Contacts of the strand formed by residues 61 - 66 (chain E) 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 LEU 61 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E ASN* 5.8 0.4 - - - +
53E PRO* 4.2 11.0 - - + +
54E ARG* 4.1 17.3 - - - -
55E GLY* 4.0 9.2 - - - +
60E VAL* 1.3 80.2 - - - +
62E TRP* 1.3 82.8 + - - +
63E GLN* 6.0 2.7 - - - +
83E ASP* 4.7 1.1 - - - +
84E THR* 2.6 51.4 + - + +
85E TYR 4.5 0.9 + - - +
118E LYS* 3.3 38.6 - - + +
119E ILE* 4.0 1.1 - - - -
120E LYS* 3.9 22.7 - - + +
144E VAL* 5.8 3.8 - - + -
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Residues in contact with TRP 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ARG* 4.0 9.0 - - + +
61E LEU* 1.3 87.9 - - - +
63E GLN* 1.3 61.5 + - - +
81E THR* 3.6 19.5 - - + -
82E VAL 3.3 6.7 - - - +
83E ASP* 3.0 36.9 + - - +
84E THR* 4.0 1.6 - - - -
106E LEU* 6.2 1.6 - - + -
109E SER* 3.9 21.3 - - - -
110E PHE* 5.1 5.4 - + - -
113E MET* 3.4 40.6 - - + -
114E GLY 3.5 22.4 - - - -
115E ILE 3.8 13.7 - - - -
116E PRO* 3.7 33.5 - - + +
118E LYS 3.0 8.9 + - - +
119E ILE* 3.3 20.0 - - + -
120E LYS 2.8 23.0 + - - -
207E HIS* 4.9 1.1 - + - -
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Residues in contact with GLN 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ASN* 3.7 19.0 + - - +
61E LEU* 5.8 2.6 - - + +
62E TRP* 1.3 76.3 - - - +
64E MET* 1.3 59.4 + - - +
81E THR* 3.3 3.0 - - - -
82E VAL 2.9 32.3 + - - +
84E THR* 3.9 13.0 - - + +
119E ILE* 4.7 0.2 - - - -
120E LYS* 3.3 16.7 - - + +
153E GLY 3.1 23.5 + - - -
154E GLN* 3.0 27.6 - - - +
156E ILE* 2.8 39.4 + - + +
157E VAL* 2.9 23.5 + - + +
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Residues in contact with MET 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E GLN* 1.3 76.8 - - - +
65E ASP* 1.3 66.3 + - - +
79E HIS* 3.7 27.6 - - + +
80E VAL 3.2 12.1 - - - +
81E THR* 3.6 15.7 - - - +
102E VAL* 4.0 14.8 - - + +
105E HIS* 3.5 23.6 - - + -
106E LEU* 4.0 16.4 - - - -
119E ILE* 4.1 15.3 - - + -
120E LYS 2.8 10.5 + - - -
121E THR* 3.4 23.9 - - + -
122E ASP 4.0 1.2 + - - -
127E TYR* 3.9 29.3 + - + +
154E GLN* 2.9 15.0 - - - +
157E VAL* 4.3 1.1 - - - -
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Residues in contact with ASP 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E MET* 1.3 78.5 - - - +
66E VAL* 1.3 94.1 + - - +
79E HIS* 3.9 0.3 - - - -
80E VAL* 2.8 31.1 + - - +
122E ASP* 3.6 23.1 - - - +
127E TYR* 3.7 9.2 + - - -
154E GLN* 3.4 24.3 - - - +
157E VAL* 3.7 20.7 - - + +
158E GLU* 4.9 5.9 - - - +
161E HIS* 4.4 9.0 - - + -
20L A 5.4 4.0 - - - +
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Residues in contact with VAL 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ASP* 1.3 100.6 + - - +
67E THR* 1.3 68.4 + - - +
68E HIS* 5.2 5.1 - - - +
77E TYR* 5.3 1.6 - - - -
78E VAL 3.1 13.9 - - - +
79E HIS* 3.5 36.1 - - + +
97E GLU* 3.6 29.6 - - + +
122E ASP* 5.9 0.2 - - - +
127E TYR* 3.7 12.1 - - + +
161E HIS* 3.5 12.1 - - - -
20L A 5.3 5.5 + - - +
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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