Contacts of the helix formed by residues 157 - 179 (chain B) in PDB entry 3EIJ
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 LEU 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B GLU* 6.6 0.2 - - - -
156B PHE* 1.3 81.0 - - + +
158B PRO* 1.3 77.0 - - + +
159B LEU* 4.1 10.8 - - + +
160B ASP* 3.2 23.8 + - + +
161B GLU* 3.0 21.4 + - - +
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Residues in contact with PRO 158 (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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156B PHE 3.8 2.7 - - - +
157B LEU* 1.3 91.3 - - + +
159B LEU* 1.3 58.2 + - + +
161B GLU* 4.6 7.9 - - + +
162B ARG* 3.0 35.5 + - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 3.2 7.5 - - + -
158B PRO* 1.3 81.5 - - + +
160B ASP* 1.3 67.3 + - - +
162B ARG* 4.6 1.8 - - - +
163B ALA* 3.4 22.3 + - - +
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Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PHE* 4.9 9.2 - - + -
157B LEU* 3.2 31.8 + - - +
159B LEU* 1.3 89.8 - - - +
161B GLU* 1.3 58.8 + - - +
162B ARG 3.3 0.4 - - - -
163B ALA* 3.3 7.4 + - - +
164B PHE* 3.0 27.9 + - - +
196B MET* 3.7 19.0 - - + +
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PHE* 4.4 24.6 - - + +
157B LEU 3.0 15.7 + - - +
158B PRO* 4.2 5.5 - - + +
160B ASP* 1.3 77.1 - - - +
162B ARG* 1.3 57.1 + - - +
164B PHE* 3.4 11.6 - - + +
165B GLU* 3.2 41.0 + - + +
196B MET* 4.7 4.5 - - + -
242B LYS* 3.6 24.4 + - - -
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PRO 3.0 18.9 + - - +
159B LEU* 4.6 2.7 - - - +
161B GLU* 1.3 73.4 - - - +
163B ALA* 1.3 64.7 + - - +
164B PHE 3.1 1.8 - - - -
165B GLU* 3.3 40.1 + - - +
166B LYS* 2.9 61.6 + - + +
169B THR* 5.6 0.6 + - - -
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Residues in contact with ALA 163 (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 LEU 3.4 19.8 + - - +
160B ASP* 3.3 9.3 + - - +
162B ARG* 1.3 77.0 - - - +
164B PHE* 1.3 57.7 - - - +
166B LYS* 3.8 7.4 - - - +
167B THR* 2.7 33.5 + - - +
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Residues in contact with PHE 164 (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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160B ASP 3.0 13.9 + - - +
161B GLU* 3.4 14.4 - - + +
162B ARG 3.1 0.2 - - - -
163B ALA* 1.3 74.2 - - - +
165B GLU* 1.3 70.4 + - + +
167B THR* 3.3 1.8 + - - -
168B LEU* 3.0 60.7 + - + +
193B LEU* 4.0 19.3 - - + -
196B MET* 3.5 41.5 - - + -
199B GLY* 3.5 21.3 - - - -
200B VAL* 3.5 23.6 - - + -
203B LEU* 4.0 18.8 - - + -
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU* 3.2 27.6 + - + +
162B ARG* 3.3 26.0 + - - +
164B PHE* 1.3 82.8 - - + +
166B LYS* 1.3 63.0 + - - +
169B THR* 2.7 35.7 + - - +
203B LEU* 4.1 29.6 - - + +
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Residues in contact with LYS 166 (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 ARG* 2.9 48.4 + - + +
163B ALA* 3.8 7.9 - - - +
165B GLU* 1.3 76.2 - - - +
167B THR* 1.3 59.3 + - - +
169B THR* 4.8 0.6 - - - -
170B PRO* 3.2 22.2 - - - +
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Residues in contact with THR 167 (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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163B ALA 2.7 23.2 + - - -
164B PHE* 3.9 2.7 - - - -
165B GLU 3.3 0.4 - - - -
166B LYS* 1.3 78.6 - - - +
168B LEU* 1.3 64.7 + - - +
170B PRO* 3.2 15.4 - - - +
171B ILE* 3.0 26.0 - - + +
191B LEU* 4.0 33.0 - - + -
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Residues in contact with LEU 168 (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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164B PHE* 3.0 48.0 + - + +
167B THR* 1.3 81.5 - - - +
169B THR* 1.3 60.1 + - - +
171B ILE* 3.0 7.4 + - + +
172B ILE* 2.9 38.4 + - + +
188B LEU* 3.9 22.0 - - + -
191B LEU* 4.0 21.8 - - + -
193B LEU* 4.3 5.6 - - + -
200B VAL* 3.7 39.3 - - + -
203B LEU* 3.7 12.6 - - + -
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Residues in contact with THR 169 (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 ARG* 5.6 0.7 + - - -
165B GLU* 2.7 27.3 + - - +
166B LYS* 4.8 0.7 - - - -
168B LEU* 1.3 76.1 - - - +
170B PRO* 1.3 59.5 - - + +
172B ILE* 3.9 0.3 - - - +
173B GLN* 2.6 67.1 + - + +
203B LEU* 4.2 12.3 - - - +
207B LEU* 4.0 22.6 - - + +
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Residues in contact with PRO 170 (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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166B LYS 3.2 17.3 - - - +
