Contacts of the helix formed by residues 179 - 195 (chain A) in PDB entry 7CE1
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 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 4.0 8.4 + - - +
178A PHE* 1.3 73.8 - - - +
180A ASN* 1.3 56.9 + - - +
181A GLU* 3.5 10.4 + - - +
182A ALA* 3.0 33.7 + - + +
183A TYR* 3.0 22.7 + - - +
338A VAL* 3.7 18.5 - - + +
339A SER 2.7 23.4 + - - +
340A ARG* 4.3 15.1 - - + +
341A PRO* 4.4 3.5 - - + +
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Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 4.5 2.6 - - - +
177A ASP* 4.3 3.0 + - - -
178A PHE* 2.7 52.1 + - + +
179A ASP* 1.3 69.8 - - - +
181A GLU* 1.3 61.3 + - - +
182A ALA 3.3 0.2 - - - -
183A TYR* 3.5 15.2 - - + +
184A ALA* 3.0 29.6 + - - +
210A PHE* 3.4 33.8 - - - +
213A HIS* 4.2 14.0 - - + +
214A ALA* 4.3 12.2 - - + +
264A ILE* 4.1 10.9 - - + +
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 5.1 6.0 + - - +
179A ASP* 3.1 8.7 + - - +
180A ASN* 1.3 78.8 - - - +
182A ALA* 1.3 64.4 + - - +
185A TYR* 3.4 8.8 + - - +
213A HIS* 3.3 30.1 + - + +
216A LYS* 4.3 12.4 - - - +
217A GLY* 3.3 27.7 - - - +
220A ARG* 2.3 35.8 + - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 3.0 35.2 + - + +
181A GLU* 1.3 78.8 - - - +
183A TYR* 1.3 57.6 + - - +
185A TYR* 3.2 6.9 + - - +
186A GLU* 2.8 43.0 + - + +
220A ARG* 6.0 0.4 - - - +
340A ARG* 5.3 1.8 - - + -
341A PRO* 4.1 14.4 - - + -
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 4.0 19.3 - + + -
179A ASP 3.0 14.2 + - - +
180A ASN* 3.5 16.2 - - + +
181A GLU 3.2 0.4 - - - -
182A ALA* 1.3 75.7 - - - +
184A ALA* 1.3 54.5 + - - +
186A GLU* 3.3 4.1 + - + +
187A ALA* 2.6 46.7 + - + +
262A VAL* 4.1 10.1 - - + +
263A SER 2.7 28.8 + - - -
264A ILE* 3.6 25.8 - - + -
290A VAL* 3.5 8.0 + - + +
291A SER* 3.3 9.0 + - - -
292A LYS* 3.2 22.5 + - + -
308A VAL* 3.7 43.1 - - + -
341A PRO* 4.3 9.8 - - + +
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASN 3.0 15.3 + - - +
183A TYR* 1.3 82.3 - - + +
185A TYR* 1.3 63.3 + - - +
187A ALA* 3.1 20.1 + - - +
188A VAL* 3.3 14.7 + - - +
201A ILE* 4.9 5.2 - - + -
214A ALA* 3.4 27.8 - - + +
217A GLY* 3.7 4.5 - - - -
218A PHE* 3.5 21.3 - - + +
262A VAL* 5.1 2.2 - - + -
264A ILE* 5.3 1.1 - - + -
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Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU 3.4 10.5 + - - +
182A ALA* 3.2 10.0 + - - +
184A ALA* 1.3 78.5 - - - +
186A GLU* 1.3 62.8 + - + +
187A ALA 3.6 0.2 + - - -
188A VAL* 4.1 3.3 - - - +
189A GLU* 3.7 19.2 + - - +
217A GLY* 3.5 19.8 + - - +
220A ARG* 5.0 13.5 - - + +
221A GLY* 4.5 11.6 - - - +
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA* 2.8 30.8 + - - +
183A TYR* 3.8 4.7 - - + +
185A TYR* 1.3 78.0 - - + +
187A ALA* 1.3 64.1 + - - +
189A GLU* 3.7 14.9 + - - +
190A ARG* 3.6 13.2 + - - +
341A PRO* 4.0 21.0 - - + +
343A TRP* 4.1 30.9 + - + +
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 2.6 27.2 + - + +
184A ALA* 3.1 13.6 + - - +
186A GLU* 1.3 77.4 - - - +
188A VAL* 1.3 61.6 + - - +
190A ARG* 3.4 8.1 + - - +
191A LEU* 3.5 2.3 + - - +
262A VAL* 4.0 19.5 - - + -
290A VAL* 3.5 44.8 - - + +
343A TRP* 4.5 3.4 - - - -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ALA 3.6 13.0 - - - +
185A TYR 4.1 2.7 - - - +
187A ALA* 1.3 71.4 - - - +
189A GLU* 1.3 58.1 + - - +
190A ARG 3.0 2.0 - - - -
