Contacts of the strand formed by residues 196 - 201 (chain N) in PDB entry 3H1J
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 VAL 196 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23N LEU* 4.6 0.2 - - - -
24N ARG* 3.3 43.1 - - - +
38N GLY 3.4 1.6 - - - +
39N VAL* 3.3 5.5 - - - -
40N TRP* 2.9 39.0 + - + +
195N MET* 1.3 82.3 - - - +
197N LEU* 1.3 67.6 + - - +
198N ALA* 3.4 2.9 + - + +
380N GLY* 4.4 16.6 - - - +
383N LEU* 3.3 37.5 - - + -
384N LEU* 3.9 13.0 - - + -
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Residues in contact with LEU 197 (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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23N LEU* 4.5 11.7 - - + +
24N ARG 2.9 10.8 + - - +
25N VAL* 3.2 19.8 - - + +
26N ALA 2.8 26.7 + - - +
37N VAL* 5.5 1.3 - - + -
38N GLY 3.5 10.3 - - - +
39N VAL* 4.5 3.6 - - + +
110N VAL* 4.1 15.3 - - + -
113N LEU* 3.7 29.8 - - + -
195N MET 4.4 0.2 - - - -
196N VAL* 1.3 70.2 - - - +
198N ALA* 1.3 61.2 + - - +
208N LEU* 4.1 19.3 - - + -
212N ALA* 3.7 29.8 - - + -
216N PHE* 4.1 20.4 - - + -
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Residues in contact with ALA 198 (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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26N ALA 3.0 5.4 - - - -
37N VAL* 3.3 3.1 - - - +
38N GLY 2.9 31.8 + - - -
40N TRP* 3.8 21.5 - - + -
196N VAL* 3.4 3.5 + - + -
197N LEU* 1.3 76.9 - - - +
199N ALA* 1.3 62.0 + - - +
208N LEU* 5.0 0.7 - - - -
376N CYS* 3.3 4.5 - - - -
379N ILE* 3.6 29.2 - - + -
380N GLY* 3.8 10.8 - - - +
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Residues in contact with ALA 199 (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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26N ALA 3.0 5.9 + - - -
27N SER* 3.0 24.8 - - - -
28N GLU 3.1 4.3 + - - -
36N THR 3.2 6.3 - - - -
37N VAL* 3.2 26.0 - - + -
198N ALA* 1.3 76.3 - - - +
200N ALA* 1.3 63.2 - - - +
203N ILE* 4.2 9.0 - - + -
208N LEU* 3.6 27.6 - - + -
376N CYS* 3.5 4.4 - - - -
379N ILE* 3.8 3.2 - - - +
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Residues in contact with ALA 200 (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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28N GLU 3.4 9.2 - - - +
35N CYS* 3.0 22.6 - - - +
36N THR 2.9 15.5 + - - -
199N ALA* 1.3 77.3 - - - +
201N GLY* 1.3 59.0 + - - +
203N ILE* 4.6 3.8 - - - -
372N THR* 3.5 31.6 - - - +
375N VAL* 4.0 22.9 - - + -
376N CYS* 4.1 5.6 - - - +
379N ILE* 4.7 0.9 - - + -
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Residues in contact with GLY 201 (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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28N GLU 3.3 7.1 + - - +
29N GLU* 3.4 4.2 - - - -
30N SER* 2.5 47.9 + - - +
32N GLN* 4.0 2.0 - - - -
35N CYS* 3.9 6.5 - - - -
200N ALA* 1.3 75.7 - - - +
202N GLY* 1.3 57.1 + - - -
203N ILE* 3.0 9.4 + - - +
372N THR* 3.9 10.9 - - - +
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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