Contacts of the strand formed by residues 70 - 75 (chain C) in PDB entry 2J3T
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 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C SER* 3.8 20.3 + - - -
64C PHE 3.5 10.1 - - - +
65C GLN* 3.9 30.9 - - + +
69C TYR* 1.3 77.5 - - - +
71C LEU* 1.3 61.1 + - - +
72C HIS* 3.5 27.4 - - + +
84C MET 3.5 1.9 - - - +
85C ASN* 3.2 6.7 - - - -
86C THR* 2.7 42.5 + - - +
87C ASP 4.1 9.2 - - - +
88C LEU* 4.0 10.9 + - + +
90C VAL 3.7 22.7 + - - +
91C GLY* 4.4 9.3 - - - -
92C PRO* 4.7 4.2 - - - +
136D MET* 5.9 0.2 - - - +
138D GLU* 5.1 5.7 + - - -
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Residues in contact with LEU 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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38C MET* 4.0 22.7 - - + -
42C LEU* 4.4 2.2 - - + -
61C PHE* 4.0 17.7 - - + -
63C SER* 2.8 36.3 - - - -
64C PHE* 2.7 49.3 + - + +
69C TYR* 4.4 3.0 - - + +
70C LYS* 1.3 72.9 - - - +
72C HIS* 1.3 67.2 + - - +
73C TYR* 4.0 12.1 - - + -
83C VAL* 3.8 24.2 - - + -
85C ASN* 3.1 23.6 - - - +
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Residues in contact with HIS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU 4.2 1.1 + - - +
63C SER* 4.1 5.8 - - - -
70C LYS* 3.5 39.6 - - + +
71C LEU* 1.3 73.2 - - - +
73C TYR* 1.3 61.2 + - - +
82C VAL 3.5 1.4 - - - +
83C VAL* 3.2 7.3 - - - +
84C MET* 2.6 58.3 + - + +
86C THR* 2.9 28.6 + - + -
90C VAL* 3.8 2.7 - - + -
91C GLY 3.3 24.5 - - - -
92C PRO* 3.7 6.2 + - - +
93C ILE* 3.4 29.6 - - + +
97C LEU* 3.8 17.9 - - + +
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Residues in contact with TYR 73 (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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42C LEU* 3.7 31.9 - - + -
46C ARG* 3.3 13.7 - - + -
61C PHE* 3.6 52.7 - + + +
62C LEU 3.3 14.1 + - - +
71C LEU* 4.0 4.0 + - + -
72C HIS* 1.3 74.7 - - - +
74C TYR* 1.3 55.0 + - - +
75C GLU* 2.5 44.9 + - + -
81C LYS* 3.2 35.3 - - + +
82C VAL 3.7 1.3 - - - -
83C VAL* 3.7 17.5 - - + -
94C ARG* 2.2 27.9 + - - -
97C LEU* 4.2 1.4 - - - +
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Residues in contact with TYR 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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64A ASN* 4.8 3.2 + - - -
73C TYR* 1.3 75.4 - - - +
75C GLU* 1.3 72.9 + - - +
76C THR* 3.5 31.5 - - + +
77C PRO* 5.6 1.6 - - - +
80C ILE 3.6 1.0 - - - +
81C LYS* 3.3 5.2 - - - +
82C VAL* 2.8 46.4 + - + +
94C ARG* 3.3 27.4 - - + +
97C LEU* 3.6 36.3 - - + -
98C HIS* 3.1 44.0 - + + -
101C TYR* 4.1 8.7 - - + -
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Residues in contact with GLU 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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67A ARG* 3.4 29.5 + - - +
46C ARG* 2.7 36.2 + - - +
73C TYR* 2.5 42.9 + - + +
74C TYR* 1.3 86.3 - - - +
76C THR* 1.3 73.5 + - - +
77C PRO* 4.5 1.6 - - - +
79C GLY* 4.5 10.0 - - - -
80C ILE 3.3 8.3 - - - +
81C LYS* 4.1 12.0 + - + -
94C ARG* 5.7 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