Contacts of the helix formed by residues 197 - 209 (chain A) in PDB entry 2XMS
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 SER 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLU 4.4 0.4 + - - -
195A GLY 3.4 4.1 + - - -
196A ASN* 1.3 78.0 - - - +
198A GLU* 1.3 64.6 + - - +
199A LEU* 3.4 9.1 + - - +
200A ILE* 3.2 27.4 + - - +
201A GLN* 2.9 22.4 + - - +
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Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A SER* 1.3 73.1 - - - +
199A LEU* 1.3 63.3 + - - +
201A GLN* 3.4 16.9 + - + +
202A LYS* 3.1 24.2 + - + +
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO* 6.2 2.2 - - + -
188A PHE* 4.1 23.6 - - + -
192A GLU* 5.3 2.0 - - - +
197A SER* 3.3 9.1 + - - +
198A GLU* 1.3 77.0 - - - +
200A ILE* 1.3 59.6 + - + +
202A LYS* 3.3 9.8 + - + +
203A TYR* 3.0 58.6 + - + +
283A LEU* 4.3 23.8 - - + +
284A THR* 3.9 27.4 - - + -
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 5.3 0.7 - - + +
188A PHE* 3.5 44.6 - - + -
192A GLU* 3.3 44.2 - - + +
193A LEU* 3.9 17.3 - - + -
196A ASN* 3.9 4.7 - - - +
197A SER* 3.2 24.1 + - - +
199A LEU* 1.3 77.1 - - + +
201A GLN* 1.3 59.0 + - - +
203A TYR* 3.4 3.6 + - - +
204A ARG* 2.8 50.4 + - - +
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Residues in contact with GLN 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ASN* 3.3 43.0 + - - +
197A SER 2.9 19.5 + - - +
198A GLU* 3.7 13.5 - - + +
199A LEU 3.4 0.2 - - - -
200A ILE* 1.3 74.9 - - - +
202A LYS* 1.3 63.9 + - - +
204A ARG* 3.5 8.0 + - - +
205A ASN* 3.1 29.5 + - - +
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLN* 5.9 3.4 - - - +
67A PRO* 6.3 1.6 - - - +
198A GLU* 3.1 15.5 + - + +
199A LEU* 3.6 13.3 - - + +
201A GLN* 1.3 76.2 - - - +
203A TYR* 1.3 82.8 + - + +
205A ASN* 3.4 8.3 + - - +
206A ILE* 3.0 41.5 + - + +
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 3.7 27.6 - - + -
63A SER* 2.6 40.0 + - - -
67A PRO* 4.8 6.2 - - - +
184A LEU* 4.1 4.7 - - + -
188A PHE* 3.7 32.3 - + + -
199A LEU* 3.0 46.5 + - + +
200A ILE 4.1 1.3 - - - +
202A LYS* 1.3 97.7 + - + +
204A ARG* 1.3 60.4 + - - +
206A ILE* 3.5 13.9 + - + +
207A ILE* 3.0 36.7 + - + +
283A LEU* 3.6 21.1 - - + +
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A GLU* 6.3 0.8 - - - +
184A LEU* 3.9 25.5 - - + +
193A LEU* 3.4 42.3 + - - +
196A ASN* 2.5 32.1 + - - +
200A ILE* 2.8 33.3 + - - +
201A GLN* 3.6 8.2 - - - +
203A TYR* 1.3 72.7 - - - +
205A ASN* 1.3 56.5 + - - +
207A ILE* 4.4 0.2 - - - +
208A THR* 2.6 46.6 + - - +
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Residues in contact with ASN 205 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A GLN* 3.1 16.4 + - - +
202A LYS* 3.6 9.9 - - - +
204A ARG* 1.3 72.5 - - - +
206A ILE* 1.3 67.9 + - - +
208A THR* 4.7 0.4 - - - -
209A HIS* 2.9 53.9 + - + +
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLY 4.4 8.7 - - - +
59A LEU* 5.1 0.4 - - + -
63A SER* 4.4 17.9 - - - +
202A LYS* 3.0 38.6 + - + +
203A TYR* 3.5 35.7 - - + +
205A ASN* 1.3 74.9 - - + +
207A ILE* 1.3 71.0 + - + +
209A HIS 3.9 0.2 - - - -
210A ALA* 3.1 31.2 + - + +
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLY* 3.4 27.4 - - - +
59A LEU* 4.4 7.9 - - + -
180A PRO* 4.0 28.9 - - + +
183A ILE* 4.4 14.4 - - + -
184A LEU* 3.7 16.4 - - + -
187A LEU* 3.5 32.5 - - + -
203A TYR* 3.0 25.8 + - + +
204A ARG 4.4 0.9 - - - +
206A ILE* 1.3 75.9 - - + +
208A THR* 1.3 67.8 + - - +
209A HIS 3.1 0.5 + - - -
210A ALA* 3.2 18.5 + - - +
213A LEU* 3.7 19.2 - - + +
216A ILE* 5.2 1.6 - - + -
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Residues in contact with THR 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PRO* 3.9 25.6 - - + +
184A LEU* 4.6 2.6 - - - +
204A ARG* 2.6 38.6 + - - +
207A ILE* 1.3 74.2 - - - +
209A HIS* 1.3 84.5 + - + +
210A ALA 3.8 0.9 + - - +
213A LEU* 4.2 13.0 - - - +
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Residues in contact with HIS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ASN* 2.9 42.4 + - + +
206A ILE 3.9 2.0 - - - -
208A THR* 1.3 99.7 + - + +
210A ALA* 1.3 66.5 + - - +
211A PRO* 3.4 6.8 - - - +
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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