Contacts of the strand formed by residues 33 - 38 (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 LEU 33 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4N MET* 3.5 31.0 - - + -
23N CYS* 4.3 4.5 - - - -
27N VAL* 4.3 11.0 - - - +
31N SER 3.0 9.6 + - - +
32N TYR* 1.3 74.6 - - - +
34N ALA* 1.3 66.7 + - - +
35N TRP* 3.7 31.2 - - + +
48N ILE 4.0 0.3 - - - +
49N TYR 3.6 0.9 - - - -
50N TRP 3.3 6.4 + - - -
51N ALA* 2.7 36.9 + - - +
71N PHE* 3.5 48.5 - - + -
88N CYS* 4.9 0.9 - - + -
89N GLN 3.5 7.2 - - - +
90N GLN* 4.9 0.2 - - - -
91N TYR* 3.2 5.9 - - - -
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Residues in contact with ALA 34 (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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100M VAL* 3.6 27.1 - - + -
33N LEU* 1.3 75.5 - - - +
35N TRP* 1.3 65.0 + - - +
36N TYR* 3.9 21.3 - - + +
46N LEU* 4.1 3.1 - - + -
48N ILE 3.0 13.0 - - - +
88N CYS* 3.2 7.3 - - - +
89N GLN* 2.8 35.2 + - - +
91N TYR* 3.7 3.8 - - + -
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Residues in contact with TRP 35 (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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6N GLN* 4.3 6.5 - - - -
21N ILE* 3.9 31.0 - - + -
22N ASN 3.9 3.4 - - - -
23N CYS* 3.6 34.1 - - + -
33N LEU* 3.7 16.2 - - + +
34N ALA* 1.3 75.8 - - - +
36N TYR* 1.3 62.3 + - - +
46N LEU* 3.7 4.5 - - - +
47N LEU* 2.9 28.4 + - + -
48N ILE* 2.9 36.5 + - + -
51N ALA 4.6 3.9 + - - -
64N GLY* 4.9 0.4 - - - -
65N SER 5.5 0.2 + - - -
71N PHE* 4.3 2.5 - - + +
72N THR* 3.8 13.4 + - - -
73N LEU* 3.4 57.2 - - + +
86N TYR* 4.8 3.1 - - + -
87N TYR 3.3 22.4 - - - -
88N CYS* 3.6 18.6 - - + -
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Residues in contact with TYR 36 (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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45M LEU* 5.6 0.2 - - + -
100M PHE* 2.9 55.2 + + - -
103M TRP* 3.9 18.2 - + - -
34N ALA* 3.9 14.3 - - + +
35N TRP* 1.3 76.5 - - - +
37N GLN* 1.3 61.1 + - - +
44N PRO* 4.1 15.5 - - + -
45N LYS 3.2 6.5 - - - +
46N LEU* 3.5 27.8 - - + -
47N LEU* 4.4 2.9 - - - -
86N TYR* 3.3 9.2 - - - +
87N TYR* 2.7 48.8 + - + +
89N GLN* 2.6 41.0 + - + -
98N PHE* 4.1 13.5 - + - -
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Residues in contact with GLN 37 (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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36N TYR* 1.3 73.7 - - - +
38N GLN* 1.3 62.6 + - - +
39N LYS* 3.6 25.8 - - + +
43N PRO 4.3 0.3 - - - +
44N PRO* 3.4 0.8 - - - -
45N LYS* 2.6 51.5 + - + +
47N LEU* 3.8 12.7 - - + +
62N PHE* 4.0 5.5 - - - -
82N ASP* 4.0 6.3 + - - +
84N ALA* 3.8 11.9 - - + -
85N VAL 3.8 3.1 - - - -
86N TYR* 2.9 40.4 + - + -
212N SO4 4.0 7.1 + - - -
213N GOL 3.1 36.0 + - - -
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Residues in contact with GLN 38 (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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39M GLN* 3.0 41.7 + - - -
91M TYR* 3.7 4.2 + - - -
37N GLN* 1.3 75.8 - - - +
39N LYS* 1.3 63.9 + - - +
40N PRO* 4.2 1.0 - - - +
42N GLN 3.0 28.0 + - - +
43N PRO 4.5 1.6 - - - -
44N PRO* 3.5 31.4 - - + +
84N ALA* 3.2 4.6 - - - +
85N VAL* 2.9 43.1 + - + +
87N TYR* 3.4 21.9 + - + -
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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