Contacts of the helix formed by residues 161 - 178 (chain B) in PDB entry 3ROT
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 HIS 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B HIS* 3.5 19.9 + + - -
89B PRO* 4.0 11.4 - - + -
113B THR* 3.1 26.0 - - + +
131B ASN* 5.7 0.7 - - - -
156B ASN* 5.7 0.2 + - - -
158B GLN* 3.2 46.2 + - - +
159B PRO 3.4 0.6 + - - -
160B GLY* 1.3 73.3 + - - +
162B ILE* 1.3 65.8 + - - +
163B GLY* 2.9 32.6 + - - -
164B LEU* 3.1 30.3 + - + +
165B GLU* 2.9 21.1 + - - +
167B ARG* 6.1 0.2 - - - -
317B GOL 2.8 29.5 + - - -
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE 3.3 13.2 - - - +
89B PRO 3.2 30.9 + - - +
90B SER* 3.3 14.8 - - - +
91B ASP* 3.2 35.7 - - - +
113B THR* 3.6 9.0 - - + -
114B ARG 3.7 12.8 - - - +
115B PRO* 4.2 1.1 - - + -
160B GLY 2.8 14.7 + - - +
161B HIS* 1.3 71.3 + - - +
163B GLY* 1.3 63.0 + - - +
165B GLU* 3.6 19.9 + - - +
166B LYS* 3.1 35.7 + - - +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B THR* 3.7 3.8 - - - +
131B ASN* 3.5 28.2 - - - +
161B HIS* 2.9 18.5 + - - -
162B ILE* 1.3 80.1 - - - +
164B LEU* 1.3 66.4 + - - +
166B LYS* 3.2 16.8 + - - -
167B ARG* 3.2 16.0 + - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASN* 3.6 22.2 - - - +
157B PRO* 4.1 12.3 - - + -
158B GLN* 4.1 5.8 - - + +
161B HIS* 3.1 42.8 + - + +
163B GLY* 1.3 71.9 - - - +
165B GLU* 1.3 60.5 + - - +
167B ARG* 3.1 39.8 + - - +
168B ALA* 2.9 30.7 + - - +
214B LEU* 3.8 18.2 - - + +
215B THR* 3.7 25.8 - - + -
217B GLN* 5.6 0.7 - - - +
317B GOL 4.6 2.5 - - - +
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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
----------------------------------------------------------
156B ASN* 5.1 5.8 - - - +
160B GLY* 5.1 9.0 - - - +
161B HIS 2.9 15.9 + - - +
162B ILE* 3.7 24.0 - - - +
163B GLY 3.2 0.2 - - - -
164B LEU* 1.3 77.7 - - - +
166B LYS* 1.3 58.1 + - + +
168B ALA* 3.6 5.5 + - - +
169B TYR* 3.0 28.9 + - + +
184B GLU* 5.8 0.7 - - - -
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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
----------------------------------------------------------
113B THR* 4.6 2.0 - - - +
114B ARG* 3.5 47.8 + - - +
116B LYS* 5.8 6.3 - - - +
130B ASP* 6.0 0.2 - - - +
131B ASN* 3.8 16.4 - - + +
132B LEU* 3.6 38.1 - - + +
162B ILE* 3.1 33.5 + - - +
163B GLY* 3.2 14.7 + - - +
165B GLU* 1.3 76.7 - - + +
167B ARG* 1.3 60.6 + - - +
169B TYR* 3.3 7.4 + - - +
170B GLY 2.9 23.7 + - - -
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASN* 2.8 37.5 + - - +
135B GLY* 3.5 4.2 - - - -
163B GLY 3.4 9.2 - - - +
164B LEU* 3.1 26.1 + - - +
166B LYS* 1.3 77.9 - - - +
168B ALA* 1.3 63.8 + - - +
170B GLY 3.1 2.6 + - - -
171B ILE* 3.0 27.8 + - - +
214B LEU* 2.7 35.6 + - + -
243B PHE* 3.5 48.8 - - + +
264B GLN* 3.0 31.0 + - - +
317B GOL 2.7 40.1 + - - -
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 4.5 4.7 - - + -
164B LEU 2.9 15.7 + - - +
165B GLU* 3.8 6.7 - - - +
167B ARG* 1.3 76.7 - - - +
169B TYR* 1.3 57.9 + - - +
171B ILE* 3.4 6.3 + - - +
172B LYS* 2.9 41.5 + - - +
184B GLU* 3.9 32.8 - - - +
214B LEU* 4.1 15.8 - - + +
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Residues in contact with TYR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 4.4 22.9 - - + -
136B LYS* 5.1 2.2 - - - -
165B GLU* 3.0 20.3 + - + +
166B LYS* 3.5 8.5 - - - +
167B ARG 3.2 0.2 - - - -
168B ALA* 1.3 78.1 - - - +
170B GLY* 1.3 62.9 + - - +
