Contacts of the helix formed by residues 81 - 88 (chain S) in PDB entry 1RZZ
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 81 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275R ILE* 3.7 22.2 - - - +
276R PRO 5.2 1.7 + - - +
75S TRP* 4.2 1.6 - - - -
78S ALA* 3.1 14.3 + - - +
79S GLY 3.0 5.4 - - - +
80S TRP* 1.3 76.9 - - - +
82S PRO* 1.3 64.8 - - - +
83S ALA* 2.9 24.8 + - - +
84S VAL* 3.0 16.6 + - + +
85S PHE* 2.9 26.3 + - - +
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Residues in contact with PRO 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S TRP* 3.7 29.4 - - + -
80S TRP 3.3 9.2 - - - +
81S ASN* 1.3 89.8 - - - +
83S ALA* 1.3 61.1 + - - +
85S PHE* 3.2 3.7 + - + +
86S LEU* 3.0 31.7 + - + +
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Residues in contact with ALA 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271R TRP* 5.3 1.1 - - + +
272R TRP* 3.6 26.3 - - + -
275R ILE* 3.4 27.1 - - + -
81S ASN* 2.9 12.3 + - - +
82S PRO* 1.3 79.4 - - - +
84S VAL* 1.3 62.1 + - - +
86S LEU* 3.6 3.1 + - - -
87S ARG* 3.1 22.5 + - - +
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Residues in contact with VAL 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275R ILE* 3.8 19.1 - - + -
276R PRO 3.9 11.9 - - - +
277R GLY 3.9 2.0 - - - +
278R GLY* 3.6 33.9 - - - +
78S ALA* 3.7 15.7 - - + +
81S ASN* 3.0 30.6 + - + +
83S ALA* 1.3 73.5 - - - +
85S PHE* 1.3 67.9 + - - +
87S ARG* 4.2 13.2 - - - +
88S ASP* 2.9 35.1 + - - +
92S PHE* 4.3 1.1 - - + -
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Residues in contact with PHE 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S GLY 4.3 0.7 - - - -
74S PHE* 3.8 23.6 - - + -
75S TRP* 3.3 67.1 - + + -
78S ALA* 3.9 4.0 - - + +
81S ASN 2.9 12.2 + - - +
82S PRO* 3.3 13.5 - - + +
84S VAL* 1.3 77.5 - - - +
86S LEU* 1.3 73.0 + - + +
89S LEU* 3.0 45.8 + - + +
92S PHE* 3.5 9.5 - + - -
2010S SPO 3.6 36.1 - - + -
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Residues in contact with LEU 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266R TRP* 3.3 20.2 + - + -
272R TRP* 3.6 28.3 - - + -
82S PRO* 3.0 21.1 + - + +
83S ALA* 4.0 2.0 - - - +
85S PHE* 1.3 91.9 - - + +
87S ARG* 1.3 65.2 + - - +
89S LEU* 3.5 23.2 - - + +
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Residues in contact with ARG 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266R TRP* 3.2 27.4 + - + +
267R VAL* 3.8 30.4 - - - +
272R TRP* 2.7 64.6 + - + +
273R ALA 4.7 3.3 - - - -
275R ILE* 3.2 20.6 + - - +
277R GLY 3.1 13.9 + - - -
280R ASN* 3.2 11.2 - - - +
281R GLY* 2.9 36.6 - - - +
83S ALA 3.1 14.0 + - - +
84S VAL* 3.8 13.3 - - - +
86S LEU* 1.3 78.9 - - - +
88S ASP* 1.3 85.2 + - - +
89S LEU 3.3 0.6 + - - -
90S PHE 5.0 0.7 + - - -
91S PHE* 4.2 3.8 - - - -
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Residues in contact with ASP 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278R GLY 3.6 1.7 - - - -
279R ILE* 2.9 27.3 + - + -
280R ASN* 2.7 37.4 + - - -
84S VAL* 2.9 19.3 + - - +
87S ARG* 1.3 106.3 + - - +
89S LEU* 1.3 54.9 + - - +
90S PHE 3.2 2.7 - - - -
91S PHE* 2.7 30.1 + - + -
92S PHE* 3.2 27.7 + - + -
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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