Contacts of the helix formed by residues 463 - 470 (chain B) in PDB entry 1U2Z
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 ASN 463 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421B CYS* 3.7 9.3 - - - -
455B SER* 3.0 24.6 + - - -
458B LYS* 3.8 15.7 - - - +
459B SER 3.0 27.7 + - - +
460B PHE 3.4 15.1 + - - +
462B ASP* 1.3 74.8 - - - +
464B ASN* 1.3 58.3 + - - +
465B ARG* 3.0 12.6 + - - +
466B VAL* 3.0 26.8 + - + +
467B ALA* 2.9 31.0 + - - +
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Residues in contact with ASN 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A LYS* 5.8 3.3 + - - -
448A ARG* 5.6 3.4 - - - +
450A ASN* 4.1 18.4 + - - +
451A ASN* 5.5 8.1 + - - +
462B ASP 3.8 7.0 + - - +
463B ASN* 1.3 74.0 + - - +
465B ARG* 1.3 59.3 + - - +
467B ALA* 3.4 7.4 + - - +
468B GLU* 2.9 31.4 + - - +
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Residues in contact with ARG 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B LEU* 4.1 6.7 - - - +
419B PHE* 3.9 19.1 - - + -
453B GLU* 3.2 39.8 + - - +
455B SER* 5.2 4.0 - - - +
463B ASN* 3.0 9.3 + - - +
464B ASN* 1.3 74.1 - - - +
466B VAL* 1.3 68.8 + - - +
468B GLU* 3.0 50.2 + - - +
469B LEU* 3.1 48.0 + - + +
472B GLN* 5.6 0.8 - - - +
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B MET* 3.7 13.6 - - - +
398B LEU* 4.0 21.5 - - + -
419B PHE* 3.9 21.5 - - + -
421B CYS* 4.1 5.6 - - + -
460B PHE* 4.0 24.2 - - + +
463B ASN* 3.0 38.9 + - + +
465B ARG* 1.3 75.9 - - - +
467B ALA* 1.3 63.3 + - - +
469B LEU* 3.1 2.6 + - - -
470B ILE* 3.0 23.4 + - + +
494B ILE* 4.1 17.7 - - + -
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Residues in contact with ALA 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ASN 2.9 17.7 + - - +
464B ASN* 3.7 9.2 - - - +
465B ARG 3.2 0.2 - - - -
466B VAL* 1.3 80.5 - - - +
468B GLU* 1.3 62.1 + - - +
470B ILE* 3.9 6.5 + - - +
471B PRO* 3.3 19.2 - - - +
494B ILE* 6.1 0.9 - - - -
497B THR* 4.6 2.6 + - - -
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Residues in contact with GLU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ASN 2.9 14.3 + - - +
465B ARG* 3.0 56.3 + - - +
467B ALA* 1.3 78.1 - - - +
469B LEU* 1.3 60.7 + - + +
471B PRO* 3.6 10.8 - - - +
472B GLN* 4.6 8.5 + - - +
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Residues in contact with LEU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B THR* 5.0 2.9 - - + -
396B MET* 3.6 13.7 - - + -
417B LEU* 3.8 20.6 - - + -
419B PHE* 3.7 40.6 - - + -
465B ARG* 3.1 58.9 + - + +
466B VAL 3.1 0.2 + - - -
468B GLU* 1.3 77.4 - - - +
470B ILE* 1.3 67.4 + - - +
471B PRO 3.2 2.7 - - - -
472B GLN* 2.9 44.5 + - + +
473B CYS* 3.3 9.8 + - - -
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Residues in contact with ILE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B MET* 3.5 28.0 - - - -
398B LEU* 5.0 0.9 - - + -
466B VAL* 3.0 21.3 + - + +
467B ALA* 4.2 5.2 - - - +
469B LEU* 1.3 74.9 - - - +
471B PRO* 1.3 68.3 - - + +
472B GLN 3.0 1.9 + - - -
473B CYS* 3.0 21.2 + - - +
476B ILE* 4.0 17.6 - - + +
494B ILE* 3.8 38.4 - - + +
495B LEU* 4.7 4.9 - - + +
497B THR* 3.2 21.5 - - - +
498B ALA* 3.7 26.8 - - + +
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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