Contacts of the helix formed by residues 420 - 426 (chain Q) in PDB entry 1HI0
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 PRO 420 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415Q LEU 3.6 8.7 - - - +
416Q ASP 5.2 2.9 - - - +
417Q HIS 5.2 0.9 - - - -
418Q THR* 3.5 8.3 - - - +
419Q ALA* 1.3 88.5 - - - +
421Q HIS* 1.3 60.1 + - + +
422Q LEU 2.9 6.1 + - - -
423Q ASN* 3.0 40.4 + - - +
424Q SER 4.5 0.9 + - - -
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Residues in contact with HIS 421 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418Q THR 4.0 2.0 + - - -
419Q ALA* 2.9 25.3 + - + +
420Q PRO* 1.3 83.1 - - - +
422Q LEU* 1.3 78.1 + - + +
423Q ASN 3.5 0.2 - - - -
424Q SER* 3.9 12.4 + - - -
425Q ARG* 5.0 1.6 - - - +
445Q GLU* 2.8 28.3 + - - -
463Q ARG* 3.6 60.8 + - + +
464Q ALA 3.8 7.4 - - - -
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Residues in contact with LEU 422 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415Q LEU* 4.0 11.2 - - + -
419Q ALA* 2.7 34.1 + - + +
421Q HIS* 1.3 98.9 - - + +
423Q ASN* 1.3 54.6 + - - +
424Q SER 3.1 3.4 - - - -
425Q ARG* 2.7 68.5 + - + +
426Q ILE* 4.1 5.4 + - - +
435Q PHE* 4.2 16.1 - - + -
444Q GLU* 4.3 5.6 - - + +
445Q GLU* 4.9 10.8 - - + +
446Q ILE* 4.0 24.2 - - + -
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Residues in contact with ASN 423 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122Q ARG* 2.5 45.8 + - - +
415Q LEU* 4.1 8.1 + - - +
419Q ALA 4.8 1.1 - - - -
420Q PRO* 3.0 38.6 + - - +
422Q LEU* 1.3 78.1 - - - +
424Q SER* 1.3 55.0 + - - +
425Q ARG 3.0 0.2 - - - -
426Q ILE* 3.0 36.0 + - - +
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Residues in contact with SER 424 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420Q PRO 4.5 1.4 + - - -
421Q HIS 3.9 14.1 + - - -
422Q LEU 4.2 0.2 + - - -
423Q ASN* 1.3 76.6 - - - +
425Q ARG* 1.3 65.2 + - - +
426Q ILE 3.2 1.2 + - - -
427Q LYS* 2.9 40.4 + - - +
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Residues in contact with ARG 425 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421Q HIS 5.0 0.9 - - - +
422Q LEU* 2.7 51.5 + - + +
424Q SER* 1.3 84.0 - - - +
426Q ILE* 1.3 62.9 + - + +
427Q LYS* 3.8 1.3 - - - -
431Q SER* 3.2 31.2 - - - +
434Q ARG* 5.5 0.2 + - - -
435Q PHE* 3.5 27.9 - - + +
438Q SER* 4.7 3.4 + - - -
444Q GLU* 3.4 30.7 + - - -
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Residues in contact with ILE 426 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122Q ARG* 4.1 29.1 - - + +
125Q LEU* 4.4 13.6 - - + +
126Q LEU* 4.2 14.4 - - + -
415Q LEU* 3.9 26.5 - - + -
422Q LEU 4.2 10.3 - - - +
423Q ASN* 3.0 15.6 + - - +
424Q SER 3.2 0.2 - - - -
425Q ARG* 1.3 82.2 - - - +
427Q LYS* 1.3 61.4 + - - +
431Q SER* 3.8 1.8 - - - -
432Q ALA* 3.8 26.7 - - + +
435Q PHE* 3.8 33.2 - - + -
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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