Contacts of the strand formed by residues 102 - 107 (chain N) in PDB entry 3INU
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 THR 102 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6N GLN* 2.8 25.2 + - - +
8N PRO* 3.0 35.2 + - + +
9N ASP 3.4 8.1 - - - +
10N SER* 4.5 0.7 - - - +
11N LEU* 4.6 3.8 - - + -
21N ILE* 3.3 39.6 - - + +
84N ALA 3.7 0.7 - - - +
85N VAL* 3.2 4.8 - - - +
86N TYR* 2.6 39.8 + - - +
101N GLY* 1.3 73.4 - - - -
103N LYS* 1.3 69.4 + - - +
104N VAL 3.7 0.5 + - - -
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Residues in contact with LYS 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N ASP 2.8 15.5 + - - +
10N SER* 3.4 9.8 - - - +
11N LEU* 3.0 28.2 + - - +
84N ALA 3.5 8.7 - - - +
85N VAL* 4.2 19.3 - - + +
101N GLY 4.3 0.2 - - - -
102N THR* 1.3 72.2 - - - +
104N VAL* 1.3 62.6 + - - +
105N GLU* 4.0 31.1 + - + +
142N ARG* 4.7 12.3 - - - +
165N GLU* 3.5 37.1 + - - -
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Residues in contact with VAL 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N LEU* 3.5 16.6 - - + +
13N VAL* 5.7 0.2 - - + -
19N ALA* 4.7 8.3 - - + -
21N ILE* 3.9 18.4 - - + -
75N ILE* 5.0 3.4 - - + -
78N LEU* 3.6 38.1 - - + -
82N ASP 4.5 3.8 - - - +
83N VAL* 3.2 24.3 - - - +
84N ALA 2.8 13.7 + - - +
86N TYR* 3.3 37.9 - - + -
102N THR* 4.8 0.4 - - + -
103N LYS* 1.3 76.6 - - - +
105N GLU* 1.3 64.7 + - - +
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Residues in contact with GLU 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N SER* 5.6 5.1 - - - -
11N LEU 2.9 12.8 + - - +
12N ALA* 3.3 10.8 - - + +
13N VAL 3.1 22.7 + - - +
78N LEU* 4.1 5.9 - - - +
83N VAL* 4.0 1.6 - - + -
103N LYS* 4.0 37.3 + - + +
104N VAL* 1.3 79.8 - - - +
106N ILE* 1.3 66.7 + - - +
142N ARG* 5.2 5.0 + - - -
165N GLU* 4.4 3.5 - - - +
166N GLN* 3.3 16.6 - - + +
173N TYR* 2.9 29.8 + - - +
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Residues in contact with ILE 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N ALA* 4.8 2.0 - - - +
13N VAL 3.3 5.8 - - - +
15N LEU* 4.1 28.7 - - + +
78N LEU* 3.6 32.5 - - + -
79N GLN 3.9 10.5 - - - +
80N ALA* 4.2 3.6 - - - -
83N VAL* 3.4 18.4 - - + -
105N GLU* 1.3 73.9 - - - +
107N LYS* 1.3 77.4 + - - +
108N ARG* 3.5 4.9 + - + +
140N TYR* 3.3 10.6 + - - -
166N GLN* 2.8 31.9 + - - +
171N SER* 3.8 25.6 - - - +
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Residues in contact with LYS 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N ALA* 3.9 32.7 - - + +
13N VAL 2.8 10.1 + - - +
14N SER* 2.9 51.4 + - - +
15N LEU* 4.0 2.1 + - - +
17N GLU* 3.9 14.1 + - - -
106N ILE* 1.3 80.4 - - - +
108N ARG* 1.3 58.2 - - - +
140N TYR* 3.7 9.0 - - - +
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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