Contacts of the strand formed by residues 62 - 70 (chain E) in PDB entry 3SKU
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 ILE 62 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E PHE* 4.5 20.2 - - + -
60E VAL* 5.1 4.5 - - + -
61E LYS* 1.3 69.4 - - - +
63E THR* 1.3 62.8 + - - +
64E GLN 3.7 14.6 - - - +
65E VAL* 4.4 2.0 - - + -
83E PRO* 5.6 2.3 - - - +
103E SER 4.5 2.2 - - - +
104E PHE* 2.9 73.4 - - + +
105E THR* 5.0 4.0 - - + -
126E PHE* 3.5 27.4 - - + -
127E ALA 3.5 7.0 - - - +
128E THR* 3.5 20.2 - - + -
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Residues in contact with THR 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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222C ARG* 5.9 3.4 - - - -
223C PHE* 4.5 27.5 - - + +
61E LYS 3.4 5.0 + - - -
62E ILE* 1.3 75.5 - - - +
64E GLN* 1.3 66.7 + - + +
81E TYR* 3.4 1.2 - - - +
82E ASN* 2.3 42.9 + - - +
83E PRO* 2.9 33.0 + - - +
104E PHE* 5.5 0.2 - - - -
127E ALA* 2.7 21.1 + - + +
129E PHE* 4.8 10.3 - - - -
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Residues in contact with GLN 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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132C GLN* 5.1 0.2 - - - +
220C LEU* 4.7 0.4 - - - +
221C PRO* 2.2 46.9 + - - +
222C ARG* 4.1 23.7 - - - +
62E ILE* 3.7 3.4 - - - +
63E THR* 1.3 89.3 - - + +
65E VAL* 1.3 74.4 + - - +
66E THR* 4.3 11.7 - - + +
80E ILE* 3.6 19.2 - - + +
81E TYR 3.0 5.2 - - - -
82E ASN* 3.2 27.8 + - + +
127E ALA* 2.9 36.2 + - + +
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Residues in contact with VAL 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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62E ILE* 4.4 2.5 - - + -
64E GLN* 1.3 76.2 - - - +
66E THR* 1.3 65.6 + - - +
67E TRP* 5.0 0.2 - - - +
79E ALA 4.0 0.9 - - - +
80E ILE* 3.4 1.9 - - - -
81E TYR* 2.6 46.8 + - + +
99E PHE* 4.3 5.5 - - + -
103E SER 4.9 5.2 - - - +
107E GLY* 3.6 30.1 - - - +
124E CYS* 4.1 17.0 - - - -
125E GLU 3.5 9.4 - - - +
126E PHE* 2.9 48.2 - - + -
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Residues in contact with THR 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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220C LEU* 3.4 38.9 - - + +
222C ARG* 4.5 1.7 + - - -
64E GLN* 4.3 12.8 + - - +
65E VAL* 1.3 77.6 - - - +
67E TRP* 1.3 64.1 + - - +
68E GLN* 4.0 6.3 - - + -
79E ALA 3.3 3.8 - - - +
80E ILE* 3.8 21.5 - - + -
123E ILE* 3.3 3.6 - - - +
124E CYS* 3.5 4.7 - - - -
125E GLU* 3.0 55.1 + - - +
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Residues in contact with TRP 67 (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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35E VAL* 5.1 2.2 - - + -
49E LEU* 3.8 41.3 - - + -
50E HIS 4.3 9.0 - - - -
51E CYS* 3.7 19.3 - - + -
65E VAL* 5.0 1.3 - - + -
66E THR* 1.3 76.0 - - - +
68E GLN* 1.3 64.0 + - - +
78E VAL* 2.9 41.1 + - + +
79E ALA* 2.9 14.9 + - + +
99E PHE* 4.0 17.7 - + - -
107E GLY* 3.0 24.4 + - - -
109E ILE* 3.9 20.4 - - + +
122E TYR* 3.9 34.1 - + + -
123E ILE 3.1 19.5 - - - -
124E CYS* 3.9 22.3 - - + -
138E LEU* 4.5 9.4 - - + -
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Residues in contact with GLN 68 (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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218C GLY* 3.3 26.7 + - - -
220C LEU* 3.4 33.1 - - + +
66E THR* 4.0 4.9 - - - -
67E TRP* 1.3 80.1 - - - +
69E LYS* 1.3 59.9 + - - +
70E SER 4.2 0.2 - - - -
75E LYS* 4.9 17.3 - - + +
76E GLN 3.3 11.9 - - - +
77E ASN* 3.5 16.6 + - + +
78E VAL* 3.9 3.2 - - - +
122E TYR* 3.9 4.2 - - - +
123E ILE* 3.1 49.0 + - + +
125E GLU* 3.7 16.7 - - - +
135E GLU* 5.8 0.2 - - - +
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Residues in contact with LYS 69 (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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68E GLN* 1.3 73.6 - - - +
70E SER* 1.3 68.1 + - - +
71E THR* 2.9 25.6 + - - +
75E LYS* 3.9 3.0 - - - -
76E GLN* 2.5 48.7 + - + +
78E VAL* 3.9 11.6 - - + +
93E TYR* 4.0 11.4 + - - +
117E GLU 2.7 30.3 + - - -
118E ASP* 3.4 2.4 - - - +
119E GLU 3.2 18.7 + - - -
120E GLY* 4.1 5.6 - - - -
121E VAL 3.8 11.7 - - - +
122E TYR* 3.4 36.6 + - + +
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Residues in contact with SER 70 (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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68E GLN 4.2 1.8 + - - -
69E LYS* 1.3 72.5 - - - +
71E THR* 1.3 58.0 + - - +
72E ASN* 3.2 22.2 + - - +
73E GLY 4.7 0.7 + - - -
74E SER 3.7 10.0 + - - -
75E LYS* 4.3 8.7 - - - -
120E GLY* 5.1 1.0 - - - -
121E VAL* 3.4 40.8 + - - +
123E ILE* 4.3 18.3 - - - +
137E GLN* 5.5 2.2 - - - -
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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