Contacts of the helix formed by residues 197 - 215 (chain A) in PDB entry 3A7H
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 ASP 197 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE* 3.6 21.9 - - - +
169A LEU* 3.5 21.1 - - + -
174A ILE* 4.4 8.9 - - - +
175A LYS* 5.4 0.8 - - + +
189A GLU* 5.4 0.2 + - - -
196A TYR* 1.3 78.7 - - - +
198A SER* 1.3 73.1 + - - +
199A LYS* 3.2 25.3 + - - +
200A ALA* 2.9 22.3 + - - +
259A PRO* 5.5 1.6 - - - +
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A HIS* 3.4 46.5 + - - -
140A LYS 5.2 0.4 - - - -
141A ILE* 3.9 10.9 - - - +
169A LEU* 4.0 7.4 - - - +
197A ASP* 1.3 83.8 + - - +
199A LYS* 1.3 68.8 + - - +
201A ASP* 3.0 26.9 + - - +
202A ILE* 3.4 5.1 + - - +
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Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 4.7 0.2 - - - +
197A ASP* 2.9 16.0 + - - +
198A SER* 1.3 87.2 + - - +
200A ALA* 1.3 64.2 + - - +
201A ASP 3.1 0.2 - - - -
202A ILE* 3.1 19.2 + - + +
203A TRP 3.2 5.7 + - - -
259A PRO* 3.2 38.4 - - + +
260A SER* 4.6 9.4 - - - +
262A ARG* 2.7 52.5 + - + +
263A PRO 3.6 16.0 + - - -
264A THR* 3.7 18.8 - - - +
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 5.1 3.8 - - + -
143A ARG* 6.3 1.8 - - + -
187A ALA* 3.9 5.5 - - + +
189A GLU* 3.6 14.7 + - - +
190A VAL* 3.5 31.4 - - + -
196A TYR* 4.1 9.6 - - + -
197A ASP 2.9 14.1 + - - +
199A LYS* 1.3 79.6 - - - +
201A ASP* 1.3 59.9 + - - +
203A TRP* 3.3 3.3 + - - +
204A SER* 3.0 30.5 + - - -
262A ARG* 3.8 2.2 - - - +
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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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132A LEU* 3.8 13.7 - - + +
136A HIS* 3.0 26.3 + - + +
141A ILE* 3.4 11.2 - - - +
142A HIS* 2.7 34.7 + - - +
143A ARG* 2.9 26.2 + - - -
145A ILE* 4.0 6.4 - - + +
197A ASP 4.2 0.2 + - - -
198A SER 3.0 10.8 + - - +
200A ALA* 1.3 81.4 - - - +
202A ILE* 1.4 58.3 + - - +
204A SER* 3.4 7.6 + - - -
205A LEU* 2.9 27.5 + - - +
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Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.7 6.3 - - + -
136A HIS* 4.0 19.3 - - + +
198A SER* 3.7 11.0 - - - +
199A LYS* 3.1 18.3 + - + +
201A ASP* 1.4 75.1 - - - +
203A TRP* 1.3 66.3 + - - +
205A LEU* 3.3 6.1 + - + +
206A GLY 3.1 16.6 + - - -
254A CYS* 3.3 16.4 - - - +
262A ARG* 4.0 17.0 - - + -
263A PRO* 3.6 27.1 - - + +
264A THR* 4.3 1.6 - - - -
265A ALA* 3.9 25.4 - - + +
268A LEU* 4.0 19.7 - - + -
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Residues in contact with TRP 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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184A PHE 5.2 0.8 + - - -
185A TRP 3.7 6.9 - - - -
186A MET 3.3 11.7 + - - -
187A ALA* 3.4 21.1 - - + -
188A PRO* 3.6 27.6 - - + -
199A LYS 3.2 3.6 + - - -
200A ALA 3.6 7.0 - - - +
202A ILE* 1.3 79.9 - - - +
204A SER* 1.3 67.1 + - - +
206A GLY 2.9 11.8 + - - -
207A ILE* 3.0 27.6 + - + +
231A ILE* 4.1 15.9 - - + +
236A PRO* 4.0 7.6 - - + -
237A PRO* 3.9 30.7 - - + -
254A CYS 3.7 9.9 - - - -
