Contacts of the helix formed by residues 169 - 186 (chain A) in PDB entry 4E2E
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 HIS 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLU* 3.4 25.5 + - - -
165A MSE 3.4 39.7 - - + +
166A GLN* 3.0 22.6 + - + +
168A THR* 1.4 79.0 + - - +
170A PRO* 1.4 80.5 - - + +
171A ILE* 3.1 39.8 + - + -
172A ARG* 3.0 7.8 + - + +
173A LEU* 2.9 20.4 + - - +
215A SER* 6.0 0.4 - - - -
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Residues in contact with PRO 170 (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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168A THR 3.7 5.4 - - - +
169A HIS* 1.4 97.2 - - + +
171A ILE* 1.4 56.1 + - + +
173A LEU* 4.3 4.0 - - + -
174A GLY* 2.9 24.6 + - - -
215A SER* 3.8 23.1 - - - +
218A ASP* 3.8 29.8 - - + -
219A SER* 3.7 15.3 - - - +
222A ILE* 3.4 21.2 - - + +
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 4.0 25.8 - - + +
121A VAL* 3.6 28.3 - - + +
122A PHE* 4.1 37.9 - - + +
125A LYS* 4.6 7.7 - - + +
165A MSE 3.8 10.3 - - + -
169A HIS* 3.1 27.3 + - + +
170A PRO* 1.4 74.2 - - + +
172A ARG* 1.3 59.6 + - - +
174A GLY* 3.9 1.2 - - - -
175A LEU* 3.0 28.6 + - - +
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A HIS* 5.9 3.6 + - + -
161A SER* 3.7 37.1 + - - +
162A LYS* 3.6 36.8 + - - +
165A MSE 3.1 24.3 + - - -
166A GLN 3.8 17.3 - - - +
167A PRO* 3.8 35.2 + - - +
169A HIS* 3.0 12.3 + - + +
171A ILE* 1.3 78.3 - - - +
173A LEU* 1.4 56.9 + - + +
175A LEU* 3.4 9.3 + - - +
176A ALA* 3.1 28.3 + - + +
200A ALA* 6.2 2.7 - - + +
203A ASP* 3.7 22.0 + - - +
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Residues in contact with LEU 173 (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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167A PRO 3.6 20.2 - - - +
168A THR* 3.4 26.0 - - - +
169A HIS 2.9 11.4 + - - +
170A PRO* 3.9 4.0 - - + +
172A ARG* 1.4 73.6 - - + +
174A GLY* 1.3 58.5 + - - +
176A ALA* 3.3 6.7 + - - +
177A LEU* 3.0 23.7 + - - +
200A ALA* 4.1 10.3 - - + +
204A ALA* 4.0 14.1 - - + -
219A SER* 3.4 31.6 - - - +
222A ILE* 3.5 20.6 - - + +
223A MSE 3.8 13.0 - - + +
226A LEU* 3.8 24.9 - - + +
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Residues in contact with GLY 174 (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 LYS* 3.7 12.7 - - - -
170A PRO 2.9 19.0 + - - -
171A ILE* 4.0 0.9 - - - -
173A LEU* 1.3 73.3 - - - +
175A LEU* 1.3 62.9 + - - +
177A LEU* 3.4 6.6 - - - +
178A ASN* 3.2 28.2 + - - +
222A ILE* 3.8 15.8 - - - +
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Residues in contact with LEU 175 (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 VAL* 4.0 8.3 - - + -
125A LYS* 3.8 22.1 - - + +
154A TYR* 3.8 28.9 - - + +
157A ALA* 3.5 29.2 - - + +
158A HIS* 3.5 39.7 - - + +
161A SER* 3.6 12.3 - - - +
171A ILE 3.0 19.1 + - - +
172A ARG 3.4 4.9 - - - +
174A GLY* 1.3 72.4 - - - +
176A ALA* 1.3 60.2 + - - +
178A ASN* 3.3 2.1 + - - +
179A TYR* 2.9 35.9 + - + +
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Residues in contact with ALA 176 (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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158A HIS* 5.5 6.3 - - + +
172A ARG* 3.1 14.3 + - + +
173A LEU* 3.3 9.4 + - - +
175A LEU* 1.3 75.0 - - - +
177A LEU* 1.4 61.3 + - - +
179A TYR* 4.1 4.4 - - - +
180A SER* 3.0 28.6 + - - -
196A LEU* 4.1 16.5 - - + +
197A ALA* 5.1 0.2 - - - -
200A ALA* 3.4 32.8 - - + -
226A LEU* 4.1 5.3 - - + +
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Residues in contact with LEU 177 (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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173A LEU 3.0 13.1 + - - +
174A GLY* 3.4 11.0 - - - +
176A ALA* 1.4 74.4 - - - +
178A ASN* 1.3 66.3 - - - +
180A SER* 2.9 17.0 + - - +
181A VAL* 3.2 19.3 + - + +
222A ILE* 4.2 11.0 - - + +
225A LEU* 3.8 44.6 - - + -
226A LEU* 3.7 19.2 - - + +
229A ASN* 3.5 25.1 - - - +
301A EDO 3.8 21.5 - - - +
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Residues in contact with ASN 178 (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 LYS* 6.2 2.4 - - - +
