Contacts of the helix formed by residues 182 - 198 (chain A) in PDB entry 2JDQ
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 PHE 182 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS 3.3 26.5 - - - -
139A GLU* 4.9 3.1 - - - -
140A ASN 4.9 1.6 - - - -
141A CYS* 3.7 51.8 - - + -
144A GLN* 3.6 15.7 - - - -
180A SER* 3.1 12.3 + - - -
181A GLU* 1.3 94.4 - - + +
183A GLU* 1.3 64.6 + - - +
184A ASP 4.6 0.9 - - - +
185A VAL* 3.3 11.5 + - + +
186A GLN* 3.1 26.8 + - - +
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU 4.1 2.1 + - - +
182A PHE* 1.3 68.7 - - - +
184A ASP* 1.3 69.6 + - - +
186A GLN* 3.1 16.6 + - - +
187A GLU* 2.9 26.3 + - - +
224A ASN* 5.2 8.6 - - - +
225A ARG* 4.1 33.8 + - - +
228A MET* 4.1 5.6 - - + +
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Residues in contact with ASP 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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141A CYS* 4.7 15.7 - - - -
145A PHE* 3.7 35.0 - - + -
183A GLU* 1.3 79.1 - - - +
185A VAL* 1.3 62.3 - - - +
187A GLU* 3.6 2.1 + - - +
188A GLN* 3.2 24.8 + - - +
225A ARG* 2.8 38.7 + - - +
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Residues in contact with VAL 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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141A CYS* 3.8 25.6 - - - +
144A GLN* 3.8 21.1 - - + +
145A PHE* 4.1 8.7 - - + +
148A ALA* 5.2 2.2 - - + +
177A LEU* 3.7 41.0 - - + +
180A SER* 3.8 8.7 - - - +
182A PHE* 3.3 28.2 + - + +
183A GLU 3.1 0.6 - - - -
184A ASP* 1.3 75.7 - - - +
186A GLN* 1.3 65.5 + - - +
188A GLN* 3.3 4.1 + - - +
189A ALA* 3.0 23.8 + - - +
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Residues in contact with GLN 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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177A LEU 3.5 20.4 - - - +
178A LEU* 2.8 31.0 + - - +
179A SER* 4.2 2.6 - - - +
180A SER* 3.4 26.9 + - - +
181A GLU 5.7 0.6 - - - -
182A PHE 3.1 12.2 + - - +
183A GLU* 3.4 18.9 - - - +
185A VAL* 1.3 75.9 - - - +
187A GLU* 1.3 61.0 + - - +
189A ALA* 3.5 3.9 + - - +
190A VAL* 3.3 19.6 + - - +
219A LEU* 3.6 11.5 - - + +
222A LYS* 3.1 35.9 + - - +
224A ASN* 4.7 1.0 - - - +
228A MET* 3.7 16.0 - - + +
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Residues in contact with GLU 187 (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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183A GLU 2.9 14.5 + - - +
184A ASP 4.0 3.6 - - - +
186A GLN* 1.3 76.1 - - - +
188A GLN* 1.3 63.1 + - - +
190A VAL* 3.6 6.5 + - - +
191A TRP* 3.4 21.4 + - + +
225A ARG* 2.8 37.5 + - - +
227A THR* 2.8 30.3 + - - -
228A MET* 3.6 33.7 + - + +
231A ASN* 3.1 23.2 + - + +
755E ARG* 6.1 4.5 - - - +
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Residues in contact with GLN 188 (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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145A PHE* 4.1 9.9 - - + +
148A ALA* 3.6 14.7 - - + +
149A TRP* 3.6 32.8 - - + +
152A THR* 2.9 35.6 + - - +
184A ASP 3.2 17.7 + - - +
185A VAL* 3.3 1.5 + - - +
187A GLU* 1.3 74.0 - - - +
189A ALA* 1.3 60.9 + - - +
190A VAL 3.3 0.2 - - - -
191A TRP* 3.7 22.3 - - - -
192A ALA* 3.0 27.0 + - - +
755E ARG* 3.1 38.8 + - - +
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Residues in contact with ALA 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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148A ALA* 4.8 1.0 - - - +
174A PHE* 3.6 43.2 - - + +
177A LEU* 3.9 11.4 - - + -
178A LEU* 4.4 4.7 - - + -
185A VAL 3.0 18.0 + - - +
186A GLN 3.5 6.7 - - - +
188A GLN* 1.3 79.0 - - - +
190A VAL* 1.3 57.8 + - - +
192A ALA* 3.3 2.8 + - - +
193A LEU* 3.0 35.5 + - - +
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Residues in contact with VAL 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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178A LEU* 3.4 13.2 - - + +
186A GLN 3.3 6.7 + - - +
187A GLU* 3.7 8.5 - - - +
189A ALA* 1.3 75.1 - - - +
191A TRP* 1.3 57.8 + - - +
193A LEU* 3.4 6.8 + - - +
194A GLY* 2.8 31.2 + - - -
212A ILE* 6.3 0.2 - - - -