191A LEU* 3.3 8.3 - - + +
192A ALA* 2.6 36.4 + - - +
199A ILE* 3.4 30.7 - - + -
218A PHE* 3.3 34.1 - - + -
221A GLY* 4.0 33.9 - - - +
222A ILE* 4.4 4.7 - - + +
225A PHE* 5.4 1.8 - - + -
227A VAL* 5.3 3.7 - - + +
262A VAL* 3.7 5.6 - - + -
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Residues in contact with GLU 189 (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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185A TYR 3.7 15.1 + - - +
186A GLU* 4.0 14.1 - - - +
187A ALA 3.4 1.4 - - - -
188A VAL* 1.3 80.5 - - - +
190A ARG* 1.3 57.4 + - - +
192A ALA* 3.3 8.9 + - - +
193A GLN* 2.7 53.1 + - + +
225A PHE* 5.2 6.7 - - + -
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Residues in contact with ARG 190 (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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186A GLU 3.6 8.3 + - - +
187A ALA 3.4 10.8 + - - +
188A VAL 3.0 0.8 - - - -
189A GLU* 1.3 81.6 - - - +
191A LEU* 1.3 57.2 + - - +
193A GLN* 3.4 22.1 + - + +
194A CYS* 3.0 28.8 + - - -
290A VAL* 4.7 3.1 - - + -
306A HIS* 3.4 30.7 + - + +
343A TRP* 2.9 61.4 - - + +
347A ALA* 4.7 3.7 + - - +
348A PRO 3.4 30.1 + - - -
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Residues in contact with LEU 191 (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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187A ALA 3.9 1.3 - - - +
188A VAL* 2.9 12.1 + - + +
190A ARG* 1.3 77.3 - - - +
192A ALA* 1.3 59.4 + - - +
194A CYS* 3.4 4.5 + - + +
195A GLY 3.1 6.1 + - - -
196A ARG* 2.9 37.3 + - + +
199A ILE* 3.8 22.4 - - + -
260A GLY* 3.9 2.7 - - - -
261A ILE 3.7 24.9 - - - +
262A VAL* 3.7 26.2 - - + -
288A ASP* 3.3 35.9 - - + +
290A VAL* 3.8 22.9 - - + -
306A HIS* 5.1 1.8 - - + -
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Residues in contact with ALA 192 (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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188A VAL 2.6 17.8 + - - +
189A GLU* 3.5 7.2 - - + +
191A LEU* 1.3 69.8 - - - +
193A GLN* 1.3 61.4 + - + +
195A GLY* 2.8 20.4 + - - +
196A ARG 4.3 8.5 + - - -
225A PHE* 4.2 14.8 - - + +
227A VAL* 4.1 22.0 - - + -
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Residues in contact with GLN 193 (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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189A GLU* 2.7 57.1 + - + +
190A ARG* 3.5 24.1 + - + +
192A ALA* 1.3 77.3 - - - +
194A CYS* 1.3 59.7 + - - +
195A GLY* 3.5 0.5 + - - -
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Residues in contact with CYS 194 (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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190A ARG* 3.0 18.6 + - - +
191A LEU* 3.6 12.3 - - - +
192A ALA 3.1 0.4 - - - -
193A GLN* 1.3 76.8 - - - +
195A GLY* 1.3 59.0 + - - +
196A ARG* 3.4 17.7 + - + +
288A ASP* 3.7 19.3 - - - +
306A HIS* 3.7 29.4 - - - -
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Residues in contact with GLY 195 (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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191A LEU 3.1 0.4 + - - -
192A ALA* 2.8 17.0 + - - -
193A GLN 3.2 0.8 - - - -
194A CYS* 1.3 78.1 - - - +
196A ARG* 1.3 66.8 + - - +
197A LYS* 3.4 7.1 + - - +
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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