Contacts of the helix formed by residues 164 - 176 (chain B) in PDB entry 5I1U
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 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A GLN* 4.8 0.3 + - - -
264A ARG* 3.1 29.4 + - - -
163B PRO* 1.3 75.6 - - - +
165B ARG* 1.3 59.2 + - - +
166B GLU* 3.2 14.9 + - - +
167B GLY* 2.8 31.6 + - - +
168B TYR* 2.8 28.6 + - - +
241B ARG* 4.6 3.8 - - - +
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Residues in contact with ARG 165 (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 PRO 3.7 1.8 + - - -
164B ASP* 1.3 74.2 + - - +
166B GLU* 1.3 77.7 + - + +
168B TYR* 3.2 4.5 + - - +
169B LEU* 2.9 57.2 + - + +
216B PHE* 4.2 5.5 - - - -
235B LEU* 4.0 14.0 - - + +
238B ILE* 3.7 24.6 - - + +
239B VAL* 3.8 25.3 - - - +
242B ASP* 4.1 11.8 + - - +
243B ARG* 5.6 3.2 - - - +
253B VAL* 5.1 6.3 - - - +
254B VAL* 5.8 0.2 - - - +
257B GLU* 3.0 37.0 + - - -
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Residues in contact with GLU 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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205A GLN* 3.3 19.7 - - - +
264A ARG* 3.7 12.1 + - - +
164B ASP* 3.2 19.1 - - - +
165B ARG* 1.3 92.8 + - + +
167B GLY* 1.3 58.1 + - - +
169B LEU* 3.9 5.1 - - - +
170B THR* 2.8 33.5 + - - +
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Residues in contact with GLY 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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201A PRO* 3.5 16.2 - - - +
205A GLN* 3.5 20.4 - - - +
163B PRO* 5.8 0.7 - - - -
164B ASP* 2.8 18.0 + - - -
166B GLU* 1.3 79.2 - - - +
168B TYR* 1.3 61.0 + - - +
170B THR* 3.4 1.7 + - - -
171B LEU* 3.0 21.8 + - - +
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Residues in contact with TYR 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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163B PRO* 4.1 21.3 - - + +
164B ASP 2.8 20.4 + - - +
165B ARG 3.6 2.0 - - - +
167B GLY* 1.3 75.6 - - - +
169B LEU* 1.3 76.6 + - + +
171B LEU* 3.2 15.6 + - + +
172B ARG* 2.8 51.7 + - + +
219B ASP* 2.6 38.8 + - - -
233B ALA* 3.4 34.7 + - + -
235B LEU* 3.8 12.3 - - + -
238B ILE* 3.5 22.7 - - + -
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Residues in contact with LEU 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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165B ARG* 2.9 56.3 + - + +
166B GLU* 4.2 4.7 - - - +
168B TYR* 1.3 94.9 - - + +
170B THR* 1.3 62.2 + - - +
172B ARG* 4.0 6.9 - - + +
173B ARG* 3.1 36.6 + - + +
215B SER* 5.9 2.5 - - - -
216B PHE* 3.8 30.7 - - + -
235B LEU* 4.1 12.3 - - + -
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Residues in contact with THR 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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201A PRO* 3.7 20.0 - - + +
204A ARG* 3.7 40.4 + - + +
205A GLN* 3.7 14.8 - - + +
145B TYR* 4.4 4.3 + - - -
149B CYS* 5.2 1.0 - - - -
166B GLU* 2.8 21.8 + - - +
167B GLY* 3.7 5.6 - - - -
169B LEU* 1.3 78.7 - - - +
171B LEU* 1.3 62.0 + - - +
173B ARG* 3.7 14.5 + - - +
174B GLY* 3.8 6.1 + - - -
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Residues in contact with LEU 171 (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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199A HIS 6.0 0.2 - - - -
201A PRO* 4.0 18.1 - - + +
149B CYS* 3.5 38.7 - - + +
152B ALA* 4.0 16.4 - - + +
153B GLU* 4.0 25.6 - - + +
156B GLY* 6.2 2.0 - - - -
167B GLY 3.0 17.9 + - - +
168B TYR* 3.6 14.4 - - + +
170B THR* 1.3 75.4 - - - +
172B ARG* 1.3 66.4 + - - +
174B GLY* 3.0 13.2 + - - -
175B THR* 3.0 20.9 + - + +
233B ALA* 6.5 0.7 - - + -
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Residues in contact with ARG 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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153B GLU* 5.3 2.6 + - - -
168B TYR* 2.8 51.0 + - + +
169B LEU* 3.4 9.8 + - + +
171B LEU* 1.3 74.9 - - - +
173B ARG* 1.3 64.1 + - - +
175B THR* 2.8 37.7 + - - -
176B ALA* 2.9 54.8 + - - +
215B SER* 3.5 32.8 + - - +
218B ASN* 4.2 18.6 + - - +
219B ASP* 4.9 6.0 + - - +
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Residues in contact with ARG 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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145B TYR* 3.5 23.0 + - - +
169B LEU* 3.1 26.0 + - + +
170B THR* 3.9 8.0 - - - +
171B LEU 3.2 0.6 - - - -
172B ARG* 1.3 76.8 - - - +
174B GLY* 1.3 61.4 + - - +
176B ALA* 4.4 4.5 - - - +
177B ALA* 4.1 8.7 + - - -
178B MET* 4.5 6.8 + - - +
179B GLU* 5.3 3.6 + - - +
208B GLN* 3.3 30.2 + - - +
211B ALA* 6.2 0.4 - - + -
212B ASP* 2.8 42.7 + - - +
215B SER* 5.5 1.3 - - - -
401B SO4 2.6 41.9 + - - -
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Residues in contact with GLY 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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145B TYR* 3.5 31.0 + - - -
146B TYR* 3.6 18.8 - - - +
149B CYS* 3.7 13.2 - - - -
170B THR 3.8 1.4 + - - -
171B LEU 3.0 7.7 + - - -
173B ARG* 1.3 77.3 - - - +
175B THR* 1.3 65.3 + - - +
176B ALA 3.2 2.9 + - - -
177B ALA* 3.2 10.9 + - - -
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Residues in contact with THR 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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80B ASP* 4.7 4.5 - - - +
146B TYR* 3.5 22.7 - - - -
149B CYS* 4.0 20.2 - - + +
150B HIS* 5.1 6.5 - - + -
153B GLU* 3.9 33.8 + - + +
171B LEU* 3.0 20.4 + - + +
172B ARG* 2.8 41.4 + - - -
174B GLY* 1.3 76.7 - - - +
176B ALA* 1.3 60.0 + - - +
177B ALA 3.4 0.5 + - - -
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Residues in contact with ALA 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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172B ARG* 2.9 36.8 + - - +
173B ARG* 4.4 4.0 - - - +
174B GLY 3.2 0.2 - - - -
175B THR* 1.3 74.6 + - - +
177B ALA* 1.3 70.7 + - - +
178B MET* 3.1 20.7 + - + +
181B ILE* 3.9 10.6 - - - +
211B ALA 5.6 0.2 - - - +
215B SER* 3.7 19.1 - - - +
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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