Contacts of the helix formed by residues 463 - 470 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421C CYS* 3.8 9.7 - - - -
455C SER* 3.0 24.7 + - - -
458C LYS* 3.6 20.7 + - - +
459C SER 3.0 26.9 + - - +
460C PHE 3.5 14.0 + - - +
461C VAL 4.2 0.2 - - - -
462C ASP* 1.3 75.3 - - - +
464C ASN* 1.3 58.5 + - - +
465C ARG* 3.1 12.6 + - - +
466C VAL* 3.1 25.9 + - + +
467C ALA* 2.9 29.0 + - - +
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Residues in contact with ASN 464 (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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416B ALA* 6.1 0.5 - - - -
450B ASN* 5.5 2.2 + - - -
451B ASN* 2.9 43.9 + - - +
458C LYS* 5.6 6.2 - - - +
462C ASP 3.8 6.8 + - - +
463C ASN* 1.3 70.3 + - - +
465C ARG* 1.3 60.8 + - - +
467C ALA* 3.8 6.7 - - - +
468C GLU* 3.0 30.8 + - - +
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Residues in contact with ARG 465 (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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417C LEU* 4.1 7.7 - - - +
419C PHE* 3.8 18.6 - - + -
453C GLU* 2.9 42.6 + - - +
455C SER* 5.2 4.9 - - - +
458C LYS* 6.1 0.4 - - - +
463C ASN* 3.1 8.9 + - - +
464C ASN* 1.3 74.4 - - - +
466C VAL* 1.3 68.1 + - - +
468C GLU* 3.1 47.4 + - - +
469C LEU* 3.1 45.3 + - + +
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Residues in contact with VAL 466 (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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396C MET* 3.6 14.8 - - - +
398C LEU* 4.0 21.1 - - + -
419C PHE* 3.9 22.0 - - + -
421C CYS* 4.1 5.2 - - + -
460C PHE* 4.0 25.6 - - + +
463C ASN* 3.1 36.1 + - + +
465C ARG* 1.3 77.4 - - - +
467C ALA* 1.3 63.0 + - - +
469C LEU 3.2 0.2 + - - -
470C ILE* 3.0 23.3 + - + +
494C ILE* 4.1 17.5 - - + -
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Residues in contact with ALA 467 (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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463C ASN 2.9 17.4 + - - +
464C ASN* 3.8 8.3 - - - +
466C VAL* 1.3 79.8 - - - +
468C GLU* 1.3 61.3 + - - +
470C ILE* 3.9 6.8 + - - +
471C PRO* 3.3 19.1 - - - +
494C ILE* 6.0 0.7 - - - -
497C THR* 4.6 2.6 + - - -
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Residues in contact with GLU 468 (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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464C ASN 3.0 15.3 + - - +
465C ARG* 3.1 55.4 + - - +
467C ALA* 1.3 78.0 - - - +
469C LEU* 1.3 61.0 + - + +
471C PRO* 3.6 11.1 - - - +
472C GLN* 4.5 9.0 + - - +
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Residues in contact with LEU 469 (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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394C THR* 5.0 2.2 - - + -
396C MET* 3.6 15.0 - - + -
417C LEU* 3.7 25.6 - - + -
419C PHE* 3.7 41.5 - - + -
465C ARG* 3.1 50.8 + - + +
466C VAL 3.2 0.2 + - - -
468C GLU* 1.3 76.7 - - - +
470C ILE* 1.3 66.7 + - - +
471C PRO* 3.3 3.4 - - - -
472C GLN* 2.9 46.2 + - + +
473C CYS* 3.3 9.5 + - - -
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Residues in contact with ILE 470 (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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396C MET* 3.5 28.2 - - - +
398C LEU* 5.0 1.3 - - + -
466C VAL* 3.0 21.3 + - + +
467C ALA* 4.1 4.5 - - - +
469C LEU* 1.3 75.0 - - - +
471C PRO* 1.3 68.8 - - + +
472C GLN 3.0 1.9 + - - -
473C CYS* 3.0 20.4 + - - +
476C ILE* 4.0 18.4 - - + +
494C ILE* 3.8 38.1 - - + +
495C LEU* 4.6 4.7 - - + +
497C THR* 3.2 21.8 - - - +
498C ALA* 3.6 27.8 - - + +
502C CYS* 5.5 0.2 - - - -
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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