Contacts of the helix formed by residues 160 - 174 (chain B) in PDB entry 2R1U
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 THR 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A VAL* 3.6 22.9 - - + +
145B ARG* 3.5 44.0 - - + +
155B SER* 2.7 24.1 + - - -
156B ARG* 3.2 4.2 + - + -
157B GLY 2.9 26.2 + - - +
159B GLY* 1.3 75.7 - - - +
161B SER* 1.3 58.8 + - - +
162B PHE 3.4 3.1 - - - -
163B GLU* 3.3 13.8 + - - +
164B PHE* 2.9 28.3 + - - +
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Residues in contact with SER 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B MET 4.3 1.1 + - - -
18B GLU* 3.7 14.6 - - - +
21B ILE* 3.6 30.1 - - - +
22B PRO* 4.6 3.8 - - - +
105B ILE* 3.6 17.2 - - - +
157B GLY 3.4 7.7 + - - -
158B PRO* 2.9 26.5 + - - +
159B GLY 3.5 0.4 - - - -
160B THR* 1.3 78.3 - - - +
162B PHE* 1.3 58.8 + - - +
164B PHE* 3.5 3.2 - - - +
165B ALA* 2.9 30.3 + - - +
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Residues in contact with PHE 162 (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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17A MET* 3.6 31.9 - - + -
21A ILE* 4.3 11.0 - - + -
158A PRO* 3.4 40.2 - - + -
159A GLY* 4.2 4.7 - - - -
162A PHE* 4.4 14.6 - + - -
21B ILE* 3.9 26.5 - - + -
25B VAL* 4.2 5.8 - - + -
159B GLY 5.3 3.5 + - - +
160B THR 3.4 0.4 - - - -
161B SER* 1.3 73.5 - - - +
163B GLU* 1.3 62.3 + - + +
165B ALA* 3.3 2.5 + - - +
166B LEU* 2.9 36.7 + - + +
185B LEU* 4.1 18.4 - - + -
187B LEU* 3.7 32.3 - - + -
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LYS* 5.0 9.2 + - - +
145B ARG* 2.9 56.9 + - - +
146B VAL* 3.7 17.0 - - + +
159B GLY 3.6 2.4 - - - +
160B THR* 3.3 16.1 + - - +
162B PHE* 1.3 79.2 - - + +
164B PHE* 1.3 56.7 + - - +
166B LEU* 3.5 7.6 + - + +
167B ALA* 3.0 29.3 + - - +
187B LEU* 6.5 0.4 - - + -
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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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22B PRO* 4.0 22.0 - - + -
71B VAL* 4.2 10.1 - - + -
103B ALA* 3.6 27.6 - - + -
104B ALA* 3.7 31.0 - - - -
105B ILE* 3.9 24.5 - - + -
146B VAL* 3.8 7.4 - - - +
153B LEU* 3.5 29.8 - - + -
155B SER* 3.5 23.8 - - - +
160B THR 2.9 17.4 + - - +
161B SER 3.5 4.0 - - - +
163B GLU* 1.3 76.7 - - - +
165B ALA* 1.3 63.7 + - - +
167B ALA* 3.2 7.0 + - - +
168B ILE* 3.1 35.1 + - + +
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Residues in contact with ALA 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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21B ILE 4.3 0.2 - - - +
22B PRO* 3.9 21.1 - - + +
25B VAL* 3.7 31.6 - - + -
26B MET* 5.0 2.7 - - + +
161B SER 2.9 18.5 + - - +
162B PHE* 3.7 3.8 - - - +
164B PHE* 1.3 78.3 - - - +
166B LEU* 1.3 57.4 + - - +
168B ILE* 3.2 15.1 + - - +
169B VAL* 3.0 29.5 + - - +
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Residues in contact with LEU 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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25B VAL* 4.0 19.7 - - + -
162B PHE* 2.9 22.3 + - - +
163B GLU* 4.0 5.8 - - + +
165B ALA* 1.3 73.7 - - - +
167B ALA* 1.3 60.3 + - - +
169B VAL* 3.4 5.9 + - + +
170B GLU* 2.9 29.0 + - - +
178B ALA* 3.8 30.0 - - + +
181B VAL* 4.2 14.4 - - + -
182B LYS* 3.9 24.0 - - + +
185B LEU* 4.7 4.3 - - + -
187B LEU* 3.9 27.6 - - + -
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Residues in contact with ALA 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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146B VAL* 4.0 19.5 - - + -
