Contacts of the strand formed by residues 78 - 86 (chain C) in PDB entry 2ZUQ
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 THR 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C SER* 4.6 4.7 - - - -
22C CYS 3.3 10.1 - - - +
23C ALA* 4.6 10.5 - - + -
29C PHE* 3.8 5.8 - - - -
72C ARG* 3.6 1.6 - - - -
73C ASP* 3.0 31.7 + - - +
76C LYS* 2.8 21.9 + - + +
77C ASN* 1.3 79.8 - - - +
79C LEU* 1.3 60.9 + - - +
80C TYR* 2.5 48.4 + - + +
197F GLN* 4.9 12.3 - - + +
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Residues in contact with LEU 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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21C SER* 3.1 6.4 - - - -
22C CYS* 2.8 37.3 + - + -
29C PHE* 4.3 10.9 - - + -
34C MET* 3.6 23.3 - - + -
35C SER 3.9 9.4 - - - +
36C TRP* 3.4 22.7 - - + +
51C ILE* 3.7 16.4 - - + -
70C ILE* 3.7 22.2 - - + -
71C SER 3.4 18.4 - - - +
72C ARG* 4.3 5.4 - - + +
77C ASN 4.0 0.6 + - - -
78C THR* 1.3 73.9 - - - +
80C TYR* 1.3 65.4 + - - +
96C CYS* 3.7 24.0 - - - -
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Residues in contact with TYR 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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19C LYS* 3.5 32.5 - - + +
20C LEU 3.3 2.2 - - - -
21C SER* 3.4 25.4 - - - -
36C TRP* 3.3 11.7 + - - -
70C ILE* 3.4 5.5 - - - +
71C SER* 2.7 60.6 + - - +
72C ARG* 4.3 3.4 - - - -
73C ASP* 3.9 25.8 + - + +
76C LYS* 5.3 2.1 - - - +
78C THR* 2.5 32.0 + - + +
79C LEU* 1.3 79.8 - - - +
81C LEU* 1.3 61.0 + - - +
82C GLN 4.1 0.4 - - - +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LYS* 3.3 4.5 - - - -
20C LEU* 2.8 44.8 + - + +
36C TRP* 3.4 42.0 - - + +
48C VAL* 3.9 20.9 - - + -
49C ALA* 3.7 22.2 - - + -
68C PHE* 3.9 20.0 - - + -
69C THR 3.9 6.5 - - - +
70C ILE* 4.0 13.9 - - + +
80C TYR* 1.3 71.2 - - - +
82C GLN* 1.3 61.3 + - - +
83C MET* 3.7 15.0 + - + +
94C TYR* 4.1 16.2 - - + -
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Residues in contact with GLN 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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17C SER* 5.0 5.1 - - - -
18C LEU* 3.3 24.0 + - - +
19C LYS* 3.2 50.0 - - + +
67C ARG 3.8 0.9 - - - +
68C PHE* 3.6 3.2 - - - -
69C THR* 3.2 49.1 + - - +
71C SER* 5.7 0.2 - - - +
80C TYR 4.1 0.4 - - - -
81C LEU* 1.3 72.2 - - - +
83C MET* 1.3 75.2 + - - +
84C SER* 4.8 6.9 + - - -
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Residues in contact with MET 83 (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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17C SER* 3.5 2.6 - - - -
18C LEU* 3.0 40.1 + - - +
20C LEU* 4.2 20.9 - - - -
68C PHE* 3.1 39.7 - - + -
81C LEU* 4.1 13.0 - - + +
82C GLN* 1.3 78.0 + - - +
84C SER* 1.3 59.3 + - - +
86C LEU* 3.5 33.7 - - + -
90C ASP* 3.9 3.6 - - + -
94C TYR* 3.1 40.8 - - + +
115C VAL* 4.4 15.0 - - + -
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Residues in contact with SER 84 (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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16C GLY 3.1 7.6 - - - +
17C SER* 3.6 14.1 - - - -
66C GLY 4.6 2.1 + - - -
67C ARG* 2.8 35.0 + - - -
68C PHE* 4.0 4.4 - - - -
82C GLN* 4.8 7.6 - - - -
83C MET* 1.3 73.9 - - - +
85C SER* 1.3 67.6 + - - -
86C LEU* 2.5 30.1 + - - +
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Residues in contact with SER 85 (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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15C GLY* 3.7 19.4 + - - -
16C GLY 3.5 1.4 + - - -
17C SER* 4.4 0.4 + - - -
67C ARG* 3.0 37.7 + - - +
84C SER* 1.3 79.1 + - - +
86C LEU* 1.3 62.9 + - - +
87C LYS* 3.1 4.0 + - - +
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Residues in contact with LEU 86 (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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12C VAL* 4.0 14.4 - - + -
13C LYS 4.3 4.7 - - - +
14C PRO* 3.4 9.2 - - - +
15C GLY 2.9 25.3 + - - -
16C GLY* 3.2 30.8 + - - +
17C SER* 3.7 15.0 - - - +
18C LEU* 4.3 2.9 - - + +
83C MET* 3.5 40.6 - - + -
84C SER 2.5 17.7 + - - +
85C SER* 1.3 68.6 - - - +
87C LYS* 1.3 61.9 - - - +
90C ASP* 3.5 19.7 - - + +
115C VAL* 4.8 1.8 - - + -
117C VAL* 3.5 26.6 - - + +
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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