Contacts of the strand formed by residues 77 - 83 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL* 5.3 3.1 - - + -
67A THR 3.8 4.5 - - - -
68A HIS* 3.8 21.2 - + - -
74A LYS* 3.2 24.7 - - + -
75A LEU 3.0 3.3 - - - -
76A LYS* 1.3 97.2 + - + +
78A VAL* 1.3 61.4 + - - +
79A HIS* 3.3 9.1 - - - +
94A ARG 2.9 27.2 + - - +
95A THR 3.6 7.2 - - - -
96A GLY* 3.5 30.7 - - - +
97A GLU* 3.5 38.4 - - + -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.1 5.8 - - - -
67A THR* 3.0 37.3 + - + +
69A VAL* 3.8 21.1 - - + -
72A PHE* 6.1 0.9 - - + -
75A LEU 3.7 12.6 - - - +
76A LYS 2.7 17.2 + - - +
77A TYR* 1.3 73.0 - - - +
79A HIS* 1.3 63.4 + - - +
80A VAL* 3.8 7.9 + - + +
91A ALA* 3.8 29.2 - - + -
92A THR 3.3 10.8 - - - +
93A ALA* 3.8 12.6 - - + +
164A ILE* 6.0 3.4 - - + -
168A LEU* 6.3 0.9 - - + -
184A LEU* 4.9 7.6 - - + -
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Residues in contact with HIS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 3.7 17.0 - - + +
65A ASP 3.9 3.6 - - - -
66A VAL* 3.6 20.9 - - + +
77A TYR* 3.3 16.5 + - - +
78A VAL* 1.3 73.4 - - - +
80A VAL* 1.3 59.8 + - - +
91A ALA* 3.1 2.9 - - - -
92A THR 2.8 33.0 + - - +
94A ARG* 3.5 17.5 - - + -
96A GLY 3.0 24.4 + - - -
97A GLU* 4.2 8.6 - - + +
101A ASP* 3.7 5.1 - - + +
102A VAL* 3.8 32.7 - - + -
105A HIS* 3.0 34.0 - - + +
127A TYR* 5.2 0.2 - - - -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN 3.7 0.5 - - - +
64A MET* 3.2 7.3 - - - +
65A ASP 2.8 33.2 + - - +
67A THR* 5.0 2.7 - - + -
78A VAL* 3.9 14.6 - - + +
79A HIS* 1.3 80.8 - - - +
81A THR* 1.3 64.8 + - - +
82A VAL* 4.1 20.2 - - + -
90A PHE 3.3 10.1 - - - +
91A ALA* 3.9 14.1 - - + -
105A HIS* 3.8 0.6 + - - -
157A VAL* 4.3 4.2 - - + +
160A THR* 4.5 2.0 - - + -
161A HIS* 3.5 38.4 - - + +
164A ILE* 4.1 17.5 - - + -
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 3.6 40.2 - - + -
63A GLN 3.3 8.7 - - - +
64A MET* 3.6 12.3 - - - +
80A VAL* 1.3 74.3 + - - +
82A VAL* 1.3 67.9 + - - +
88A PHE 3.8 0.5 - - - +
89A THR* 3.7 1.0 - - - -
90A PHE* 2.8 33.3 + - - -
105A HIS* 2.8 30.9 + - - -
106A LEU* 5.1 1.1 - - + +
109A SER* 4.7 3.9 + - - +
113A MET* 3.7 16.1 - - - +
119A ILE* 4.5 6.2 - - + +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 3.3 2.1 - - - -
63A GLN 2.9 33.4 + - - -
80A VAL* 4.1 4.3 - - + -
81A THR* 1.3 82.2 - - - +
83A ASP* 1.3 77.5 + - - +
84A THR* 3.2 4.0 + - - +
87A HIS* 3.9 13.7 - - + -
88A PHE 3.2 8.5 - - - +
89A THR* 3.8 16.2 - - + -
113A MET* 3.8 3.6 - - - -
156A ILE* 3.9 21.1 - - + -
157A VAL* 3.8 20.4 - - + -
160A THR* 3.7 26.0 - - + +
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LYS 5.2 0.2 - - - -
58A PRO* 3.7 3.5 - - - +
59A ARG 2.8 27.6 + - - -
60A VAL 4.3 1.1 + - - -
61A LEU 4.8 0.7 - - - -
62A TRP* 2.9 27.2 + - - +
82A VAL* 1.3 69.2 - - - +
84A THR* 1.3 59.0 + - - +
85A TYR* 3.4 10.8 + - - +
86A SER* 2.8 40.8 + - - +
87A HIS* 2.7 35.9 + - - -
88A PHE* 2.9 19.6 + - + -
113A MET* 3.3 7.2 - - + +
207A HIS* 3.7 10.4 - - - +
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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