167B THR* 3.2 19.3 - - - +
169B THR* 1.3 95.8 - - + +
171B ILE* 1.3 58.5 + - + +
173B GLN* 4.1 7.4 - - + +
174B GLU* 3.0 48.5 + - - +
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B THR* 3.0 37.9 - - + +
168B LEU* 3.0 11.3 + - + +
170B PRO* 1.3 79.2 - - + +
172B ILE* 1.3 64.4 + - + +
174B GLU* 3.3 5.1 + - - +
175B TYR* 2.8 27.9 + - - +
178B HIS* 4.7 1.6 - - - -
184B VAL* 3.8 28.5 - - + +
187B MET* 3.8 39.8 - - + +
188B LEU* 4.5 14.1 - - + -
191B LEU* 4.9 9.0 - - + -
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Residues in contact with ILE 172 (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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168B LEU* 2.9 32.2 + - + +
171B ILE* 1.3 77.9 - - + +
173B GLN* 1.3 64.4 + - - +
174B GLU 3.3 0.7 + - - -
175B TYR* 3.6 7.0 - - + +
176B PHE* 3.2 50.9 + - + -
184B VAL* 5.6 2.0 - - + -
188B LEU* 6.5 0.2 - - + -
200B VAL* 4.2 9.4 - - + +
203B LEU* 4.1 20.0 - - + -
204B ALA* 3.9 41.3 - - + +
207B LEU* 4.0 11.2 - - + -
222B LEU* 4.8 12.8 - - + -
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Residues in contact with GLN 173 (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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169B THR* 2.6 49.0 + - + +
170B PRO* 4.1 5.5 - - + +
172B ILE* 1.3 73.7 - - - +
174B GLU* 1.3 60.2 + - + +
176B PHE* 4.1 18.0 - - + +
177B GLU* 4.2 8.3 + - - +
207B LEU* 4.2 16.9 - - + +
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Residues in contact with GLU 174 (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 PRO* 3.0 35.2 + - + +
171B ILE* 3.8 5.6 - - - +
172B ILE 3.1 0.2 - - - -
173B GLN* 1.3 77.4 - - + +
175B TYR* 1.3 60.2 + - - +
176B PHE 3.2 1.6 - - - -
177B GLU* 2.8 26.8 + - + +
178B HIS* 3.1 25.4 + - + +
187B MET* 5.6 5.3 - - + +
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Residues in contact with TYR 175 (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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402A LYS* 4.7 3.6 + - - -
171B ILE 2.8 17.4 + - - +
172B ILE* 3.6 7.6 - - - +
174B GLU* 1.3 75.4 - - - +
176B PHE* 1.3 87.3 + + - +
178B HIS* 2.9 12.3 + - - -
179B GLY* 2.5 65.3 + - - -
180B ASP 3.9 0.9 - - - -
181B THR* 3.8 13.4 + - - -
184B VAL* 3.5 28.9 - - + -
218B MET* 2.4 44.0 + - + +
221B LYS* 4.0 6.4 - - - +
222B LEU* 3.8 28.8 + - + -
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Residues in contact with PHE 176 (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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398A VAL* 3.7 6.8 - - - +
172B ILE* 3.2 39.9 + - + +
173B GLN* 4.1 13.9 - - + +
174B GLU 3.2 0.6 - - - -
175B TYR* 1.3 100.3 - + - +
177B GLU* 1.3 60.3 + - - +
204B ALA* 4.0 4.9 - - + -
207B LEU* 4.5 7.4 - - + -
208B ALA* 4.1 13.9 - - + -
215B HIS* 3.3 53.1 - + + +
218B MET* 2.8 34.3 - - + +
219B THR* 3.0 30.3 - - - -
222B LEU* 5.6 0.2 - - + -
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Residues in contact with GLU 177 (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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391A TRP* 4.3 7.8 - - - -
398A VAL* 3.1 21.7 - - - +
173B GLN 4.2 5.4 + - - +
174B GLU* 2.8 21.4 + - + +
176B PHE* 1.3 83.6 - - - +
178B HIS* 1.3 55.7 + - + -
215B HIS* 5.1 7.8 + - - -
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Residues in contact with HIS 178 (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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391A TRP* 5.8 0.9 - - - -
398A VAL* 3.5 15.2 - - - +
440A SER* 3.9 18.5 + - - -
171B ILE 4.7 1.3 - - - -
174B GLU* 3.1 20.0 + - + +
175B TYR* 2.9 31.0 + - + +
177B GLU* 1.3 78.6 - - + +
179B GLY* 1.3 62.5 - - - +
180B ASP* 3.0 57.9 + - + -
183B GLU* 3.7 28.1 + - - +
184B VAL* 3.9 6.6 - - + +
187B MET* 5.1 5.6 - - + -
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Residues in contact with GLY 179 (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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398A VAL* 4.4 5.8 - - - -
402A LYS* 3.1 30.7 + - - -
440A SER* 4.9 1.8 - - - -
442A GLN* 3.5 1.1 - - - +
175B TYR* 2.5 31.8 + - - -
177B GLU 3.8 0.6 - - - -
178B HIS* 1.3 69.5 - - - +
180B ASP* 1.3 58.0 + - - +
181B THR 3.0 9.5 + - - -
218B MET* 3.7 18.3 - - - +
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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