Contacts of the strand formed by residues 82 - 88 (chain C) in PDB entry 1NZ0
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 PHE 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C PHE* 4.0 9.4 - + + -
37C ARG 3.3 5.2 - - - +
38C LYS* 3.8 25.4 - - - -
39C ASN* 3.4 8.0 - - - +
44C SER* 3.0 10.9 + - - +
45C ARG 3.0 24.4 + - - +
79C PRO* 4.0 17.5 - - + -
80C LYS 3.5 22.4 - - - -
81C GLY* 1.3 78.7 - - - +
83C ASP* 1.3 59.5 + - - +
84C ILE* 3.8 17.3 - - + +
115C ILE* 3.6 29.4 - - + -
116C GLU* 3.8 8.7 - - - -
117C GLY* 3.7 31.6 - - - -
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Residues in contact with ASP 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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11C LEU* 3.3 26.2 - - + +
16C ASP* 4.0 12.1 - - - +
20C ILE* 3.9 19.6 - - + +
35C LEU 3.9 0.2 - - - +
36C PHE* 3.1 5.5 - - - +
37C ARG* 2.9 35.3 + - + +
39C ASN* 2.9 22.4 + - - +
45C ARG* 2.9 42.4 + - - +
82C PHE* 1.3 69.9 - - - +
84C ILE* 1.3 60.1 + - - +
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Residues in contact with ILE 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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11C LEU* 3.6 3.9 - - - +
34C VAL* 3.7 27.4 - - + -
35C LEU 3.4 2.9 - - - +
36C PHE* 4.3 1.6 - - + -
44C SER* 4.2 15.0 - - - +
45C ARG 2.8 11.6 + - - +
46C LEU* 3.3 21.0 - - + -
47C GLY 2.8 26.3 + - - +
71C PHE* 4.3 8.3 - - + -
78C ILE* 4.3 16.2 - - + -
79C PRO 5.0 1.1 - - - +
82C PHE* 3.8 23.8 - - + +
83C ASP* 1.3 78.2 - - - +
85C VAL* 1.3 66.5 - - - +
86C VAL* 4.1 1.6 - - + -
112C LEU* 3.9 5.4 - - + -
115C ILE* 3.8 20.0 - - + -
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Residues in contact with VAL 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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11C LEU* 3.8 6.5 - - + -
13C LEU* 3.7 24.9 - - + -
17C PHE* 4.1 14.8 - - + -
20C ILE* 3.9 21.5 - - + -
33C VAL 3.8 0.9 - - - +
34C VAL* 3.3 5.5 - - - -
35C LEU* 2.8 44.4 + - + +
47C GLY 3.4 5.6 - - - +
49C VAL* 3.7 29.8 - - + -
84C ILE* 1.3 78.0 - - - +
86C VAL* 1.4 64.9 - - - +
87C ILE* 4.0 14.1 - - + +
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Residues in contact with VAL 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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32C PHE* 3.6 32.5 - - + -
33C VAL 3.8 3.8 - - - +
34C VAL* 4.5 4.0 - - + +
46C LEU* 3.9 31.0 - - + -
47C GLY 2.9 10.5 + - - +
48C ILE* 3.4 8.4 - - + +
49C VAL 2.9 25.6 + - - +
67C VAL* 4.2 19.5 - - + -
84C ILE* 4.3 5.8 - - + -
85C VAL* 1.4 75.7 - - - +
87C ILE* 1.3 61.7 + - - +
88C PRO* 4.1 1.1 - - + -
108C LEU* 3.9 25.8 - - + -
112C LEU* 4.7 0.2 - - + -
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Residues in contact with ILE 87 (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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21A PHE* 4.0 36.8 - - + -
17C PHE* 4.5 2.7 - - + -
21C PHE* 6.1 0.2 - - + -
32C PHE* 3.6 2.6 - - - -
33C VAL* 2.9 53.4 + - + +
35C LEU* 3.8 33.7 - - + -
49C VAL* 3.4 17.7 - - + +
51C LYS* 4.7 9.6 - - + +
85C VAL* 4.0 14.1 - - + +
86C VAL* 1.3 77.7 - - - +
88C PRO* 1.3 71.6 - - - +
89C ARG* 4.1 0.9 - - + +
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Residues in contact with PRO 88 (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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31C TYR 3.5 7.2 - - - +
32C PHE* 3.8 9.8 - - + -
48C ILE* 4.9 3.1 - - + -
49C VAL 3.3 14.4 - - - +
50C VAL* 4.0 19.5 - - + -
51C LYS* 5.3 7.6 + - - +
54C PHE* 3.6 21.8 - - + -
63C LEU* 3.4 34.3 - - + -
86C VAL* 4.0 4.7 - - + +
87C ILE* 1.3 94.1 - - - +
89C ARG* 1.3 60.7 + - - +
92C LEU* 3.9 9.4 - - + -
5003C SO4 4.7 1.0 + - - -
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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