Contacts of the helix formed by residues 73 - 82 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D CYS* 3.5 4.6 - - - -
53D CYS* 4.2 3.8 - - - -
55D CYS* 3.8 12.3 - - - -
57D LEU* 3.6 23.4 - - + +
60D VAL* 5.4 9.4 - - + +
63D ARG 5.6 0.9 - - - -
64D LEU* 5.4 1.3 - - - +
65D TYR* 4.1 1.3 - - - -
72D LEU* 1.3 75.4 - - - +
74D ARG* 1.3 61.1 + - - +
75D ARG* 3.8 12.1 - - - -
76D ASP* 3.4 15.9 - - - -
77D TYR* 2.9 26.7 + - - +
203D ZN 2.4 34.3 - - - -
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Residues in contact with ARG 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ARG 5.3 2.9 + - - +
65D TYR* 3.7 40.6 - - + +
73D CYS* 1.3 71.7 - - - +
75D ARG* 1.4 52.6 + - - +
77D TYR* 3.4 1.2 + - - +
78D LEU* 2.8 55.7 + - + +
97D TYR* 4.3 11.4 + - + +
345L LEU* 3.7 29.0 - - - +
348L GLY* 6.1 2.2 - - - -
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Residues in contact with ARG 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D CYS* 4.3 14.5 - - - +
73D CYS* 3.4 9.3 - - - +
74D ARG* 1.4 77.1 - - - +
76D ASP* 1.4 83.3 + - - +
78D LEU* 3.4 1.4 + - - +
79D ARG* 2.9 64.8 + - + +
97D TYR* 3.6 49.6 + - + +
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Residues in contact with ASP 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D CYS* 3.5 4.1 - - - -
52D LEU* 3.8 24.1 - - + +
53D CYS* 3.2 13.3 - - - +
72D LEU* 4.5 2.9 - - + -
73D CYS* 3.4 5.4 - - - +
75D ARG* 1.4 90.3 + - - +
77D TYR* 1.4 64.7 + - - +
79D ARG* 2.8 32.2 + - - -
80D LEU* 3.2 32.4 + - - +
203D ZN 1.9 39.1 - - - -
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Residues in contact with TYR 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D TYR* 3.6 41.3 - + + -
67D LYS* 4.1 10.5 - - + -
72D LEU* 4.2 13.3 - - + +
73D CYS 2.9 19.7 + - - +
74D ARG 3.6 3.4 - - - +
76D ASP* 1.4 77.0 - - - +
78D LEU* 1.3 75.6 + - + +
81D PHE* 2.7 71.5 + + + +
82D GLY* 4.8 3.4 - - - -
347L GLY 5.4 0.2 - - - -
351L GLY* 3.5 22.4 - - - -
354L ASP* 2.6 41.9 + - + -
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C VAL* 5.4 1.4 + - - +
65D TYR* 5.5 2.9 - - + +
74D ARG* 2.8 36.6 + - + +
75D ARG 3.9 2.5 - - - +
77D TYR* 1.3 98.4 - - + +
79D ARG* 1.4 62.2 + - - +
82D GLY* 3.0 29.6 + - - +
96D ALA* 3.5 34.3 - - + +
97D TYR* 3.6 31.2 - - + -
345L LEU* 4.0 12.6 - - + -
347L GLY 4.0 18.6 - - - +
348L GLY* 4.6 6.3 - - - +
351L GLY* 5.8 0.2 - - - -
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Residues in contact with ARG 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C HIS* 4.3 18.3 + - - +
122C PHE 3.2 22.8 + - - +
123C CYS* 3.3 31.5 - - - +
124C VAL 3.0 26.9 + - - -
52D LEU* 4.5 10.5 - - - +
75D ARG* 2.9 49.9 + - + +
76D ASP* 2.8 25.5 + - - +
77D TYR 3.4 0.2 - - - -
78D LEU* 1.4 75.9 - - - +
80D LEU* 1.3 78.5 + - - +
97D TYR* 5.3 8.3 - - + +
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C MET* 4.5 4.3 - - + -
101C MET* 5.7 4.5 - - + -
110C LEU* 4.0 24.0 - - + -
122C PHE 5.2 1.3 - - - +
124C VAL* 2.9 23.7 - - - +
52D LEU* 3.4 28.7 - - + -
72D LEU* 4.5 2.9 - - + -
76D ASP 3.2 15.9 + - - +
79D ARG* 1.3 112.0 - - - +
81D PHE* 1.4 80.5 + - + +
342K GLU* 3.8 1.4 - - - -
343K PRO* 3.4 30.9 - - + +
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Residues in contact with PHE 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C MET* 3.7 13.2 - - + -
124C VAL* 4.8 0.7 - - - -
67D LYS* 3.8 31.0 - - + -
68D LEU* 3.8 12.3 - - + -
72D LEU* 3.7 22.2 - - + -
77D TYR* 2.7 55.7 + + + +
80D LEU* 1.4 86.7 - - + +
82D GLY* 1.3 67.6 + - - +
83D GLN* 5.3 0.2 - - - +
342K GLU* 3.5 40.0 - - - +
343K PRO* 3.6 34.5 - - + -
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Residues in contact with GLY 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C VAL* 3.5 23.6 - - - +
77D TYR* 3.6 5.2 + - - -
78D LEU* 3.0 34.2 + - - -
80D LEU 3.9 0.6 - - - -
81D PHE* 1.3 83.0 - - - +
83D GLN* 1.3 60.5 + - - -
84D ASP* 4.0 1.0 + - - +
96D ALA* 3.5 12.3 - - - +
347L GLY* 4.9 0.9 - - - -
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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