148B LYS* 5.4 3.6 - - + +
153B LEU* 4.0 18.6 - - + +
163B GLU 3.0 18.1 + - - +
164B PHE 3.2 5.8 + - - +
166B LEU* 1.3 74.9 - - - +
168B ILE* 1.3 61.1 + - - +
170B GLU* 3.4 9.9 + - - +
171B ALA* 3.0 28.2 + - - +
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Residues in contact with ILE 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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22B PRO* 5.2 2.7 - - + -
26B MET* 3.9 26.7 - - + -
31B ILE* 5.1 0.2 - - + -
69B VAL* 4.3 19.3 - - + -
71B VAL* 4.2 14.1 - - + -
101B LEU* 4.7 3.4 - - + -
103B ALA* 3.8 29.4 - - + -
153B LEU* 4.2 12.3 - - + -
164B PHE* 3.1 33.2 + - + +
165B ALA* 3.2 11.6 + - - +
167B ALA* 1.3 76.7 - - - +
169B VAL* 1.3 63.8 + - - +
171B ALA* 3.2 4.5 + - - +
172B LEU* 3.0 31.4 + - + +
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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
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25B VAL* 4.2 20.2 - - + +
26B MET* 4.4 5.2 - - + -
29B ALA* 3.6 35.2 - - + -
31B ILE* 4.3 15.0 - - + -
165B ALA 3.0 18.1 + - - +
166B LEU* 3.6 11.4 - - + +
168B ILE* 1.3 77.9 - - - +
170B GLU* 1.3 54.6 + - - +
173B ASN* 2.7 33.7 + - + -
174B GLY 3.5 0.5 + - - -
177B VAL* 4.0 11.9 - - + +
178B ALA* 3.9 23.3 - - + +
181B VAL* 5.0 1.8 - - + -
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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
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166B LEU 2.9 18.4 + - - +
167B ALA* 3.8 8.8 - - - +
168B ILE 3.3 0.2 - - - -
169B VAL* 1.3 76.7 - - - +
171B ALA* 1.3 61.4 + - - +
174B GLY* 3.0 31.0 + - - -
175B LYS* 3.1 51.4 - - + +
178B ALA* 4.1 9.0 - - + +
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Residues in contact with ALA 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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101B LEU* 4.0 23.3 - - + -
148B LYS* 4.1 21.1 - - - +
153B LEU* 5.0 0.4 - - + -
167B ALA 3.0 18.1 + - - +
168B ILE* 3.6 5.2 - - - +
170B GLU* 1.3 79.4 - - - +
172B LEU* 1.3 61.4 + - - +
174B GLY 5.1 0.2 + - - -
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Residues in contact with LEU 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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4B LYS* 3.8 37.5 + - + +
5B ARG 4.9 0.4 - - - +
31B ILE* 4.0 24.9 - - + -
68B ASP* 3.9 30.1 - - + +
69B VAL* 3.8 24.2 - - + -
101B LEU* 4.3 14.6 - - + -
168B ILE* 3.0 21.6 + - + +
169B VAL 4.2 0.4 - - - +
171B ALA* 1.3 84.5 - - + +
173B ASN* 1.3 75.0 + - - +
174B GLY 3.7 0.7 - - - -
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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
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4B LYS* 3.4 26.1 + - - +
29B ALA* 3.1 24.8 - - - +
30B GLY 4.8 1.4 - - - +
31B ILE* 3.7 18.6 + - - +
169B VAL* 2.7 18.6 + - + +
172B LEU* 1.3 82.7 + - - +
174B GLY* 1.3 58.6 + - - +
177B VAL* 3.6 33.9 - - + +
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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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169B VAL 3.5 0.9 + - - +
170B GLU* 3.0 28.7 + - - -
171B ALA 4.8 0.2 - - - -
172B LEU 3.7 1.2 - - - -
173B ASN* 1.3 80.5 - - - +
175B LYS* 1.3 65.3 + - - -
176B GLU* 3.4 2.9 + - - -
177B VAL* 3.6 0.9 + - - +
178B ALA 3.2 16.3 + - - -
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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
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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