Contacts of the strand formed by residues 77 - 83 (chain F) in PDB entry 3JCA
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 TYR 77 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F VAL* 4.3 1.3 - - + -
67F THR 3.4 7.2 - - - -
68F HIS* 3.7 28.7 - + - -
73F GLY 5.6 0.2 - - - -
74F LYS* 3.9 7.9 - - - -
75F LEU 3.1 1.6 + - - -
76F LYS* 1.3 102.9 + - + +
78F VAL* 1.3 62.8 + - - +
79F HIS* 3.3 10.8 - - + -
94F ARG 2.8 28.8 + - - +
95F THR 3.4 26.0 - - - -
96F GLY* 3.4 22.9 - - - +
97F GLU* 3.7 23.1 - - + -
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Residues in contact with VAL 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F VAL* 3.3 3.3 - - - -
67F THR* 3.0 35.5 + - + -
69F VAL* 3.6 21.1 - - + -
72F PHE* 4.4 4.9 - - + -
75F LEU 3.8 12.1 - - - +
76F LYS 2.7 18.7 + - - +
77F TYR* 1.3 70.6 - - - +
79F HIS* 1.3 72.4 + - - +
80F VAL* 3.7 11.0 + - + +
91F ALA* 3.7 19.7 - - + -
92F THR 3.5 9.4 - - - +
93F ALA* 3.9 12.3 - - + +
164F ILE* 5.5 4.3 - - + -
168F LEU* 6.4 0.2 - - + -
184F LEU* 4.5 9.4 - - + -
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Residues in contact with HIS 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F MET* 3.8 7.6 - - + +
65F ASP 3.6 4.3 - - - -
66F VAL* 3.7 24.1 - - + +
77F TYR 3.3 15.3 - - - -
78F VAL* 1.3 72.6 - - - +
80F VAL* 1.3 60.7 + - - +
91F ALA* 3.1 4.5 - - - -
92F THR 2.8 35.6 + - - +
94F ARG* 3.6 8.0 - - + +
96F GLY 2.9 21.6 + - - -
97F GLU* 4.2 3.9 - - - -
101F ASP* 3.6 16.3 + - + -
102F VAL* 3.6 49.2 - - + +
105F HIS* 3.2 24.8 - - + +
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Residues in contact with VAL 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F GLN 3.5 1.5 - - - +
64F MET* 3.2 8.9 - - - +
65F ASP* 2.7 40.8 + - + +
67F THR* 5.2 0.7 - - + -
78F VAL* 3.8 23.1 - - + +
79F HIS* 1.3 82.0 - - - +
81F THR* 1.3 66.3 + - - +
82F VAL* 3.8 23.1 - - + -
89F THR* 3.9 4.9 - - + -
90F PHE 3.4 7.6 - - - +
91F ALA* 4.0 6.1 - - + -
105F HIS* 3.8 0.9 + - - -
157F VAL* 6.2 2.0 - - + -
160F THR* 3.9 15.9 - - + -
161F HIS* 4.0 23.3 - - + +
164F ILE* 4.2 8.1 - - + -
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Residues in contact with THR 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F TRP* 3.5 42.8 - - + -
63F GLN 3.5 4.7 - - - +
64F MET* 3.5 9.0 - - - -
80F VAL* 1.3 72.7 - - - +
82F VAL* 1.3 63.9 + - - +
88F PHE 3.6 1.9 - - - +
90F PHE 2.8 35.7 + - - -
105F HIS* 2.6 30.6 + - - -
106F LEU* 5.7 2.8 - - + +
109F SER* 4.4 8.2 + - - +
113F MET* 3.8 18.4 - - - +
119F ILE* 5.7 4.0 - - + -
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Residues in contact with VAL 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F TRP* 3.3 3.3 - - - -
63F GLN* 2.8 42.4 + - + +
80F VAL* 3.8 9.4 - - + -
81F THR* 1.3 80.5 - - - +
83F ASP* 1.3 75.8 + - - +
84F THR 3.1 1.4 + - - -
87F HIS* 3.9 17.3 - - + +
88F PHE 3.2 8.5 - - - +
89F THR* 3.7 11.9 - - + +
113F MET* 4.2 2.0 - - - -
156F ILE* 4.0 24.5 - - + -
157F VAL* 5.7 3.4 - - + -
160F THR* 3.6 32.1 - - + +
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Residues in contact with ASP 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F PRO* 3.9 3.8 - - - +
59F ARG 2.8 20.0 + - - -
60F VAL 4.2 1.0 + - - -
61F LEU 4.7 0.5 - - - +
62F TRP* 2.8 32.0 + - - +
82F VAL* 1.3 71.7 - - - +
84F THR* 1.3 61.4 + - - +
85F TYR* 3.3 10.7 - - - +
86F SER* 2.8 41.5 + - - +
87F HIS* 2.7 32.6 + - - -
88F PHE* 3.0 10.2 + - + -
113F MET* 3.6 6.6 - - + +
207F HIS* 3.5 19.5 + - - +
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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