Contacts of the strand formed by residues 66 - 73 (chain B) in PDB entry 1N54
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 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A ASP* 5.1 3.8 - - - +
610A ARG* 4.9 2.3 + - - -
57B TYR* 3.4 38.9 + - + +
60B PHE* 3.7 21.5 - - + +
61B SER* 2.9 27.2 + - - +
64B GLY 3.7 7.6 - - - +
65B ASP* 1.3 71.1 - - - +
67B LYS* 1.3 66.3 + - - +
68B LYS 4.1 6.7 - - - +
69B ILE* 4.2 15.0 - - + -
86B VAL* 3.7 21.3 - - + -
87B GLU 3.3 13.7 - - - +
88B TYR* 4.0 6.3 - - + +
89B TYR* 2.9 17.4 + - - -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LYS* 3.2 26.7 + - - -
1556A GOL 3.6 33.3 + - - -
57B TYR* 3.6 9.3 + - - -
66B ILE* 1.3 74.2 - - - +
68B LYS* 1.3 59.3 + - - +
87B GLU* 2.6 52.7 + - + +
88B TYR 4.5 3.4 - - - +
89B TYR* 3.4 42.3 - - + +
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A SER* 5.8 3.4 - - - -
563A PHE* 6.5 0.7 - - + -
607A LYS* 5.7 1.1 - - - +
1556A GOL 3.1 29.8 + - - +
57B TYR* 4.2 4.5 - - - +
66B ILE* 4.7 0.2 - - - -
67B LYS* 1.3 84.5 - - - +
69B ILE* 1.3 72.0 + - - +
70B ILE* 4.1 29.7 - - + +
85B PHE 3.7 2.1 - - - +
87B GLU* 3.1 38.4 + - - +
119B PHE* 6.1 2.0 - - + -
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A SER* 5.7 0.2 + - - -
53B GLU* 3.8 20.3 + - + +
56B ILE* 3.5 33.7 - - + -
57B TYR* 3.3 50.0 + - + +
66B ILE* 4.2 18.2 - - + -
68B LYS* 1.3 85.8 - - - +
70B ILE* 1.3 63.4 + - - +
71B MET* 3.8 13.6 + - - +
84B CYS* 4.0 20.9 - - - -
85B PHE 3.3 8.7 - - - +
86B VAL* 4.5 6.3 - - + -
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LYS* 4.1 37.5 - - + +
69B ILE* 1.3 74.1 - - - +
71B MET* 1.3 65.0 + - - +
84B CYS* 3.3 5.0 - - - -
85B PHE* 3.0 44.8 + - + +
87B GLU* 5.7 4.7 - - + +
119B PHE* 3.6 42.6 - - + -
124B GLN* 3.5 38.1 - - + +
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Residues in contact with MET 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A SER* 6.5 0.2 - - - -
47B LEU* 4.6 8.7 - - + -
51B THR 4.0 18.6 - - - +
52B THR* 5.4 0.2 - - - -
53B GLU* 4.0 40.4 - - + +
56B ILE* 4.2 15.7 - - + -
69B ILE* 3.8 7.5 + - - +
70B ILE* 1.3 73.0 - - - +
72B GLY* 1.3 70.2 + - - +
73B LEU* 3.4 19.6 + - + +
80B ALA* 5.2 10.8 - - + -
83B PHE 4.0 14.4 - - - +
84B CYS* 3.9 4.0 - - + -
124B GLN* 4.0 8.1 - - - +
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ILE 3.4 3.2 + - - -
71B MET* 1.3 75.6 - - - +
73B LEU* 1.3 63.3 + - - +
79B THR 3.4 2.3 - - - +
80B ALA* 3.5 6.6 - - - -
81B CYS* 3.2 19.5 + - - -
83B PHE* 3.0 50.9 + - - +
124B GLN* 4.1 2.9 - - - -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B MET* 3.7 18.2 - - + +
72B GLY* 1.3 77.9 - - - +
74B ASP* 1.3 63.0 + - - +
78B LYS* 4.3 9.4 - - + +
79B THR* 3.0 33.0 - - - +
80B ALA* 4.6 0.9 - - - +
81B CYS* 3.4 9.5 - - - +
83B PHE* 4.5 0.5 - - - -
124B GLN* 2.7 27.0 + - - +
125B TYR* 3.8 29.8 - - + +
126B GLY 2.9 23.0 + - - -
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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