Contacts of the helix formed by residues 172 - 185 (chain B) in PDB entry 1TU8
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 PHE 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PRO* 3.4 21.5 - - + -
125B LEU* 3.5 23.6 - - + -
126B ALA* 3.6 23.1 - - + -
129B GLU* 3.3 30.7 - - + +
168B CYS 3.4 20.2 - - - -
169B LEU* 3.0 16.5 + - - +
170B ASP 3.2 0.4 - - - -
171B LYS* 1.3 119.5 - - + +
173B PRO* 1.3 61.4 - - - +
174B LEU 3.3 2.7 - - - -
175B LEU* 3.3 13.8 + - + -
176B LYS* 2.9 23.0 + - - +
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Residues in contact with PRO 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU* 3.2 10.8 - - - +
169B LEU 4.9 0.4 - - - +
170B ASP 4.8 4.0 - - - +
171B LYS 3.3 12.6 - - - +
172B PHE* 1.3 85.6 - - - +
174B LEU* 1.3 61.7 + - + +
176B LYS* 3.8 7.8 - - + +
177B VAL* 2.9 40.1 + - + +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU* 3.0 31.4 + - + +
132B LEU* 3.7 11.2 - - + +
133B ALA* 3.8 32.3 - - + +
137B ASN 3.7 14.6 - - - +
138B GLY* 3.6 24.4 - - - +
139B ARG* 4.1 22.7 - - + +
173B PRO* 1.3 78.2 - - + +
175B LEU* 1.3 61.1 + - - +
177B VAL* 3.5 5.4 + - + +
178B PHE* 2.9 30.0 + - - +
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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
----------------------------------------------------------
125B LEU* 3.5 36.6 - - + +
128B PHE* 3.9 25.6 - - + -
129B GLU* 3.0 23.1 + - - +
132B LEU* 4.1 17.0 - - + -
154B LEU* 4.4 9.0 - - + -
158B LEU* 3.7 35.1 - - + +
169B LEU* 4.1 7.2 - - + -
172B PHE* 3.3 16.6 + - + +
174B LEU* 1.3 72.0 - - - +
176B LYS* 1.3 66.4 + - - +
178B PHE* 3.6 4.2 - - - +
179B HIS* 2.9 25.5 + - - +
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Residues in contact with LYS 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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162B GLN* 5.0 10.5 - - - +
169B LEU* 3.8 34.4 - - + +
170B ASP* 5.2 12.4 + - - +
172B PHE 2.9 16.7 + - - +
173B PRO* 3.8 8.5 - - + +
174B LEU 3.3 0.2 - - - -
175B LEU* 1.3 78.4 - - - +
177B VAL* 1.3 65.3 + - + +
179B HIS* 3.4 4.3 + - - +
180B GLN* 3.2 22.3 + - + +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLY 6.1 0.4 - - - +
139B ARG* 5.2 5.4 - - + +
173B PRO* 2.9 26.9 + - + +
174B LEU* 4.0 4.9 - - + +
176B LYS* 1.3 79.4 - - + +
178B PHE* 1.3 60.9 + - - +
180B GLN* 3.3 5.7 + - + +
181B ARG* 2.9 52.7 + - - +
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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
----------------------------------------------------------
132B LEU* 3.9 20.4 - - + -
138B GLY 5.3 1.1 - - - +
140B ASN 3.6 21.3 - - - +
141B LEU* 4.2 9.2 - - + -
142B ILE* 4.5 1.6 - - + -
151B ASP* 3.4 44.0 - - - -
154B LEU* 3.7 24.2 - - + -
155B PHE* 3.7 20.2 - - - -
158B LEU* 3.7 15.0 - - + -
174B LEU 2.9 19.1 + - - +
175B LEU 3.6 2.7 - - - +
177B VAL* 1.3 74.4 - - - +
179B HIS* 1.3 68.8 + - - +
181B ARG* 3.2 6.9 + - - +
182B MET* 2.9 43.4 + - + +
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Residues in contact with HIS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE* 3.5 22.7 - + - -
158B LEU* 3.9 13.7 - - + +
159B ASP* 2.8 52.4 + - + -
162B GLN* 3.3 28.0 + - - -
169B LEU* 4.4 4.5 - - + -
175B LEU 2.9 18.5 + - - +
176B LYS 3.6 5.8 - - - +
178B PHE* 1.3 84.8 - - - +
180B GLN* 1.3 67.7 + - + +
182B MET 3.3 0.5 + - - -
183B LYS* 3.0 39.9 + - + +
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Residues in contact with GLN 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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176B LYS* 3.2 15.0 + - + +
177B VAL* 3.9 6.7 - - + +
179B HIS* 1.3 83.2 - - + +
181B ARG* 1.3 61.6 + - - +
183B LYS* 3.3 23.7 + - - +
184B ASP* 2.9 67.0 + - - +
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Residues in contact with ARG 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 3.0 28.6 + - - +
140B ASN* 3.4 38.7 + - - +
141B LEU* 4.4 9.4 - - + -
177B VAL* 2.9 40.0 + - + +
178B PHE* 3.4 7.5 - - - +
180B GLN* 1.3 76.1 - - - +
182B MET* 1.3 63.8 + - + +
184B ASP* 3.2 15.7 + - - +
185B ARG* 3.3 18.3 + - + +
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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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141B LEU* 4.0 20.2 - - + -
147B ILE* 4.2 3.1 - - + -
151B ASP* 3.7 28.0 - - + +
152B TYR* 3.6 35.2 - - + -
155B PHE* 3.6 26.2 - - + -
178B PHE* 2.9 41.6 + - + +
181B ARG* 1.3 77.7 - - + +
183B LYS* 1.3 60.5 + - - +
185B ARG* 3.2 34.0 + - - +
188B LEU* 3.5 24.3 - - + +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE* 3.8 19.2 - - + -
159B ASP* 5.0 6.5 + - - +
179B HIS* 3.0 36.3 + - + +
180B GLN* 3.6 24.1 + - - +
182B MET* 1.3 75.9 - - - +
184B ASP* 1.3 59.3 + - - +
188B LEU* 4.8 2.2 - - - -
189B LYS* 3.2 34.8 + - + +
192B CYS* 4.6 21.1 - - + -
196B ASP* 5.4 7.1 + - - -
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Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLN* 2.9 52.4 + - - +
181B ARG* 3.7 9.0 + - - +
182B MET 3.2 0.4 - - - -
183B LYS* 1.3 75.8 - - - +
185B ARG* 1.3 65.6 + - - +
186B PRO* 3.2 8.0 - - - +
189B LYS* 4.4 20.2 + - - +
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Residues in contact with ARG 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP* 3.0 45.7 + - - +
24B GLN* 4.7 2.6 - - - +
141B LEU* 4.1 16.9 - - - +
147B ILE* 3.5 30.1 - - - +
181B ARG* 3.3 15.3 + - + +
182B MET* 3.2 37.1 + - - +
184B ASP* 1.3 75.1 - - - +
186B PRO* 1.3 75.9 - - + +
187B LYS 3.3 1.8 - - - -
188B LEU* 3.1 9.1 + - + -
189B LYS 2.8 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