Contacts of the strand formed by residues 68 - 75 (chain C) in PDB entry 4J1R
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 GLY 68 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C ASN* 3.5 7.4 - - - +
65C GLY 3.0 29.8 + - - +
66C SER 3.5 0.6 - - - -
67C PHE* 1.3 87.7 - - - +
69C VAL* 1.3 67.9 + - - -
86C LYS 3.4 6.3 - - - -
127C TYR* 6.3 2.2 - - - -
288D TYR* 4.6 1.5 + - - -
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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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61C VAL* 3.7 21.1 - - + -
63C GLY 3.4 13.2 - - - +
67C PHE* 3.9 1.5 - - - -
68C GLY* 1.3 80.8 - - - +
70C VAL* 1.3 67.7 + - - +
71C TYR* 3.8 30.3 - - + +
84C ILE 3.6 0.6 - - - +
85C LYS* 3.5 2.3 - - - -
86C LYS* 2.7 45.9 + - + +
288D TYR* 3.2 38.4 - - + +
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Residues in contact with VAL 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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61C VAL* 3.7 2.3 - - - -
62C ILE* 2.7 48.3 + - + +
63C GLY* 3.0 18.5 + - - +
67C PHE* 3.6 15.7 - - + -
69C VAL* 1.3 81.0 - - - +
71C TYR* 1.3 61.2 + - - +
83C ALA* 4.2 9.6 - - + -
84C ILE 3.3 7.2 - - - +
85C LYS* 4.1 9.2 - - + +
502C I5R 3.5 53.4 - - + +
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Residues in contact with TYR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C THR* 3.6 31.0 - - + -
60C LYS* 3.3 5.8 - - - -
61C VAL* 3.6 32.1 - - + -
62C ILE* 3.9 2.4 - - - +
69C VAL* 3.8 29.8 - - + +
70C VAL* 1.3 78.6 - - - +
72C GLN* 1.3 63.0 - - - +
83C ALA* 3.2 8.5 - - - +
84C ILE* 2.8 55.5 + - + +
86C LYS* 4.0 31.8 + - + +
129C ASN* 5.5 0.7 - - - -
288D TYR* 4.3 11.0 - - + +
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Residues in contact with GLN 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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58C ASP* 3.0 21.3 - - - +
59C THR* 3.3 1.3 - - - -
60C LYS* 2.8 46.7 + - - +
62C ILE* 3.6 25.4 - - + -
71C TYR* 1.3 75.4 - - - +
73C ALA* 1.3 64.5 + - - +
81C LEU* 3.3 44.7 - - - +
82C VAL 3.5 4.7 - - - +
134C TYR* 3.5 34.0 - - + +
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Residues in contact with ALA 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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56C TYR* 3.5 34.5 - - + -
57C THR 3.6 8.5 - - - +
58C ASP* 3.8 2.5 - - - -
59C THR* 3.9 5.6 - - - +
71C TYR 4.2 0.4 + - - -
72C GLN* 1.3 76.9 + - - +
74C LYS* 1.3 60.8 + - - +
81C LEU* 3.4 11.3 - - - +
82C VAL* 2.9 36.6 + - + +
84C ILE* 4.0 15.7 - - + +
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Residues in contact with LYS 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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56C TYR* 3.2 3.7 - - - -
57C THR* 2.9 51.4 + - - +
58C ASP* 3.6 24.8 + - + +
73C ALA* 1.3 73.4 - - - +
75C LEU* 1.3 68.9 + - - +
76C CYS* 3.4 2.0 + - - +
79C GLY* 3.1 36.1 - - - +
80C GLU 3.4 4.0 - - - +
81C LEU* 3.6 16.2 - - + -
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Residues in contact with LEU 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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54C VAL* 4.2 17.5 - - + -
55C SER 3.5 11.2 - - - +
56C TYR* 4.2 8.5 - - + -
74C LYS* 1.3 72.9 - - - +
76C CYS* 1.3 59.1 + - - +
77C ASP* 3.5 14.1 - - - +
78C SER* 3.4 24.2 - - - +
79C GLY* 2.8 32.6 + - - -
80C GLU* 2.8 16.3 + - + +
82C VAL* 4.0 29.8 - - + -
113C ARG* 3.8 22.7 - - - +
114C TYR* 4.4 17.0 - - + +
131C VAL* 5.2 3.8 - - + -
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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