Contacts of the helix formed by residues 165 - 182 (chain B) in PDB entry 4AQD
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 ASN 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLY 4.2 0.4 + - - -
153B PHE* 3.9 19.5 + - - +
164B GLY* 1.3 71.7 - - - +
166B MET* 1.3 64.9 + - - +
167B GLY 3.2 3.4 - - - -
168B LEU* 3.1 20.8 + - + +
169B PHE* 3.1 25.7 + - + -
291B GLY 5.1 0.8 + - - -
292B PRO* 3.1 12.1 - - - +
293B THR* 2.7 46.9 + - - -
295B ASP* 3.2 30.0 + - - +
298B PHE* 4.0 8.6 - - + +
299B LEU* 4.4 3.4 - - - +
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Residues in contact with MET 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.2 38.8 - - + +
44B LYS 3.9 12.8 - - - +
45B LYS* 4.3 3.1 - - + +
46B PRO* 5.2 0.9 - - - -
147B ARG* 3.9 18.6 + - - +
150B ALA 4.0 2.5 - - - +
151B LEU 3.5 19.5 - - - +
152B GLY 2.9 21.3 + - - +
153B PHE 3.8 1.3 - - - +
154B LEU 3.5 20.0 - - - +
163B PRO* 3.9 6.5 - - + -
164B GLY 3.3 32.1 - - - +
165B ASN* 1.3 77.0 - - - +
167B GLY* 1.3 55.0 + - - +
169B PHE* 3.1 11.2 + - - +
170B ASP* 3.0 33.0 + - - +
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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
----------------------------------------------------------
146B TYR* 3.5 4.7 - - - +
147B ARG* 3.5 24.9 - - - -
152B GLY* 2.9 10.9 + - - -
153B PHE* 3.9 9.6 - - - -
165B ASN 3.2 0.2 - - - -
166B MET* 1.3 72.9 - - - +
168B LEU* 1.3 64.4 + - - +
170B ASP* 3.2 15.0 - - - +
171B GLN* 3.1 26.3 + - - +
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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
----------------------------------------------------------
118B PHE* 4.9 2.5 - - + -
153B PHE* 3.9 12.2 - - + -
165B ASN* 3.1 41.1 + - + +
167B GLY* 1.3 77.7 - - - +
169B PHE* 1.3 57.3 + - - +
171B GLN* 3.3 19.3 + - - +
172B GLN* 3.0 26.7 + - - +
203B SER* 3.8 32.3 - - - +
206B LEU* 4.0 20.6 - - + -
207B HIS* 4.0 1.3 - - - +
292B PRO* 4.1 8.1 - - + -
298B PHE* 3.9 38.1 - - + -
299B LEU* 6.0 0.7 - - + -
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LYS* 3.5 36.6 - - + -
46B PRO* 3.6 20.8 - - + +
163B PRO* 6.0 0.7 - - + -
164B GLY 4.5 3.1 - - - -
165B ASN* 3.1 29.7 + - + -
166B MET 3.1 6.7 + - - +
168B LEU* 1.3 74.1 - - - +
170B ASP* 1.3 57.1 + - - +
172B GLN* 3.6 25.0 - - - +
173B LEU* 2.8 35.2 + - - +
295B ASP* 3.5 17.9 - - - -
297B ASP* 3.5 29.4 - - - -
298B PHE* 3.5 27.1 - + + -
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 3.3 27.3 + - - +
46B PRO* 3.3 16.3 - - - +
93B LEU* 3.6 10.9 - - - +
146B TYR* 3.7 7.6 - - + -
147B ARG* 2.8 64.3 + - - +
166B MET 3.0 15.2 + - - +
167B GLY* 3.2 9.5 - - - +
169B PHE* 1.3 75.8 - - - +
171B GLN* 1.3 63.7 + - - +
173B LEU* 3.1 1.9 + - - +
174B ALA* 2.9 19.4 + - - +
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Residues in contact with GLN 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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113B ILE* 3.6 14.1 - - + +
118B PHE* 5.1 0.4 - - - -
144B MET* 4.0 22.2 - - + -
146B TYR* 3.5 48.9 - - + +
153B PHE* 5.4 0.4 - - - -
167B GLY 3.1 12.5 + - - +
168B LEU* 3.3 15.0 + - - +
170B ASP* 1.3 78.1 - - - +
172B GLN* 1.3 57.3 + - - +
174B ALA* 3.1 4.5 + - - +
175B LEU* 2.9 33.9 + - + +
203B SER* 3.3 32.3 + - - -
207B HIS* 3.1 23.1 + - - +
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Residues in contact with GLN 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 3.0 16.2 + - - +
169B PHE* 3.7 25.8 - - - +
170B ASP 3.2 0.2 - - - -
171B GLN* 1.3 77.1 - - - +
173B LEU* 1.3 58.4 + - - +
175B LEU* 3.3 6.8 + - - +
176B GLN* 3.0 33.0 + - - +
207B HIS* 3.9 11.2 - - + -
210B SER* 3.4 13.7 + - - -
212B GLY* 3.2 25.8 - - - +
213B SER* 2.7 27.4 + - - +
216B LEU* 3.6 14.2 - - + +
298B PHE* 3.4 11.2 - - + -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 3.9 13.9 - - + +
34B ALA* 3.6 31.0 - - + -
46B PRO* 3.6 28.9 - - + +
47B GLN 4.2 6.7 - - - +
48B SER* 4.4 9.4 - - - +
169B PHE 2.8 17.4 + - - +
170B ASP 3.5 4.7 - - - +
172B GLN* 1.3 76.2 - - - +
174B ALA* 1.3 59.4 + - - +
176B GLN* 3.2 18.0 + - + +
177B TRP* 3.0 26.2 + - - +
1533B EDO 3.8 23.3 - - - +
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 3.8 16.2 - - + -
95B LEU* 4.0 9.7 - - + +
142B VAL* 6.2 1.1 - - + -
144B MET* 3.6 36.8 - - + -
170B ASP 2.9 11.6 + - - +
