Contacts of the helix formed by residues 198 - 212 (chain A) in PDB entry 2GWU
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 THR 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A PRO 5.9 0.4 - - - +
197A ARG* 1.3 76.3 - - - +
199A ILE* 1.3 66.4 + - - +
200A GLU* 3.1 30.6 - - - +
201A ASP* 3.0 24.9 + - - +
202A PHE* 3.0 14.4 - - - -
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Residues in contact with ILE 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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50A LEU* 2.9 32.6 - - + +
51A GLY* 4.7 2.9 - - - +
73A HIS* 3.6 9.6 - - + +
77A TRP* 5.5 9.0 - - + -
197A ARG 4.1 0.2 + - - -
198A THR* 1.3 71.5 - - - +
200A GLU* 1.3 82.4 + - + +
202A PHE* 2.9 11.5 + - - -
203A GLU* 2.9 49.3 + - + +
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Residues in contact with GLU 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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198A THR* 3.1 20.2 + - - +
199A ILE* 1.3 85.9 - - + +
201A ASP* 1.3 72.7 + - - +
203A GLU* 3.2 18.9 + - - +
204A SER* 3.1 23.4 + - - -
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Residues in contact with ASP 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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197A ARG* 3.6 33.1 - - + -
198A THR* 3.0 25.8 + - - +
200A GLU* 1.3 92.5 - - - +
202A PHE* 1.3 64.0 + - + +
204A SER* 3.3 14.8 + - - -
205A MET* 3.3 17.8 + - - +
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Residues in contact with PHE 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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50A LEU* 2.9 21.3 - - + -
69A LEU* 3.3 5.5 - - - +
73A HIS* 3.5 3.4 - + + -
88A MET* 3.0 44.4 - - + -
89A LEU 3.7 7.6 - - - -
90A GLY 4.4 0.2 - - - -
108A LEU* 2.9 48.0 - - + -
197A ARG* 2.8 50.7 - - + -
198A THR 3.0 18.8 - - - -
199A ILE* 2.9 6.3 + - - -
201A ASP* 1.3 75.6 - - - +
203A GLU* 1.3 57.0 + - - +
205A MET* 3.0 13.1 + - - +
206A ASN 2.8 25.3 + - - -
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Residues in contact with GLU 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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48A MET* 3.6 36.7 - - + +
49A ASP* 4.4 2.3 - - - +
50A LEU* 3.0 27.3 + - + +
199A ILE* 2.9 45.1 + - + +
200A GLU* 3.2 17.5 + - - +
202A PHE* 1.3 76.1 - - - +
204A SER* 1.3 57.1 + - - +
206A ASN* 3.2 1.9 + - - +
207A THR* 2.8 34.2 + - - -
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Residues in contact with SER 204 (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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200A GLU 3.1 10.1 + - - -
201A ASP* 3.6 10.1 - - - -
202A PHE 3.2 0.4 - - - -
203A GLU* 1.3 78.1 - - - +
205A MET* 1.3 63.4 + - - +
207A THR* 3.2 8.1 + - - -
208A TYR* 3.1 21.3 + - - +
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Residues in contact with MET 205 (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 TRP* 5.1 1.8 - - + -
69A LEU* 5.7 0.2 - - + -
90A GLY* 4.6 3.8 - - - -
105A MET* 2.8 56.1 - - + +
106A ILE* 3.5 7.4 - - - +
107A HIS 3.4 14.8 - - - +
108A LEU* 3.2 36.6 - - + -
197A ARG* 6.2 2.2 - - - -
201A ASP* 3.3 12.1 + - - +
202A PHE* 3.0 19.4 + - - +
204A SER* 1.3 80.0 - - - +
206A ASN* 1.3 62.4 + - - +
208A TYR* 3.1 8.4 + - - +
209A LEU* 3.0 23.1 + - - +
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Residues in contact with ASN 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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47A ALA* 2.7 37.2 + - - +
49A ASP 5.7 0.8 + - - -
50A LEU* 4.0 5.2 - - + +
67A TRP* 3.0 39.4 + - - +
69A LEU* 2.9 42.4 - - + +
70A GLN* 5.1 2.6 - - - +
202A PHE 2.8 5.5 + - - -
203A GLU 3.5 6.3 - - - +
205A MET* 1.3 73.3 - - - +
207A THR* 1.3 67.1 + - - +
209A LEU* 3.9 0.2 - - - -
210A GLN* 2.8 22.3 + - - +
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Residues in contact with THR 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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46A ASP* 5.4 2.9 - - + +
47A ALA 4.2 4.2 + - - -
48A MET* 4.7 19.0 - - + +
203A GLU* 2.8 19.3 + - - +
204A SER* 3.5 10.6 - - - -
205A MET 3.2 0.2 - - - -
206A ASN* 1.3 77.4 - - - +
208A TYR* 1.3 57.7 + - - +
210A GLN* 4.5 1.8 - - - -
211A THR* 2.8 54.6 + - + +
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Residues in contact with TYR 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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106A ILE* 4.1 17.9 - - + -
204A SER 3.1 8.1 + - - +
205A MET* 3.1 10.6 + - - +
207A THR* 1.3 81.2 - - - +
209A LEU* 1.3 60.3 + - - +
211A THR* 4.0 3.8 - - - -
212A SER* 2.9 62.4 + - - -
214A SER* 4.6 8.4 - - - -
215A SER* 5.7 3.6 - - - -
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Residues in contact with LEU 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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42A ILE* 3.8 1.6 - - - +
67A TRP* 3.2 42.0 - - + -
106A ILE* 2.9 41.1 - - + -
205A MET 3.0 8.1 + - - +
208A TYR* 1.3 76.7 - - - +
210A GLN* 1.3 64.4 + - - +
215A SER* 2.9 36.8 + - - -
216A VAL* 4.7 2.0 - - + -
217A PHE* 2.9 52.7 - - + -
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Residues in contact with GLN 210 (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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41A ASN* 3.5 5.9 - - - +
42A ILE* 2.7 69.0 + - + +
45A GLY 3.4 1.8 - - - +
46A ASP* 2.9 21.0 - - - +
47A ALA* 2.8 50.4 + - - +
67A TRP* 3.7 13.7 - - - +
206A ASN* 2.8 22.8 + - - +
207A THR* 3.7 3.1 - - - +
209A LEU* 1.3 82.8 - - - +
211A THR* 1.4 58.9 + - + +
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Residues in contact with THR 211 (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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46A ASP* 3.1 40.8 - - + +
207A THR* 2.8 39.4 + - + +
208A TYR* 3.8 4.7 + - - -
210A GLN* 1.4 79.7 - - + +
212A SER* 1.3 73.3 + - - +
213A PRO* 3.3 8.0 - - - +
218A THR* 4.8 4.0 + - - -
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Residues in contact with SER 212 (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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208A TYR* 2.9 57.7 + - - -
210A GLN 3.9 0.2 - - - -
211A THR* 1.3 78.9 + - - +
213A PRO* 1.3 74.8 - - - +
214A SER* 3.3 12.9 + - - -
215A SER* 3.0 27.8 + - - -
218A THR* 3.0 5.0 - - - +
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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