - - +
471C SER* 4.7 3.0 + - - -
1502C K 3.2 20.1 - - - -
438D PHE* 3.4 35.8 + - - -
439D GLY* 3.5 7.4 - - - -
464D GLY 3.4 8.1 + - - -
465D GLY 2.7 18.8 + - - -
466D PHE 3.2 0.4 - - - -
467D HIS* 1.3 76.4 - - - +
469D ASN* 1.3 58.3 + - - +
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Residues in contact with ASN 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D HIS* 4.3 12.8 - - - +
58D PHE* 3.5 19.1 - - + -
59D THR* 3.1 27.9 + - - -
439D GLY* 2.9 38.7 + - - +
442D ILE* 3.7 13.7 - - + +
443D PRO* 3.5 13.3 - - - +
466D PHE 3.1 6.2 + - - +
468D SER* 1.3 82.2 + - - +
470D SER* 1.3 61.0 + - - +
471D SER* 3.3 4.8 + - - -
472D ASP* 3.8 9.8 + - - +
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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