Contacts of the helix formed by residues 197 - 208 (chain N) in PDB entry 1H2I
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 GLU 197 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192N LYS* 2.5 43.1 - - - +
195N ASP 3.5 3.1 + - - +
196N LEU* 1.3 75.0 - - - +
198N PRO* 1.3 72.8 - - - +
199N SER* 3.3 12.5 + - - -
200N VAL* 2.8 27.6 + - + -
201N GLU* 2.9 12.5 + - - +
42O ALA* 3.7 20.9 - - - +
45O GLN* 3.2 19.5 + - - +
77O GLU* 4.5 10.4 + - - +
78O MET* 4.2 14.6 - - + -
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Residues in contact with PRO 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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194N GLN* 5.7 3.4 - - - +
196N LEU* 3.2 28.6 - - + +
197N GLU* 1.3 85.3 - - - +
199N SER* 1.3 54.5 + - - +
201N GLU* 3.0 8.2 + - + +
202N GLU* 2.8 39.2 + - - +
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Residues in contact with SER 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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197N GLU* 3.9 15.2 + - - -
198N PRO* 1.3 77.8 - - - +
200N VAL* 1.3 67.6 + - - +
202N GLU* 3.5 11.0 + - - +
203N ALA* 3.2 23.2 + - - +
34O GLU* 5.3 0.5 - - - +
38O ALA* 4.1 12.2 + - - +
42O ALA* 5.6 1.0 - - - +
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Residues in contact with VAL 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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197N GLU* 2.8 27.4 + - + +
199N SER* 1.3 78.1 + - - +
201N GLU* 1.3 51.5 + - + +
203N ALA* 3.4 4.2 + - - +
204N ARG* 2.8 66.6 + - - +
35O GLU* 4.8 1.4 - - + +
38O ALA* 3.8 36.6 - - + +
39O ILE* 3.9 13.9 - - + +
42O ALA* 4.1 9.2 - - + -
77O GLU 4.2 4.5 - - - +
78O MET* 3.5 13.2 - - - +
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Residues in contact with GLU 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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196N LEU* 5.3 7.6 - - + -
197N GLU 2.9 12.6 + - - +
198N PRO* 3.0 12.8 + - + +
200N VAL* 1.3 74.9 - - + +
202N GLU* 1.3 68.9 + - - +
204N ARG* 3.7 13.3 + - - +
205N TYR* 3.0 24.3 + - - +
77O GLU* 4.7 4.0 - - - +
36P TYR* 3.2 37.0 + - - -
37P GLN* 5.4 5.2 - - - +
40P GLN* 3.7 16.2 - - - +
44P ARG* 4.6 19.1 + - - +
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Residues in contact with GLU 202 (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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198N PRO 2.8 18.4 + - - +
199N SER* 3.8 12.5 - - - +
201N GLU* 1.3 72.1 - - - +
203N ALA* 1.3 57.6 + - - +
205N TYR* 2.6 31.3 + - - +
206N ASN* 3.0 25.8 + - - +
34O GLU* 4.9 6.8 - - - +
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Residues in contact with ALA 203 (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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199N SER 3.2 11.0 + - - +
200N VAL 3.5 7.9 - - - +
202N GLU* 1.3 81.6 - - - +
204N ARG* 1.3 57.4 + - - +
206N ASN* 3.1 4.5 + - - +
207N SER* 3.0 26.5 + - - -
32O THR* 4.8 1.7 + - - -
34O GLU* 3.8 35.7 + - + +
35O GLU* 3.7 28.3 - - - +
38O ALA* 4.2 4.9 - - + -
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Residues in contact with ARG 204 (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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200N VAL* 2.8 35.3 + - - +
201N GLU* 3.7 14.7 + - - +
203N ALA* 1.3 71.0 - - - +
205N TYR* 1.3 63.8 + - - +
207N SER* 3.4 12.0 + - - -
208N CYS* 3.7 15.2 + - - -
35O GLU* 2.6 52.4 + - - +
39O ILE* 4.2 1.2 - - - +
76O ASN 4.5 0.2 + - - -
77O GLU 3.0 27.3 + - - -
78O MET 3.0 19.6 + - - -
79O PHE* 3.4 20.5 + - - +
80O GLY* 3.4 9.5 - - - +
82O ASN* 5.2 1.3 - - - +
116O LYS* 4.2 9.2 - - - +
36P TYR* 2.8 43.2 + - - -
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Residues in contact with TYR 205 (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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201N GLU* 3.0 16.4 + - - +
202N GLU* 2.6 19.0 + - - +
204N ARG* 1.3 74.6 - - - +
206N ASN* 1.3 75.1 + - - +
207N SER 3.6 0.5 + - - -
208N CYS* 3.7 13.7 + - - +
209N ARG* 2.9 47.0 + - - +
33P ALA* 3.8 32.2 - - + +
34P GLU* 4.9 5.6 + - - +
36P TYR* 5.0 8.3 - + - -
37P GLN* 3.0 42.7 + - + -
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Residues in contact with ASN 206 (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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202N GLU* 3.0 30.0 + - - +
203N ALA 3.1 6.0 + - - +
205N TYR* 1.3 97.3 - - - +
207N SER* 1.3 62.1 + - - +
209N ARG* 3.5 37.4 + - - +
34O GLU* 3.8 22.9 + - - +
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Residues in contact with SER 207 (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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203N ALA 3.0 14.1 + - - -
204N ARG 3.4 7.1 + - - -
205N TYR 3.3 0.4 - - - -
206N ASN* 1.3 74.2 - - - +
208N CYS* 1.3 60.2 + - - +
209N ARG 2.8 22.4 + - - +
32O THR* 3.5 37.3 - - - +
35O GLU* 3.4 21.9 + - - -
116O LYS* 4.2 8.0 + - - -
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Residues in contact with CYS 208 (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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204N ARG* 3.7 13.6 + - - -
205N TYR* 3.9 6.7 - - - +
206N ASN 3.4 0.4 - - - -
207N SER* 1.3 81.6 + - - +
209N ARG* 1.3 57.3 + - - +
82O ASN* 5.5 3.8 - - - -
116O LYS* 5.6 5.4 - - - -
30P GLN* 5.4 9.6 - - - +
31P TYR 4.5 12.8 - - - +
32P THR* 4.8 1.1 - - - -
33P ALA* 3.6 32.9 + - + +
36P TYR* 4.1 33.2 - - - -
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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