255A LEU* 3.3 40.6 - - + +
256A ASN 3.6 28.3 - - - -
257A LYS* 4.1 10.5 - - + -
262A ARG* 3.6 18.1 - - - +
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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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143A ARG 5.3 4.7 + - - -
145A ILE* 3.7 30.9 + - - +
185A TRP* 2.6 28.5 + - - +
186A MET* 4.6 2.1 - - - -
187A ALA 4.7 0.3 + - - -
200A ALA 3.0 14.6 + - - -
201A ASP* 3.6 12.2 + - - -
202A ILE 3.3 0.2 - - - -
203A TRP* 1.3 78.0 - - - +
205A LEU* 1.3 55.0 + - - +
207A ILE* 3.2 4.4 + - - +
208A THR* 2.8 32.5 + - - -
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Residues in contact with LEU 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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125A LEU* 3.7 23.3 - - + -
128A ILE* 3.7 34.3 - - + -
129A LEU* 3.3 34.3 - - + -
132A LEU* 4.2 10.3 - - + -
145A ILE* 4.2 5.1 - - + +
201A ASP 2.9 14.1 + - - +
202A ILE* 3.5 9.9 - - + +
203A TRP 3.1 0.2 - - - -
204A SER* 1.3 73.2 - - - +
206A GLY* 1.3 62.0 + - - +
208A THR* 3.3 8.0 + - - -
209A ALA* 2.9 25.8 + - - +
250A PHE* 4.1 11.7 - - + -
254A CYS* 4.3 3.1 - - - -
268A LEU* 4.0 16.4 - - + -
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Residues in contact with GLY 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 ILE 3.1 7.1 + - - -
203A TRP 2.9 9.0 + - - -
205A LEU* 1.3 77.6 - - - +
207A ILE* 1.3 60.0 + - - -
209A ALA* 3.1 17.1 + - - +
210A ILE* 3.1 17.2 + - - +
251A VAL* 4.3 4.9 - - - +
254A CYS* 3.5 25.3 - - - +
255A LEU* 3.9 12.6 - - - +
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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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184A PHE 3.6 15.9 - - - +
185A TRP* 3.5 23.8 - - + -
203A TRP* 3.0 38.8 + - + +
204A SER 3.6 5.8 - - - +
206A GLY* 1.3 74.2 - - - +
208A THR* 1.3 63.7 + - - +
210A ILE* 3.2 7.7 + - - +
211A GLU* 3.0 19.9 + - - +
217A PRO* 3.5 23.1 - - + -
218A PRO* 3.7 12.5 - - + +
237A PRO* 4.1 18.4 - - + -
255A LEU* 3.8 19.5 - - + -
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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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125A LEU* 5.1 0.7 - - + -
128A ILE* 4.6 15.0 - - + -
145A ILE* 3.5 8.7 + - + +
146A LYS* 3.3 23.7 + - - +
147A ALA* 3.7 25.4 - - - +
150A VAL* 5.2 0.2 - - + -
185A TRP* 3.8 1.9 - - - +
204A SER 2.8 20.4 + - - -
205A LEU* 3.5 12.8 - - - -
206A GLY 3.3 0.4 - - - -
207A ILE* 1.3 75.2 - - - +
209A ALA* 1.4 55.6 + - - +
211A GLU* 3.2 10.5 + - - +
212A LEU* 2.9 42.1 + - + +
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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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121A ILE* 4.9 2.9 - - - +
125A LEU* 3.9 31.9 - - + -
205A LEU 2.9 13.6 + - - +
206A GLY* 3.1 10.9 + - - +
208A THR* 1.4 71.9 - - - +
210A ILE* 1.3 67.9 + - - +
212A LEU* 3.3 5.5 + - - +
213A ALA* 3.2 22.7 + - - +
247A LEU* 4.9 4.9 - - + +
250A PHE* 4.2 10.8 - - + -
251A VAL* 3.9 18.6 - - + -