125A LYS* 3.6 13.2 - - - +
129A ASP* 2.9 41.7 + - - +
132A ARG* 3.5 17.2 + - - +
133A TYR* 5.0 1.6 + - - -
154A TYR* 3.8 7.4 - - + +
174A GLY 3.2 16.1 + - - +
175A LEU 4.1 1.8 - - - +
177A LEU* 1.3 87.8 - - - +
179A TYR* 1.3 56.4 + - - +
181A VAL* 3.2 11.0 + - - +
182A PHE* 2.9 32.1 + - - +
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Residues in contact with TYR 179 (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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151A GLU* 3.1 13.2 + - - -
154A TYR* 3.4 53.7 - + + -
155A SER* 2.7 26.7 + - - -
158A HIS* 4.1 27.4 - + + -
175A LEU* 2.9 21.2 + - + +
176A ALA* 4.1 0.7 - - - +
178A ASN* 1.3 74.3 - - - +
180A SER* 1.3 57.4 + - - +
182A PHE* 3.3 11.2 + + - +
183A TYR* 2.9 59.5 + + - -
196A LEU* 3.6 20.4 - - + -
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Residues in contact with SER 180 (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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176A ALA 3.0 15.6 + - - -
177A LEU* 2.9 21.8 + - - -
179A TYR* 1.3 72.1 - - - +
181A VAL* 1.3 59.2 + - - +
183A TYR* 3.2 2.2 + - - -
184A TYR* 3.0 24.6 + - - +
193A ALA* 3.3 37.9 - - - +
196A LEU* 3.5 13.1 - - - +
197A ALA* 4.0 11.2 - - - +
226A LEU* 4.5 0.7 - - - +
229A ASN* 5.1 1.0 + - - -
233A TRP* 3.4 16.0 - - - -
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Residues in contact with VAL 181 (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 ARG* 3.7 23.6 - - - +
177A LEU* 3.2 15.5 + - + +
178A ASN* 3.2 12.9 + - - +
180A SER* 1.3 74.8 + - - +
182A PHE* 1.4 54.3 + - - +
185A GLU* 2.8 64.2 + - + +
229A ASN* 3.8 22.7 - - - +
233A TRP* 4.0 13.5 - - + -
301A EDO 3.8 12.3 - - - +
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Residues in contact with PHE 182 (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 ARG* 3.8 14.4 - - + +
135A ALA* 5.6 0.2 - - + -
147A VAL* 3.3 22.9 - - + -
150A SER* 3.4 27.6 - - - -
151A GLU* 3.2 37.7 - - + -
154A TYR* 3.6 20.9 - + + -
178A ASN 2.9 8.4 + - - +
179A TYR* 3.3 22.9 - + - +
180A SER 3.3 0.2 - - - -
181A VAL* 1.4 75.2 - - - +
183A TYR* 1.3 60.6 + + - +
186A ILE* 2.9 59.4 + - + +
187A GLN* 3.0 32.7 + - + -
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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
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151A GLU* 3.4 22.3 + - - -
179A TYR* 2.9 63.9 + + - -
180A SER* 3.2 6.5 + - - +
182A PHE* 1.3 75.9 - + - +
184A TYR* 1.3 53.7 + - - +
187A GLN* 3.4 21.3 - - + +
188A ASN 2.9 12.0 + - - -
189A ALA* 2.8 37.7 + - + +
192A GLN* 3.6 42.7 + - + -
193A ALA* 3.8 11.9 - - + +
196A LEU* 3.7 21.1 - - + -
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Residues in contact with TYR 184 (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 SER 3.0 16.1 + - - +
181A VAL 3.2 2.9 + - - +
183A TYR* 1.3 77.0 - - - +
185A GLU* 1.3 71.2 + - + +
188A ASN* 3.4 22.9 - - - +
189A ALA 4.4 2.7 - - - +
190A PRO* 4.0 33.9 - - + +
193A ALA* 3.7 8.0 - - + +
232A LEU* 5.4 1.2 + - + -
233A TRP* 3.5 66.7 + + + -
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Residues in contact with GLU 185 (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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57A ARG* 5.3 1.7 + - - -
132A ARG* 4.7 3.3 + - - -
136A GLU* 4.4 12.8 - - - +
143A ARG* 4.8 2.1 + - - -
181A VAL* 2.8 42.9 + - + +
184A TYR* 1.3 88.7 - - + +
186A ILE* 1.3 72.4 + - + +
188A ASN* 4.4 2.1 + - - +
233A TRP* 5.6 3.2 + - + -
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Residues in contact with ILE 186 (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 ARG* 3.7 33.0 - - + +
135A ALA* 4.0 4.7 - - + -
136A GLU* 3.8 39.0 - - + +
143A ARG* 2.8 38.3 + - - +
147A VAL* 3.6 26.5 - - + -
182A PHE* 2.9 39.9 + - + +
185A GLU* 1.3 82.1 - - + +
187A GLN* 1.3 62.0 + - - +
188A ASN* 3.3 3.9 + - - +
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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