Contacts of the helix formed by residues 472 - 479 (chain C) 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 472 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C THR* 3.5 5.2 - - - -
55C ARG* 2.8 19.7 + - - +
56C HIS* 3.4 15.1 + - - +
59C THR* 2.6 38.2 + - + +
442C ILE* 3.8 21.8 - - + +
446C ILE* 5.0 0.2 - - + -
469C ASN* 3.8 10.8 + - - +
470C SER 3.2 1.8 - - - -
471C SER* 1.3 74.2 - - - +
473C LEU* 1.3 64.4 + - - +
474C GLU 3.1 1.1 - - - +
475C THR* 2.7 38.9 + - - -
476C ILE* 3.2 16.3 + - - +
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Residues in contact with LEU 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C ILE* 3.8 8.7 - - + +
466C PHE* 3.8 35.4 - - + -
470C SER 3.1 20.4 + - - +
472C ASP* 1.3 76.5 - - - +
474C GLU* 1.3 56.4 + - - +
476C ILE* 3.1 18.5 + - + +
477C ALA* 3.0 27.9 + - - +
485C THR* 5.1 4.5 - - - +
519C PHE 5.6 0.2 - - - +
522C LEU* 4.4 7.0 - - + -
523C ALA* 4.0 24.5 - - - +
526C ASN* 3.8 22.0 - - + +
528C VAL* 3.7 22.8 - - + +
554C LEU* 4.0 13.9 - - + -
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Residues in contact with GLU 474 (chain C).
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* 2.9 25.2 + - + +
471C SER 3.3 10.5 + - - +
472C ASP 3.1 0.4 - - - -
473C LEU* 1.3 78.4 - - - +
475C THR* 1.3 51.1 + - - +
477C ALA* 3.3 2.3 + - + +
478C ARG* 2.8 68.5 + - - +
526C ASN* 3.4 29.0 + - - +
514D PHE* 3.7 0.5 - - - -
515D GLY* 2.8 33.2 + - - +
516D GLY 4.4 5.6 - - - +
517D VAL* 3.6 25.6 - - + -
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Residues in contact with THR 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL* 5.1 1.3 - - + -
53C LEU 3.7 16.4 - - - +
54C THR* 3.8 7.1 - - + -
55C ARG* 3.8 7.4 + - - +
446C ILE* 4.1 13.9 - - + -
472C ASP* 2.7 34.8 + - - +
474C GLU* 1.3 76.4 + - - +
476C ILE* 1.3 58.9 + - - +
478C ARG* 3.1 21.1 + - - +
479C LEU* 2.9 59.2 + - + +
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Residues in contact with ILE 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C ILE* 3.7 35.7 - - + -
445C ALA* 5.6 0.9 - - + -
446C ILE* 3.9 20.6 - - + -
459C LEU* 5.8 0.4 - - + -
472C ASP 3.2 8.0 + - - +
473C LEU* 3.1 19.6 + - + +
475C THR* 1.3 76.8 - - - +
477C ALA* 1.3 62.9 + - - +
479C LEU 3.6 0.3 + - - -
480C ASN* 3.1 16.3 + - - -
481C LEU* 3.1 40.2 + - - +
483C ILE* 4.1 25.6 - - + -
485C THR* 5.0 4.3 - - - +
528C VAL* 5.0 2.7 - - + -
552C PRO* 3.4 19.4 - - + +
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Residues in contact with ALA 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C LEU 3.0 9.0 + - - +
474C GLU* 3.4 8.1 - - + +
476C ILE* 1.3 77.1 - - - +
478C ARG* 1.3 57.6 + - - +
480C ASN* 2.9 24.8 + - - +
526C ASN 3.5 22.7 - - - +
527C GLY* 3.8 17.3 - - - +
528C VAL* 4.0 4.0 - - + +
552C PRO* 4.2 11.0 - - - +
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Residues in contact with ARG 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LEU* 2.8 42.2 + - - +
55C ARG* 4.0 3.0 - - - +
474C GLU* 2.8 52.5 + - - +
475C THR* 3.1 20.4 + - - +
477C ALA* 1.3 73.0 - - - +
479C LEU* 1.3 75.8 + - + +
480C ASN* 3.2 2.0 + - - +
513D LYS 3.7 16.3 + - - -
514D PHE* 3.8 19.7 - - - +
515D GLY* 3.7 12.6 - - - +
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Residues in contact with LEU 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL* 3.7 33.7 - - + -
53C LEU 5.8 0.2 - - - +
446C ILE* 4.6 3.6 - - + -
450C MET* 4.6 10.3 - - - -
475C THR* 2.9 32.9 + - + +
478C ARG* 1.3 93.6 - - + +
480C ASN* 1.3 69.8 + - - +
481C LEU* 3.4 35.1 + - + +
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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