Contacts of the strand formed by residues 66 - 72 (chain C) in PDB entry 3P1M
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 LYS 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C ASP* 1.3 74.3 - - - +
67C ILE* 1.3 63.7 + - - +
82C LYS* 4.7 28.8 + - + +
83C GLY 3.5 11.0 - - - +
84C LYS* 5.2 3.6 - - + -
161C ASP* 4.7 1.9 - - - +
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Residues in contact with ILE 67 (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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189A TYR* 6.5 0.2 - - + -
65C ASP 5.0 0.7 - - - -
66C LYS* 1.3 79.3 - - - +
68C THR* 1.3 60.8 + - - +
69C VAL* 4.2 7.1 - - + +
82C LYS* 3.2 6.8 - - - -
83C GLY 2.9 40.3 + - - +
85C VAL* 4.2 21.8 - - + -
156C LEU* 3.5 38.4 - - + -
157C THR 3.6 22.4 - - - +
158C LYS* 4.3 12.6 - - + +
160C MET* 3.9 13.5 - - + -
161C ASP* 3.4 21.1 - - + +
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Residues in contact with THR 68 (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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67C ILE* 1.3 73.2 - - - +
69C VAL* 1.3 66.6 + - - +
70C HIS* 3.9 20.6 - - + +
80C THR* 3.9 19.9 - - + +
81C THR 3.4 3.7 + - - -
82C LYS* 3.6 27.9 + - - +
160C MET 3.9 0.2 - - - +
161C ASP* 2.8 15.7 + - - -
162C ASN* 2.6 52.3 + - - +
163C MET 3.8 1.4 + - - -
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Residues in contact with VAL 69 (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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67C ILE* 4.2 11.9 - - + +
68C THR* 1.3 81.9 - - - +
70C HIS* 1.3 75.4 + - - +
71C PHE* 4.0 19.9 + - + -
79C LEU 3.9 0.7 - - - +
80C THR* 3.7 1.2 - - - +
81C THR* 3.1 36.5 + - + +
83C GLY 5.3 2.5 - - - +
89C LEU* 4.2 7.0 - - + -
92C VAL* 5.5 3.4 - - + -
156C LEU* 3.9 29.8 - - + -
163C MET* 3.5 36.1 - - + +
165C VAL* 4.3 4.0 - - + -
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Residues in contact with HIS 70 (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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191A GLN* 5.7 1.4 + - - -
68C THR* 3.9 11.3 - - + +
69C VAL* 1.3 74.0 - - - +
71C PHE* 1.3 60.4 + - - +
72C ILE* 4.1 0.7 - - + -
78C THR* 4.1 15.2 - - + +
79C LEU 3.3 3.8 - - - -
80C THR* 2.7 42.6 + - + +
162C ASN* 3.8 22.4 + - - +
163C MET 2.9 17.8 + - - +
164C THR* 3.3 18.2 - - + +
165C VAL* 2.9 30.5 + - - +
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Residues in contact with PHE 71 (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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69C VAL* 4.0 16.4 - - + -
70C HIS* 1.3 76.7 - - - +
72C ILE* 1.3 62.2 + - - +
73C ASN* 3.6 1.1 + - - +
77C GLU 3.5 0.9 - - - +
78C THR* 3.5 1.5 - - - -
79C LEU* 2.7 53.1 + - + +
81C THR* 3.9 14.4 - - + -
89C LEU* 3.6 22.0 - - + -
92C VAL* 4.0 8.5 - - + -
93C VAL* 3.7 29.6 - - + -
98C LEU* 3.8 23.1 - - + -
100C ILE* 4.7 4.5 - - + -
117C LEU* 4.1 15.5 - - + -
165C VAL* 3.4 23.1 - - + -
167C VAL* 4.5 20.2 - - + -
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Residues in contact with ILE 72 (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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71C PHE* 1.3 71.0 - - - +
73C ASN* 1.3 71.1 + - - +
76C GLY* 4.2 20.2 - - - +
77C GLU 3.5 3.6 - - - +
78C THR* 4.0 17.3 - - + +
164C THR* 3.7 29.4 - - + -
165C VAL 2.9 11.8 + - - +
166C ARG* 3.5 17.8 - - + +
167C VAL* 2.8 30.9 + - - +
183F THR* 3.6 24.2 - - - +
184F SER* 4.9 7.9 - - - -
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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