Contacts of the helix formed by residues 197 - 212 (chain A) in PDB entry 2BWG
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 PRO 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LYS* 3.4 27.4 - - + +
10A LEU 3.2 27.4 - - - +
11A ASP* 3.6 11.9 - - + +
182A PRO* 4.7 0.4 - - + -
196A TYR* 1.3 91.3 - - + +
198A GLN* 1.3 59.3 + - - +
199A LEU 3.4 0.2 - - - -
200A SER* 4.4 0.4 - - - -
201A ALA* 3.0 26.2 + - - +
16C LEU* 4.6 0.4 - - + -
334C ILE* 3.4 20.6 - - + -
336C VAL* 3.5 22.7 - - + -
337C THR* 5.4 0.9 - - - +
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Residues in contact with GLN 198 (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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11A ASP* 3.1 22.6 + - - +
12A PHE* 3.6 20.2 - - + -
178A VAL* 2.8 29.2 + - - +
179A GLY* 3.1 21.2 - - - -
182A PRO* 3.4 21.9 - - + +
196A TYR 3.5 2.1 + - - +
197A PRO* 1.3 70.1 - - - +
199A LEU* 1.3 66.9 + - - +
201A ALA* 3.4 4.3 - - - +
202A VAL* 3.1 33.4 + - - +
218A SER* 3.0 18.0 + - - +
219A ASP 3.7 2.8 - - - +
220A GLY 3.3 22.4 - - - +
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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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10A LEU* 3.4 16.0 + - + +
11A ASP* 3.7 18.4 + - - +
12A PHE* 3.8 27.0 - - + -
15A VAL* 3.8 34.3 - - + -
197A PRO 3.4 0.2 - - - -
198A GLN* 1.3 77.5 - - - +
200A SER* 1.3 57.4 + - - +
202A VAL* 3.2 5.0 + - - +
203A ILE* 2.9 38.2 + - + +
230A LYS 4.2 1.8 - - - +
234A ALA* 4.0 19.3 - - + -
333A PHE* 4.1 22.4 - - + -
4B ILE* 4.1 20.2 - - + -
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Residues in contact with SER 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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8A LEU 4.7 0.7 + - - -
9A LYS* 3.4 19.2 - - - +
10A LEU* 2.7 41.0 + - - +
196A TYR* 4.0 5.6 - - - -
197A PRO 3.5 2.0 + - - -
198A GLN 3.4 0.2 - - - -
199A LEU* 1.3 76.6 - - - +
201A ALA* 1.3 61.2 + - - +
203A ILE* 3.9 7.4 - - - +
204A GLU* 3.0 46.4 + - - +
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Residues in contact with ALA 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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160A VAL* 3.8 26.0 - - + +
178A VAL* 3.6 21.1 - - + -
196A TYR* 3.9 7.1 - - + -
197A PRO 3.0 19.1 + - - +
198A GLN* 3.4 14.1 - - - +
200A SER* 1.3 78.5 - - - +
202A VAL* 1.3 63.1 + - - +
204A GLU* 3.8 0.3 - - - +
205A CYS* 2.9 28.6 + - - +
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Residues in contact with VAL 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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12A PHE* 5.1 0.7 - - + -
178A VAL* 4.4 4.0 - - + -
198A GLN* 3.1 25.0 + - + +
199A LEU* 3.6 4.7 - - - +
201A ALA* 1.3 79.6 - - - +
203A ILE* 1.3 57.6 + - - +
206A ALA* 2.8 36.0 + - - +
216A ILE* 4.2 9.6 - - + -
218A SER* 3.1 34.5 - - - +
231A ALA* 3.6 17.3 - - + +
234A ALA* 3.6 23.6 - - + -
236A ALA* 3.7 19.1 - - + +
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Residues in contact with ILE 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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199A LEU* 2.9 31.8 + - + +
200A SER* 3.9 7.2 - - - +
202A VAL* 1.3 77.2 - - - +
204A GLU* 1.3 68.4 + - + +
206A ALA* 4.2 1.2 - - - +
207A ASP* 3.5 19.8 + - - +
234A ALA* 3.7 28.2 - - + +
333A PHE* 4.8 4.7 - - + -
2B PRO* 4.4 17.7 - - + +
4B ILE* 3.6 37.2 - - + -
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Residues in contact with GLU 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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7A ASP* 4.7 1.2 - - - +
9A LYS* 3.2 17.3 + - - +
160A VAL 4.3 4.0 - - - +
161A THR* 4.7 5.9 - - - +
162A GLY* 4.6 7.1 - - - +
196A TYR* 2.8 36.0 + - - -
200A SER* 3.0 26.3 + - - +
