Contacts of the helix formed by residues 182 - 193 (chain B) in PDB entry 1EQB
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 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B TYR* 2.9 24.4 + - + +
180B VAL* 3.9 1.5 + - - -
181B VAL* 1.3 73.1 - - - +
183B TRP* 1.3 61.1 + - - +
184B ALA* 3.3 10.6 + - - +
185B LYS* 2.8 44.5 + - + +
186B MET* 3.1 22.5 + - - +
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Residues in contact with TRP 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLY* 4.2 11.7 - - - -
173B GLY* 4.4 10.8 - - - -
174B PHE* 4.6 3.6 - + - -
181B VAL* 3.1 42.5 + - + -
182B ASP* 1.3 71.0 + - - +
184B ALA* 1.3 63.8 + - - +
186B MET* 3.1 10.8 + - + +
187B ARG* 2.9 22.9 + - - +
197B LEU* 3.8 5.7 - - + +
199B VAL* 3.7 36.6 - - + -
200B ASP 5.6 0.4 - - - -
201B MET* 5.4 1.6 - - + -
204B VAL* 5.0 7.6 - - + -
213B TYR* 3.9 19.9 - + - -
214B PRO* 2.9 39.6 + - + +
215B ASN 3.6 5.4 - - - -
216B PRO* 3.3 37.3 - - + +
219B HIS* 3.9 21.8 - + + -
220B ALA* 6.5 0.2 - - + -
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ASP* 3.3 7.0 + - - +
183B TRP* 1.3 79.2 - - - +
185B LYS* 1.3 57.5 + - - +
187B ARG* 3.3 4.9 + - - +
188B GLU* 3.0 32.3 + - - +
219B HIS* 3.6 33.7 - - + +
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Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B TYR* 3.9 35.9 - - + -
159B GLU* 4.0 19.8 + - - -
182B ASP* 2.8 40.1 + - + +
184B ALA* 1.3 71.3 - - - +
186B MET* 1.3 65.1 + - - +
188B GLU* 3.3 34.3 + - - +
189B ILE* 3.2 29.3 + - + +
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Residues in contact with MET 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B TYR* 3.6 24.0 - - + +
153B ILE* 5.7 2.2 - - + -
155B TYR* 4.1 13.9 - - + -
158B LEU* 3.9 18.8 - - + -
170B ILE* 3.9 26.4 - - + +
172B GLY* 3.9 20.9 - - - +
181B VAL* 3.7 25.6 - - - -
182B ASP 3.1 10.8 + - - +
183B TRP* 3.1 15.5 + - - +
185B LYS* 1.3 73.0 - - - +
187B ARG* 1.3 61.5 + - - +
189B ILE* 3.3 10.1 + - - +
190B ALA* 2.9 28.2 + - - +
197B LEU* 3.9 16.5 - - + +
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TRP 2.9 11.5 + - - +
184B ALA* 3.6 10.1 - - - +
186B MET* 1.3 76.2 - - - +
188B GLU* 1.3 65.2 + - - +
190B ALA* 3.2 1.5 + - - -
191B ASP* 2.8 52.6 + - - +
197B LEU* 3.5 9.6 - - + +
218B PRO 5.0 1.6 + - - -
219B HIS* 2.6 60.0 + - + +
220B ALA 4.2 9.1 + - - +
221B HIS* 3.5 36.3 + - - +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B ALA* 3.0 15.8 + - - +
185B LYS* 3.3 41.8 + - + +
187B ARG* 1.3 80.2 - - - +
189B ILE* 1.3 63.9 + - + +
191B ASP* 3.2 7.8 + - - +
192B SER* 3.1 21.2 + - - -
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B TYR* 3.7 30.1 - - + +
158B LEU* 3.7 25.8 - - + +
159B GLU* 3.9 30.7 - - + +
162B ALA* 3.6 28.7 - - + -
163B LYS* 6.4 0.2 - - + -
170B ILE* 4.0 9.6 - - + -
185B LYS* 3.2 21.6 + - - +
186B MET* 3.3 8.7 + - - +
188B GLU* 1.3 78.1 - - + +
190B ALA* 1.3 61.2 + - - +
192B SER* 2.7 24.2 + - - +
193B ILE* 3.8 6.9 - - - +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ILE* 4.1 17.5 - - + +
186B MET 2.9 16.7 + - - +
187B ARG* 3.6 7.9 - - - +
189B ILE* 1.3 77.1 - - - +
191B ASP* 1.3 64.1 + - - +
193B ILE* 3.0 5.3 + - - +
194B GLY 2.9 4.2 + - - -
195B ALA* 2.9 45.8 + - + +
196B TYR 4.5 0.9 - - - -
197B LEU* 4.2 20.9 - - + +
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Residues in contact with ASP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ARG* 2.8 55.4 + - - +
188B GLU* 3.2 7.6 + - - +
190B ALA* 1.3 77.5 - - - +
192B SER* 1.3 61.0 + - - +
193B ILE 3.2 1.0 + - - -
194B GLY* 3.3 11.5 + - - +
195B ALA 4.9 0.9 - - - +
221B HIS* 4.4 5.7 + - - -
120C ASN* 5.7 0.5 + - - -
144C PRO* 3.5 14.2 - - - +
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B GLU* 5.4 1.6 - - - +
163B LYS* 3.7 26.7 + - - +
188B GLU 3.1 10.6 + - - -
189B ILE* 2.7 27.6 + - - +
191B ASP* 1.3 77.1 - - - +
193B ILE* 1.3 63.7 + - - +
143C VAL* 4.2 10.0 - - - +
144C PRO* 3.9 13.3 - - - +
161C GLN* 4.3 10.9 + - - +
165C HIS* 5.1 1.7 + - - -
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ALA* 3.6 26.9 - - + +
163B LYS* 4.2 16.2 - - + +
166B LYS* 2.8 40.4 - - + +
167B PRO* 3.4 48.0 - - + +
170B ILE* 4.5 2.2 - - + -
189B ILE 3.8 6.5 - - - +
190B ALA 3.4 10.3 - - - +
192B SER* 1.3 88.3 + - - +
194B GLY* 1.3 61.9 + - - +
195B ALA* 3.8 9.5 - - + -
142C ILE 4.1 0.7 - - - +
143C VAL* 5.3 2.2 - - - -
144C PRO* 4.1 7.0 - - - -
165C HIS* 4.4 15.5 - - + +
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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