172B LYS* 3.4 13.2 + - + +
173B THR* 3.0 50.0 + - + +
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Residues in contact with GLY 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.7 27.8 - - - -
136B LYS* 3.7 16.7 - - - +
166B LYS 2.9 11.5 + - - -
167B ARG 3.1 3.7 + - - -
169B TYR* 1.3 76.2 - - - +
171B ILE* 1.3 61.9 + - - +
173B THR* 2.7 23.7 + - - -
174B ILE* 3.4 7.4 + - - +
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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
----------------------------------------------------------
135B GLY* 3.3 23.3 + - - +
138B LEU* 4.6 2.0 - - + -
139B GLY* 4.4 9.0 - - - +
154B VAL* 4.6 6.7 - - + -
167B ARG 3.0 14.4 + - - +
168B ALA* 3.7 7.0 - - - +
170B GLY* 1.3 73.1 - - - +
172B LYS* 1.3 64.5 + - + +
174B ILE* 3.0 14.6 + - - +
175B LEU* 3.0 21.7 + - + +
212B PHE* 3.7 61.5 - - + -
214B LEU* 4.2 19.1 - - + -
243B PHE* 4.4 12.8 - - + -
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Residues in contact with LYS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 5.2 9.0 - - + -
168B ALA* 2.9 33.0 + - - +
169B TYR* 3.7 13.4 - - + +
171B ILE* 1.3 78.7 - - + +
173B THR* 1.3 57.4 + - + +
175B LEU* 3.8 8.8 - - + +
176B GLN* 3.0 32.2 + - - +
182B PHE* 3.8 37.9 - - + -
184B GLU* 2.5 44.9 + - - +
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Residues in contact with THR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 2.9 25.9 + - - +
169B TYR* 3.0 47.3 - - + +
170B GLY 2.7 16.6 + - - -
172B LYS* 1.3 77.0 - - + +
174B ILE* 1.3 62.6 + - - +
176B GLN* 4.8 5.2 - - - -
177B ASP* 2.6 39.3 + - - +
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 3.5 29.6 - - + +
139B GLY* 3.6 26.9 - - - -
140B GLU* 3.6 31.2 - - + +
143B LEU* 3.8 14.6 - - + -
170B GLY 3.6 12.1 - - - +
171B ILE 3.0 8.3 + - - +
173B THR* 1.3 82.1 + - - +
175B LEU* 1.3 65.0 + - + +
177B ASP* 3.9 4.0 - - + +
178B LYS* 3.2 31.4 + - + +
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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
----------------------------------------------------------
139B GLY* 4.9 2.9 - - - +
143B LEU* 4.2 27.6 - - + -
152B ALA* 3.9 15.5 - - + -
154B VAL* 4.9 3.4 - - + -
171B ILE* 3.0 35.7 + - + +
172B LYS* 3.4 3.3 + - + +
174B ILE* 1.3 78.9 - - + +
176B GLN* 1.3 59.8 + - - +
178B LYS 3.3 1.9 + - - -
179B GLY 3.0 3.8 + - - -
180B ILE* 2.8 43.4 + - + +
181B PHE 5.0 0.2 - - - +
182B PHE* 3.7 41.3 - - + -
210B ILE* 6.1 0.4 - - + -
212B PHE* 3.9 20.4 - - + -
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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 LYS 3.0 17.5 + - - +
173B THR* 4.4 4.7 - - - +
175B LEU* 1.3 72.2 - - - +
177B ASP* 1.3 64.5 + - - +
178B LYS 3.0 1.8 - - - -
179B GLY* 2.8 23.1 + - - -
180B ILE 4.4 6.5 - - - -
182B PHE* 4.2 14.8 - - + -
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B THR* 2.6 31.2 + - - +
174B ILE* 3.9 6.3 - - + +
175B LEU 3.4 0.2 - - - -
176B GLN* 1.3 84.0 - - - +
178B LYS* 1.3 66.1 + - + +
179B GLY 3.3 0.4 + - - -
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Residues in contact with LYS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 6.6 0.4 - - - -
143B LEU* 3.3 28.9 - - + -
174B ILE* 3.2 22.9 + - + +
175B LEU 3.9 2.7 - - - +
176B GLN 3.0 0.8 - - - -
177B ASP* 1.3 82.6 - - + +
179B GLY* 1.3 58.5 + - - +
180B ILE* 3.3 13.7 + - + +
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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