171B GLN 3.4 8.1 - - - +
173B LEU* 1.3 75.3 - - - +
175B LEU* 1.3 64.4 + - - +
177B TRP* 3.2 7.7 + - - +
178B VAL* 3.2 25.6 + - - +
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 3.7 35.4 - - + -
113B ILE* 5.3 3.6 - - + -
144B MET* 4.1 6.5 - - + -
171B GLN 2.9 23.2 + - - +
172B GLN* 3.5 7.2 - - - +
174B ALA* 1.3 72.8 - - - +
176B GLN* 1.3 65.0 + - - +
178B VAL* 3.3 8.1 + - - +
179B GLN* 3.2 25.8 + - - +
194B LEU* 3.7 34.5 - - + -
207B HIS* 4.3 18.2 - - + +
213B SER* 5.0 0.7 - - - -
216B LEU* 3.9 31.8 - - + +
217B PHE* 4.4 4.7 - - + -
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Residues in contact with GLN 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 GLN* 3.0 22.3 + - - +
173B LEU* 3.2 25.2 + - + +
175B LEU* 1.3 76.9 - - - +
177B TRP* 1.3 62.3 + - - +
179B GLN* 3.4 4.6 + - + +
180B LYS* 3.2 35.7 + - + +
212B GLY 5.3 2.5 + - - +
216B LEU* 4.3 28.7 - - + +
1533B EDO 4.5 10.1 - - - +
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Residues in contact with TRP 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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8B THR* 4.2 14.5 + - + -
10B ASN* 4.2 11.1 - - - +
31B ILE* 4.0 22.3 - - + +
32B PRO 4.4 8.8 + - - -
33B TYR* 4.2 13.0 - - + -
52B TRP* 6.2 1.0 - - - -
95B LEU* 3.5 38.1 - - + -
97B VAL* 3.9 15.0 - - + -
142B VAL* 5.2 0.4 - - + -
173B LEU 3.0 11.5 + - - +
174B ALA* 3.3 13.9 - - - +
175B LEU 3.2 0.2 - - - -
176B GLN* 1.3 75.3 - - - +
178B VAL* 1.3 75.2 + - + +
180B LYS* 3.3 0.9 + - - -
181B ASN* 2.7 71.4 + - + +
182B ILE* 4.7 6.7 - - + -
185B PHE* 3.7 23.1 - + - -
1533B EDO 4.0 25.1 - - - -
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Residues in contact with VAL 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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109B VAL* 4.5 3.8 - - + -
111B ILE* 3.7 29.6 - - + -
142B VAL* 4.3 20.0 - - + -
174B ALA 3.2 14.6 + - - +
175B LEU 3.5 7.6 - - - +
177B TRP* 1.3 90.6 - - + +
179B GLN* 1.3 63.0 + - - +
182B ILE* 2.7 60.0 + - + +
192B VAL* 4.5 17.3 - - + -
216B LEU 5.9 0.4 - - - +
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Residues in contact with GLN 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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175B LEU 3.2 12.3 + - - +
176B GLN* 3.5 10.5 - - + +
177B TRP 3.3 0.4 - - - -
178B VAL* 1.3 83.8 - - - +
180B LYS* 1.3 62.3 + - + +
181B ASN 3.6 0.2 + - - -
182B ILE 4.7 0.3 + - - -
183B ALA* 5.6 0.3 + - - +
189B PRO* 3.0 53.1 + - - +
192B VAL* 3.8 11.5 - - - +
215B SER 3.7 15.1 - - - +
216B LEU* 3.5 38.9 + - + -
217B PHE* 5.0 0.2 - - - +
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Residues in contact with LYS 180 (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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9B LYS* 3.1 43.3 + - + +
10B ASN* 5.3 6.6 + - - +
176B GLN* 3.2 18.7 + - + +
177B TRP 3.3 0.2 + - - -
178B VAL 3.2 0.4 - - - -
179B GLN* 1.3 79.5 - - + +
181B ASN* 1.3 71.6 + - - +
182B ILE 4.0 0.2 - - - -
183B ALA* 5.6 1.5 - - - +
1533B EDO 2.7 41.6 + - - +
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Residues in contact with ASN 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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8B THR* 3.2 11.3 - - - +
9B LYS* 2.8 37.1 + - - +
10B ASN* 4.4 3.3 + - - +
177B TRP* 2.7 69.6 + - + +
180B LYS* 1.3 96.8 - - - +
182B ILE* 1.3 63.9 + - - +
183B ALA* 3.3 3.8 - - - -
184B ALA* 3.2 18.3 + - - +
185B PHE* 3.3 13.9 - - + -
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Residues in contact with ILE 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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97B VAL* 4.3 9.4 - - + -
109B VAL* 3.7 19.3 - - + -
140B ILE* 4.0 23.3 - - + -
142B VAL* 4.1 18.4 - - + -
177B TRP* 4.7 9.4 - - + -
178B VAL* 2.7 37.5 + - + +
179B GLN 4.7 0.4 + - - -
181B ASN* 1.3 68.4 - - - +
183B ALA* 1.3 66.2 + - - +
184B ALA 3.1 2.2 - - - -
185B PHE* 3.0 17.7 + - + +
187B GLY* 2.8 34.7 + - - +
188B ASN 4.3 0.7 - - - -
189B PRO* 3.7 30.7 - - + -
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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
------------------------------------------------------------
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