201A ALA 3.8 2.0 - - - +
203A ILE* 1.3 82.2 - - + +
205A CYS* 1.3 65.6 + - - +
207A ASP* 3.4 7.4 - - - +
208A SER* 3.3 21.4 + - - -
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Residues in contact with CYS 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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159A VAL* 4.8 0.2 - - - -
160A VAL* 3.2 42.6 - - - -
161A THR* 3.3 15.0 - - - -
162A GLY* 4.5 0.9 - - - -
165A VAL* 3.7 16.7 - - + +
178A VAL* 3.6 26.9 - - + -
201A ALA 2.9 16.3 + - - +
202A VAL 4.3 0.7 - - - +
204A GLU* 1.3 76.0 - - - +
206A ALA* 1.3 59.7 + - - +
208A SER* 3.6 4.1 - - - -
209A ALA* 3.0 28.9 + - - +
216A ILE* 3.7 3.4 - - + +
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Residues in contact with ALA 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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202A VAL 2.8 24.4 + - - +
203A ILE 4.2 0.9 - - - +
205A CYS* 1.3 70.3 - - - +
207A ASP* 1.3 64.6 + - - +
209A ALA 3.2 0.5 + - - -
210A HIS* 2.9 38.8 + - + -
216A ILE* 3.9 14.2 - - + +
234A ALA 4.1 2.9 - - - +
235A GLY* 3.5 37.9 - - - +
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Residues in contact with ASP 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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203A ILE 3.5 12.2 + - - +
204A GLU* 3.4 12.1 - - - +
206A ALA* 1.3 76.8 - - - +
208A SER* 1.3 56.9 + - - +
210A HIS* 3.9 5.3 - - - +
211A GLY* 3.0 27.2 + - - -
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Residues in contact with SER 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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162A GLY* 2.6 45.1 + - - -
165A VAL* 3.8 4.5 - - - +
166A GLU* 3.4 16.7 + - - +
204A GLU 3.3 6.7 + - - -
205A CYS 3.6 6.7 - - - -
206A ALA 3.2 0.4 - - - -
207A ASP* 1.3 82.4 - - - +
209A ALA* 1.3 63.8 + - - +
210A HIS 3.6 0.2 + - - -
211A GLY* 3.6 6.6 + - - -
212A LEU* 3.8 17.2 + - - +
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Residues in contact with ALA 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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165A VAL* 3.5 15.0 - - + +
169A ILE* 3.7 13.9 - - + -
205A CYS 3.0 8.4 + - - +
206A ALA 3.8 2.5 - - - +
208A SER* 1.3 77.6 - - - +
210A HIS* 1.3 53.3 + - + +
212A LEU* 3.1 12.8 + - - +
214A GLY* 2.7 30.2 + - - -
215A HIS* 4.0 10.1 - - - +
216A ILE* 3.3 34.5 - - + -
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Residues in contact with HIS 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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34A ARG* 6.2 0.7 - - - -
206A ALA* 2.9 32.9 + - + +
207A ASP* 4.0 5.4 + - - +
209A ALA* 1.3 73.2 - - + +
211A GLY* 1.3 60.0 + - - +
212A LEU 3.0 2.0 - - - -
213A LYS* 3.0 22.1 + - - +
214A GLY 3.4 16.8 - - - -
215A HIS* 5.1 0.9 - + - -
216A ILE 4.9 0.2 + - - -
235A GLY* 3.1 26.0 + - - -
237A ASP* 2.5 35.5 + - - -
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Residues in contact with GLY 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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207A ASP 3.0 16.4 + - - -
208A SER 4.0 3.4 - - - -
209A ALA 3.3 0.6 - - - -
210A HIS* 1.3 76.6 - - - +
212A LEU* 1.3 62.7 + - - +
213A LYS* 3.4 11.0 + - - -
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Residues in contact with LEU 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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39A ARG* 3.2 32.7 + - - +
166A GLU* 3.7 54.3 - - + +
169A ILE* 4.1 18.8 - - + -
170A LEU* 4.1 22.0 - - + -
208A SER 3.8 9.2 + - - +
209A ALA 3.1 9.2 + - - +
210A HIS 3.0 1.0 - - - -
211A GLY* 1.3 79.9 - - - +
213A LYS* 1.3 74.5 + - - +
214A GLY 4.2 1.6 - - - +
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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