216A LEU* 3.3 20.0 - - + -
219A LEU* 3.3 33.9 - - + -
228A MET* 5.1 2.0 - - - +
231A ASN* 3.1 45.5 - - + +
232A ALA* 3.8 3.8 - - + +
235A ALA* 3.9 7.6 - - + +
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Residues in contact with TRP 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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152A THR* 3.4 12.2 - - + +
187A GLU* 3.4 11.5 + - + +
188A GLN* 3.7 28.5 - - - +
190A VAL* 1.3 79.2 - - - +
192A ALA* 1.3 66.9 + - - +
194A GLY* 3.3 1.2 + - - -
195A ASN* 3.1 20.6 + - - -
231A ASN* 3.6 24.7 - - - +
234A TRP* 3.7 18.7 - + - -
753E ARG* 3.0 57.1 + - - +
754E ILE 3.7 5.8 - - - -
755E ARG* 3.5 55.4 - - + -
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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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151A LEU 5.2 0.4 - - - -
152A THR* 3.4 31.6 + - - +
155A ALA* 4.3 1.5 - - + +
174A PHE* 3.5 33.9 - - + -
188A GLN 3.0 14.8 + - - +
189A ALA 3.3 5.6 + - - +
191A TRP* 1.3 75.0 - - - +
193A LEU* 1.3 56.9 + - - +
195A ASN* 3.1 7.8 + - - +
196A ILE* 3.0 31.8 + - + +
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Residues in contact with LEU 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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171A VAL* 3.9 32.3 - - + -
174A PHE* 3.7 39.3 - - + +
175A ILE* 4.0 12.1 - - + +
178A LEU* 4.2 13.9 - - + -
189A ALA 3.0 26.9 + - - +
190A VAL* 3.7 5.2 - - - +
192A ALA* 1.3 73.5 - - - +
194A GLY* 1.3 56.4 + - - +
196A ILE* 3.9 5.5 - - - +
197A ALA* 2.8 36.0 + - - +
207A VAL* 4.3 12.4 - - + +
212A ILE* 3.9 25.1 - - + +
235A ALA* 5.3 0.7 - - + -
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Residues in contact with GLY 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 VAL 2.8 17.9 + - - -
192A ALA 3.3 0.2 - - - -
193A LEU* 1.3 76.4 - - - +
195A ASN* 1.3 55.1 + - - +
197A ALA* 3.5 4.4 + - - +
198A GLY 2.9 21.8 + - - -
234A TRP* 3.6 21.1 - - - -
235A ALA* 4.1 17.6 - - - +
238A ASN* 3.0 14.4 + - - -
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Residues in contact with ASN 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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152A THR* 3.1 31.9 + - - +
155A ALA* 3.8 18.2 - - + +
156A SER* 3.6 8.8 - - - +
191A TRP 3.1 11.3 + - - -
192A ALA 3.1 9.6 + - - +
194A GLY* 1.3 73.0 - - - +
196A ILE* 1.3 64.6 + - - +
198A GLY* 3.1 10.2 + - - -
199A ASP 3.2 9.4 + - - -
234A TRP* 3.1 13.7 - - - -
752E LYS* 3.5 20.7 - - + -
753E ARG 2.8 44.2 + - - +
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Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ALA* 4.2 14.1 - - + -
162A THR* 4.2 14.4 - - + -
165A VAL* 4.1 22.4 - - + -
166A ILE* 3.8 31.2 - - + -
171A VAL* 3.6 21.3 - - + -
174A PHE* 4.5 14.6 - - + -
192A ALA* 3.0 25.8 + - + +
193A LEU* 3.9 7.6 - - + +
195A ASN* 1.3 74.2 - - - +
197A ALA* 1.3 62.8 + - - +
198A GLY 3.3 0.5 + - - -
199A ASP* 3.3 6.4 + - - +
203A CYS* 3.1 25.1 - - + +
207A VAL* 3.9 18.4 - - + -
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Residues in contact with ALA 197 (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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193A LEU 2.8 23.4 + - - +
194A GLY* 3.8 6.1 - - - +
196A ILE* 1.3 72.0 - - - +
198A GLY* 1.3 59.9 + - - +
199A ASP 3.5 0.7 + - - -
200A SER 3.5 5.7 - - - +
203A CYS 4.4 1.8 - - - -
204A ARG* 3.5 33.7 - - - +
207A VAL* 4.3 4.7 - - + +
212A ILE* 6.2 0.2 - - + -
235A ALA 5.1 0.2 - - - +
238A ASN* 4.2 18.2 - - + +
239A LEU* 3.9 27.4 - - + -
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Residues in contact with GLY 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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194A GLY 2.9 15.3 + - - -
195A ASN 3.1 7.3 + - - -
197A ALA* 1.3 76.0 - - - +
199A ASP* 1.3 64.6 + - - +
200A SER* 3.4 0.8 - - - -
238A ASN* 3.8 13.7 - - - -
241A ARG* 6.3 0.7 - - - -
751E THR* 2.7 32.5 + - - +
752E LYS* 4.0 6.2 - - - -
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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