Contacts of the helix formed by residues 73 - 82 (chain C) in PDB entry 2XJZ
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 CYS 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C CYS* 3.3 13.5 - - + +
53C CYS* 4.2 2.5 - - - -
55C CYS* 4.2 15.7 - - + -
57C LEU* 6.0 3.6 - - + -
60C VAL* 5.5 8.3 - - + +
63C ARG 5.7 2.0 - - - -
64C LEU* 5.4 2.7 - - - -
65C TYR* 4.1 1.3 - - - -
72C LEU* 1.3 77.2 - - - +
74C ARG* 1.4 56.2 + - - +
75C ARG* 3.8 11.0 - - - -
76C ASP* 3.4 16.6 - - - -
77C TYR* 2.9 32.1 + - - +
203C ZN 2.4 36.1 - - - -
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Residues in contact with ARG 74 (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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61C GLY* 5.6 6.7 - - - -
63C ARG 5.2 3.6 + - - +
65C TYR* 3.7 40.4 - - + +
73C CYS* 1.4 71.4 - - - +
75C ARG* 1.3 53.2 + - - +
77C TYR* 3.4 0.7 + - - +
78C LEU* 2.8 54.9 + - + +
97C TYR* 4.3 5.6 + - + +
66D TYR* 6.0 1.8 - - - -
68D LEU* 3.7 32.9 - - - +
69D GLY* 3.9 7.9 - - - +
1148D CL 3.3 26.4 - - - +
345K LEU* 3.7 23.4 - - + +
348K GLY* 6.3 1.3 - - - -
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Residues in contact with ARG 75 (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 CYS* 6.3 1.2 - - - +
73C CYS* 3.4 9.7 - - - -
74C ARG* 1.3 78.8 - - - +
76C ASP* 1.3 64.9 + - - +
78C LEU* 3.8 1.7 - - - +
79C ARG* 2.9 68.9 + - + +
97C TYR* 3.6 47.9 + - + +
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Residues in contact with ASP 76 (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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50C CYS* 3.5 1.0 - - - -
52C LEU* 3.4 21.2 - - + +
53C CYS* 3.2 13.0 + - - +
72C LEU* 4.1 13.5 - - + -
73C CYS* 3.4 5.0 - - - +
75C ARG* 1.3 83.6 + - - +
77C TYR* 1.4 65.0 + - - +
79C ARG* 2.8 36.8 + - - +
80C LEU* 3.2 30.9 + - - +
203C ZN 1.9 39.0 - - - -
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Residues in contact with TYR 77 (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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65C TYR* 3.6 42.2 - + + -
67C LYS* 4.1 10.8 - - + -
72C LEU* 4.3 9.5 - - + +
73C CYS 2.9 20.1 + - - +
74C ARG 3.6 3.1 - - - +
76C ASP* 1.4 77.4 - - - +
78C LEU* 1.3 75.0 + - + +
81C PHE* 2.7 75.4 + + + +
82C GLY* 5.1 0.7 - - - -
351K GLY* 3.4 24.3 - - - -
354K ASP* 2.5 44.7 + - + -
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Residues in contact with LEU 78 (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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124B VAL* 5.0 0.2 - - - +
65C TYR* 5.6 2.5 - - + +
74C ARG* 2.8 30.3 + - + +
75C ARG 3.9 2.9 - - - +
77C TYR* 1.3 96.4 - - + +
79C ARG* 1.3 62.1 - - - +
82C GLY* 3.0 24.0 + - - +
96C ALA* 3.2 36.5 - - + +
97C TYR* 3.6 29.6 - - + -
345K LEU* 3.7 22.4 - - + -
347K GLY* 3.8 24.0 - - - +
348K GLY* 4.4 6.5 - - - +
351K GLY* 5.6 0.2 - - - -
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Residues in contact with ARG 79 (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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121B HIS* 4.2 20.4 - - - +
122B PHE 3.1 24.1 + - - +
123B CYS* 3.3 32.4 - - - +
124B VAL* 3.0 26.9 + - - -
52C LEU* 3.4 20.2 - - - +
75C ARG* 2.9 58.9 + - + +
76C ASP* 2.8 25.6 + - - +
77C TYR 3.4 0.2 - - - -
78C LEU* 1.3 75.5 - - - +
80C LEU* 1.3 71.3 + - - +
96C ALA* 5.2 1.1 - - - -
97C TYR* 5.2 8.7 - - + +
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Residues in contact with LEU 80 (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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99B MET* 4.3 6.7 - - + -
101B MET* 5.6 3.1 - - + -
110B LEU* 3.9 31.0 - - + -
122B PHE 5.2 0.9 - - - +
124B VAL* 3.1 19.0 - - - +
52C LEU* 4.0 13.7 - - + -
72C LEU* 4.8 6.7 - - + -
76C ASP 3.2 18.6 + - - +
78C LEU 3.2 0.4 - - - -
79C ARG* 1.3 112.4 - - - +
81C PHE* 1.3 82.7 + - + +
341J GLY 5.6 0.2 - - - -
342J GLU* 3.5 2.6 - - - -
343J PRO* 3.2 35.8 - - + +
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Residues in contact with PHE 81 (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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99B MET* 3.6 12.3 - - + -
124B VAL* 4.7 0.9 - - - -
67C LYS* 3.7 37.2 - - + -
68C LEU* 3.9 7.4 - - + -
72C LEU* 4.0 11.0 - - + -
77C TYR* 2.7 57.8 + + + +
80C LEU* 1.3 93.3 - - + +
82C GLY* 1.3 65.2 + - - +
83C GLN 4.0 0.3 + - - -
342J GLU* 3.6 37.0 - - + +
343J PRO* 3.4 39.7 - - + -
350K PHE* 6.1 0.7 - - - +
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Residues in contact with GLY 82 (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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124B VAL* 3.2 25.8 - - - +
77C TYR* 3.6 4.3 + - - -
78C LEU* 3.0 35.3 + - - +
80C LEU 3.9 0.2 - - - -
81C PHE* 1.3 82.7 - - - +
83C GLN* 1.3 60.8 + - - -
96C ALA* 3.7 9.6 - - - -
342J GLU* 5.5 0.3 - - - +
347K GLY* 4.5 3.1 - - - -
350K PHE* 5.9 0.7 - - - -
351K GLY 6.3 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