Contacts of the strand formed by residues 34 - 38 (chain N) in PDB entry 3SDI
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 34 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2181 GLY* 5.1 0.5 - - - -
2221 GLN* 3.4 16.6 + - - +
14N LEU* 3.7 13.9 - - + +
15N GLY 4.0 2.9 - - - -
16N ALA* 3.8 21.5 - - + -
32N ASP* 3.2 20.9 + - - +
33N LYS* 1.3 78.5 - - - +
35N THR* 1.3 60.3 + - - +
42N TRP* 3.8 6.4 - - + -
43N CYS 3.8 1.8 - - - -
44N CYS* 3.7 28.5 - - - -
174N ARG* 3.6 39.7 - - + +
175N MET* 3.6 12.6 - - - +
176N VAL* 3.7 26.2 - - + -
186N ARG* 4.3 2.5 - - - +
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Residues in contact with THR 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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2181 GLY* 6.0 0.3 - - - -
2191 TYR* 3.8 24.6 - - + +
2221 GLN* 3.7 10.5 + - - +
32N ASP 4.6 0.9 + - - -
33N LYS 3.8 2.4 + - - -
34N LEU* 1.3 74.6 + - - +
36N ARG* 1.3 72.3 + - - +
37N VAL* 3.7 2.3 + - + -
42N TRP* 3.1 7.1 - - - -
43N CYS* 2.7 55.3 + - - -
45N ARG* 2.9 25.8 + - - -
56N ALA* 4.1 19.1 - - + -
60N GLN* 6.0 0.9 - - - +
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Residues in contact with ARG 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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2221 GLN* 3.1 22.1 + - + +
2241 ILE* 3.8 33.0 - - - +
72G ARG* 5.6 1.8 - - - +
35N THR* 1.3 78.7 - - - +
37N VAL* 1.3 64.0 + - - +
38N HIS* 3.1 45.8 + - - +
39N ASP* 3.3 25.6 + - - +
41N ILE 3.9 0.4 - - - -
42N TRP* 3.3 33.5 - - + +
60N GLN* 4.0 31.4 + - - +
64N GLU* 5.8 1.8 + - - -
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Residues in contact with VAL 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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35N THR* 3.7 1.7 + - + -
36N ARG* 1.3 79.4 + - - +
38N HIS* 1.3 64.5 + - - +
41N ILE* 2.9 38.6 + - + +
42N TRP* 4.4 5.4 - - - +
43N CYS* 4.6 8.1 - - - -
56N ALA* 3.8 26.5 - - + +
59N VAL* 4.0 17.9 - - + -
60N GLN* 3.9 25.6 - - + +
63N LEU* 3.8 20.2 - - + +
79N ALA* 5.0 0.2 - - + -
83N PHE* 4.0 24.5 - - + -
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Residues in contact with HIS 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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72G ARG* 4.7 5.4 - - - -
36N ARG* 3.1 32.3 + - - +
37N VAL* 1.3 79.4 + - - +
39N ASP* 1.3 92.1 + - + +
40N LYS 3.1 5.1 + - - -
41N ILE* 3.1 35.1 + - + +
42N TRP* 3.7 0.3 + - - -
63N LEU* 4.4 12.3 + - + +
64N GLU* 5.2 2.5 + - - -
67N THR* 3.0 37.2 + - + +
73N THR* 4.5 14.5 + - + +
74N PRO* 3.7 23.1 - - + +
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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