Contacts of the helix formed by residues 168 - 186 (chain B) in PDB entry 5HJS
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 GLN 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY 3.9 1.0 + - - -
167B LEU* 1.3 72.6 - - - +
169B VAL* 1.4 59.6 + - - +
170B GLU* 3.5 29.8 + - - +
171B PHE* 3.0 26.4 + - + +
172B ILE* 3.1 13.9 + - - +
256B VAL 5.1 0.7 - - - +
259B GLU* 4.2 7.8 - - - +
260B GLN* 2.9 42.2 + - - +
263B ALA* 3.5 26.6 - - - +
267B GLN* 5.6 1.0 + - - -
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA* 5.5 5.4 - - + -
167B LEU 4.0 0.4 + - - +
168B GLN* 1.4 71.8 - - - +
170B GLU* 1.3 74.7 + - + +
171B PHE 3.1 0.4 - - - -
172B ILE* 3.9 17.7 - - + +
173B ASN* 3.1 45.3 + - - +
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLN* 3.2 36.5 + - - +
169B VAL* 1.3 83.8 + - + +
171B PHE* 1.3 57.8 + - - +
173B ASN* 5.6 0.2 - - - +
174B PRO* 3.3 15.4 - - - +
256B VAL* 3.2 19.0 - - + +
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 4.5 4.9 - - + -
135B LEU* 4.5 9.2 - - + -
167B LEU* 3.7 18.2 - - + -
168B GLN* 3.0 6.8 + - + +
170B GLU* 1.3 78.1 - - - +
172B ILE* 1.3 63.7 + - - +
173B ASN 3.5 0.4 - - - -
174B PRO* 3.2 10.0 - - - +
175B ILE* 3.2 39.7 + - + +
253B LEU* 4.0 10.8 - - + -
256B VAL* 3.6 18.8 - - + +
257B HIS* 3.6 40.6 - + + -
260B GLN* 3.6 37.0 - - + +
301B 668 3.7 28.7 - - - -
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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
----------------------------------------------------------
159B ARG* 3.8 25.4 - - + +
162B PHE* 3.9 7.4 - - + -
163B ALA* 3.6 28.9 - - + +
167B LEU* 3.3 40.2 - - + +
168B GLN 3.1 14.8 + - - +
169B VAL* 3.4 14.3 + - + +
171B PHE* 1.3 75.9 - - - +
173B ASN* 1.3 66.3 + - - +
175B ILE* 3.1 10.4 + - - +
176B PHE* 3.1 52.4 + - + -
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Residues in contact with ASN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG* 3.9 23.5 + - - +
169B VAL* 3.1 30.2 + - - +
172B ILE* 1.3 77.0 - - - +
174B PRO* 1.4 65.0 - - + +
176B PHE* 3.2 5.4 + - - +
177B GLU* 2.9 30.1 + - - +
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Residues in contact with PRO 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLU* 3.3 24.2 - - - +
171B PHE 3.2 11.4 - - - +
173B ASN* 1.4 92.7 - - + +
175B ILE* 1.4 53.7 + - - +
177B GLU* 4.2 7.2 - - + -
178B PHE* 2.9 31.0 + - - +
253B LEU* 3.7 21.4 - - + +
256B VAL* 4.5 12.8 - - + -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.9 20.0 - - + -
138B THR* 4.0 26.2 - - + -
149B ILE* 4.4 1.6 - - + -
162B PHE* 4.2 19.5 - - + -
167B LEU* 4.0 14.1 - - + -
171B PHE* 3.2 58.8 + - + +
172B ILE* 3.1 9.2 + - - +
174B PRO* 1.4 74.8 - - - +
176B PHE* 1.3 64.3 + - + +
178B PHE* 3.7 4.6 - - - +
179B SER* 2.8 34.2 + - - +
253B LEU* 4.3 6.5 - - + -
301B 668 5.4 3.4 - - + -
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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
----------------------------------------------------------
142B TYR* 4.2 13.6 + + - -
147B GLU 3.2 28.7 - - - -
148B SER* 4.3 0.4 - - - -
149B ILE* 3.6 25.4 - - + -
157B TYR 3.9 2.5 - - - -
158B ASN* 3.6 8.1 - - - -
159B ARG* 3.5 62.3 + - + +
162B PHE* 3.6 28.5 - + - -
172B ILE* 3.1 42.3 + - + +
173B ASN 3.8 1.3 - - - +
175B ILE* 1.3 80.5 - - + +
177B GLU* 1.3 57.9 + - - +
179B SER* 3.5 5.5 + - - -
180B ARG* 3.0 29.1 + - - +
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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
----------------------------------------------------------
204A ASP* 6.6 0.2 - - - -
211A GLN* 3.1 28.2 + - - +
159B ARG* 4.7 5.0 + - - +
173B ASN 2.9 18.0 + - - +
174B PRO* 3.9 7.9 - - + +
176B PHE* 1.3 71.7 - - - +
178B PHE* 1.4 63.9 + - - +
180B ARG* 2.7 46.9 + - - +
181B ALA* 3.0 23.4 + - + +
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Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.9 16.6 - - + -