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Residues in contact with ILE 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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206A GLY 3.1 6.1 + - - +
207A ILE* 3.6 7.6 - - - +
209A ALA* 1.3 76.2 - - - +
211A GLU* 1.3 54.5 + - - +
213A ALA* 3.1 2.4 + - - +
214A ARG* 2.8 44.0 + - + +
216A GLU 4.1 7.6 - - - +
217A PRO 5.0 0.2 - - - -
218A PRO* 3.8 35.2 - - + -
237A PRO* 4.1 6.7 - - + -
238A THR 4.1 12.8 - - - +
239A LEU* 4.3 22.4 - - + -
251A VAL* 3.7 24.7 - - + -
255A LEU* 3.6 28.5 - - + -
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Residues in contact with GLU 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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108A LEU* 3.5 20.3 - - - +
111A LEU* 3.6 6.6 - - + +
146A LYS* 3.9 0.3 - - - -
147A ALA* 2.8 41.2 + - + +
148A ALA* 4.7 1.9 + - - +
185A TRP* 3.0 36.6 + - - +
207A ILE 3.0 12.6 + - - +
208A THR* 3.4 9.7 - - - +
209A ALA 3.2 0.2 - - - -
210A ILE* 1.3 77.9 - - - +
212A LEU* 1.3 56.8 + - - +
215A GLY* 2.6 35.9 + - - +
216A GLU* 3.7 27.3 + - - +
217A PRO* 4.3 2.7 - - - +
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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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107A ALA* 4.0 26.2 - - + +
111A LEU* 3.7 15.6 - - + +
116A LEU* 3.7 35.9 + - + +
121A ILE* 3.8 23.5 - - + +
124A ILE* 3.9 23.8 - - + -
125A LEU* 3.9 30.5 - - + -
128A ILE* 4.6 0.7 - - + -
147A ALA* 4.1 12.6 - - + -
208A THR* 2.9 28.8 + - + +
209A ALA* 3.3 5.1 + - - +
211A GLU* 1.3 76.6 - - - +
213A ALA* 1.3 60.4 + - - +
215A GLY 4.4 0.4 - - - -
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Residues in contact with ALA 213 (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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115A PRO* 5.2 9.9 - - - +
116A LEU 5.5 1.8 - - - +
121A ILE* 3.7 17.0 - - + -
209A ALA 3.2 14.3 + - - +
210A ILE 3.1 4.4 + - - +
212A LEU* 1.3 80.8 - - - +
214A ARG* 1.3 58.3 + - - +
239A LEU* 3.9 22.4 - - + -
243A TYR* 2.8 39.3 + - + -
247A LEU* 4.5 2.2 - - + -
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Residues in contact with ARG 214 (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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210A ILE* 2.8 26.2 + - + +
213A ALA* 1.3 73.1 - - - +
215A GLY* 1.3 60.4 + - - +
216A GLU* 3.6 12.5 + - + +
239A LEU* 3.8 14.1 - - + +
240A GLU* 3.2 45.4 + - - +
243A TYR* 3.2 22.9 - - - -
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Residues in contact with GLY 215 (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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108A LEU* 4.4 12.8 - - - +
111A LEU* 4.2 17.1 - - - +
211A GLU* 2.6 30.4 + - - +
212A LEU 4.4 1.2 + - - -
213A ALA 3.7 0.8 - - - -
214A ARG* 1.3 72.0 - - - +
216A GLU* 1.3 71.7 + - - +
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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
------------------------------------------------------------
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