136B LEU* 4.1 7.6 - - + -
139B SER* 3.9 15.7 - - - -
174B PRO 2.9 19.2 + - - +
175B ILE* 3.7 5.6 - - - +
177B GLU* 1.4 77.1 - - - +
179B SER* 1.3 52.6 + - - +
181B ALA* 3.3 7.1 + - + +
182B MET* 2.8 63.8 + - + +
246B LYS* 3.9 31.6 - - + -
249B SER* 4.1 14.1 - - - -
250B LEU* 3.7 28.7 - - + -
253B LEU* 3.5 24.9 - - + -
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU 5.0 0.2 + - - -
138B THR* 4.2 10.7 - - - +
139B SER* 3.5 28.2 + - - +
142B TYR* 3.5 34.5 - - - +
149B ILE* 4.2 3.5 - - - +
175B ILE* 2.8 22.1 + - - +
176B PHE* 3.6 5.2 - - - -
178B PHE* 1.3 77.1 - - - +
180B ARG* 1.4 56.4 + - - +
182B MET* 3.5 1.6 + - - +
183B ASN* 3.1 29.6 + - - +
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Residues in contact with ARG 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN* 4.3 11.9 + - - +
142B TYR* 3.7 26.4 - - + +
159B ARG* 6.1 1.6 - - - +
176B PHE 3.0 17.9 + - - +
177B GLU* 2.7 42.0 + - - +
179B SER* 1.4 73.7 - - - +
181B ALA* 1.3 79.1 + - - +
183B ASN* 3.5 4.0 + - - +
184B GLU* 3.3 59.5 + - + +
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Residues in contact with ALA 181 (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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177B GLU* 3.0 18.2 + - - +
178B PHE* 3.5 8.3 - - + +
180B ARG* 1.3 94.1 - - - +
182B MET* 1.3 64.1 + - - +
184B GLU* 3.4 18.9 + - - +
185B LEU* 3.7 5.9 + - - +
246B LYS* 4.0 27.2 - - + +
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Residues in contact with MET 182 (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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136B LEU* 3.8 13.0 - - + -
139B SER* 3.4 25.1 - - - +
178B PHE* 2.8 43.9 + - + +
179B SER 3.8 0.7 - - - +
181B ALA* 1.3 72.5 - - - +
183B ASN* 1.3 57.5 + - - +
185B LEU* 3.1 29.0 + - - +
186B GLN* 3.5 3.5 + - - -
187B LEU* 3.7 27.7 + - + -
192B PHE* 3.6 34.0 - - + -
195B LEU* 4.6 2.0 - - + -
246B LYS* 3.6 33.9 - - + +
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Residues in contact with ASN 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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139B SER 4.9 4.9 + - - +
142B TYR* 3.8 27.3 + - + +
144B PRO* 3.8 33.1 - - - +
179B SER 3.1 18.6 + - - +
180B ARG 3.6 5.9 - - - +
181B ALA 3.4 0.2 - - - -
182B MET* 1.3 72.5 - - - +
184B GLU* 1.3 66.4 + - - +
186B GLN* 2.8 48.9 + - - +
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Residues in contact with GLU 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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212A LEU* 5.9 2.6 - - - +
215A GLU* 5.5 2.8 - - - +
180B ARG* 3.3 42.7 + - + +
181B ALA* 3.5 10.4 - - - +
182B MET 3.3 1.0 - - - -
183B ASN* 1.3 79.9 - - - +
185B LEU* 1.4 61.4 + - - +
186B GLN* 3.5 8.2 + - - +
242B ARG* 5.2 11.5 + - - +
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Residues in contact with LEU 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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181B ALA 3.7 6.9 + - - +
182B MET* 3.1 18.3 + - - +
184B GLU* 1.4 77.5 - - - +
186B GLN* 1.4 68.2 + - - +
187B LEU* 3.7 20.1 - - + +
233B HIS* 5.0 2.1 + - - -
239B MET* 3.4 34.5 - - + +
242B ARG* 3.5 54.5 - - + +
243B MET* 4.3 11.7 - - + +
246B LYS* 3.8 35.7 - - + -
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Residues in contact with GLN 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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182B MET 3.5 2.2 + - - -
183B ASN* 2.8 48.2 + - - +
184B GLU* 4.0 7.4 - - - +
185B LEU* 1.4 79.1 - - - +
187B LEU* 1.3 65.9 + - - +
188B ASN 3.8 1.2 + - - -
191B GLU* 4.3 2.8 - - - +
232B HIS* 4.5 9.5 - - - -
233B HIS* 5.0 3.0 + - + -
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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