Contacts of the helix formed by residues 166 - 180 (chain B) in PDB entry 3T06
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 GLY 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B MET* 4.3 3.4 - - - +
158B GLU 4.2 6.7 - - - -
159B CYS* 3.7 8.1 - - - -
164B LYS 3.2 2.6 + - - -
165B ASP* 1.3 77.1 + - - +
167B VAL* 1.3 61.9 + - - +
168B ARG 3.6 0.9 - - - -
169B GLU* 3.3 30.6 + - - +
170B VAL* 2.9 31.2 + - - +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.6 28.5 - - + -
24B VAL* 3.9 20.0 - - + -
25B ASN* 3.7 33.0 - - + +
159B CYS* 4.4 4.3 - - + -
160B SER 4.0 18.6 - - - +
161B ALA* 4.4 2.2 - - - -
164B LYS* 3.4 18.9 + - + +
165B ASP 3.3 0.4 - - - -
166B GLY* 1.3 73.8 - - - +
168B ARG* 1.3 61.3 + - - +
170B VAL* 2.7 33.2 + - - +
171B PHE* 3.2 7.9 + - + -
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Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASN* 4.6 9.4 - - - +
28B ASP* 5.6 7.4 - - - +
46B ILE* 5.5 0.3 - - - +
164B LYS 4.7 2.1 + - - +
167B VAL* 1.3 80.2 - - - +
169B GLU* 1.3 96.4 + - - +
170B VAL 3.2 0.2 + - - -
171B PHE* 3.3 2.1 + - - +
172B GLU* 3.1 54.0 + - + +
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Residues in contact with GLU 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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157B MET* 4.2 16.2 - - - -
164B LYS 5.0 0.9 - - - +
165B ASP* 5.0 3.8 - - - +
166B GLY* 3.3 33.8 + - - +
167B VAL 3.0 1.2 + - - -
168B ARG* 1.3 118.3 + - - +
170B VAL* 1.3 61.5 + - - +
172B GLU* 3.7 12.9 + - - +
173B MET* 3.2 24.1 + - - +
176B ARG* 4.5 3.2 + - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 5.0 4.7 - - + -
81B LEU* 3.9 19.3 - - + -
113B ILE* 4.2 3.3 - - + +
115B VAL* 3.6 28.9 - - + -
157B MET* 3.1 30.1 - - + +
159B CYS* 4.1 15.9 - - + -
166B GLY 2.9 25.5 + - - +
167B VAL* 2.7 18.9 + - - +
169B GLU* 1.3 69.4 - - - +
171B PHE* 1.3 70.4 + - + +
173B MET* 3.4 5.3 + - - +
174B ALA* 3.1 20.1 + - - +
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.8 22.9 - - + -
21B LEU* 4.2 17.5 - - + -
22B LEU* 3.9 21.1 - - + -
25B ASN* 3.2 50.7 - - + +
46B ILE* 3.9 15.3 - - + -
55B LEU* 4.7 3.8 - - + +
57B LEU* 3.8 24.7 - - + -
81B LEU* 4.0 13.5 - - + -
167B VAL* 3.2 21.6 + - + -
168B ARG 4.1 2.7 - - - +
170B VAL* 1.3 78.5 - - + +
172B GLU* 1.3 67.5 + - - +
174B ALA* 3.0 4.8 + - - +
175B THR* 2.9 27.4 + - - +
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 4.0 13.9 - - + +
47B GLU 4.8 3.8 - - - +
48B VAL* 4.1 21.9 - - + +
168B ARG* 3.1 52.6 + - + +
169B GLU* 3.8 10.3 - - - +
171B PHE* 1.3 76.9 - - - +
173B MET* 1.3 62.9 + - - +
175B THR* 3.4 1.6 + - - -
176B ARG* 2.9 47.2 + - - +
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Residues in contact with MET 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.0 17.7 - - + -
154B PHE* 3.9 16.2 - - + -
155B GLY* 3.7 29.8 - - - -
156B TYR 4.3 4.5 - - - +
157B MET* 3.4 43.5 - - + -
169B GLU 3.2 8.7 + - - +
170B VAL 3.6 7.4 - - - +
171B PHE 3.2 0.4 - - - -
172B GLU* 1.3 78.9 - - - +
174B ALA* 1.3 57.0 + - - +
176B ARG* 3.2 27.7 + - - +
177B ALA* 2.8 27.4 + - - +
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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
----------------------------------------------------------
8B LEU* 3.9 27.4 - - + -
55B LEU* 5.6 0.2 - - - -
79B VAL* 3.6 26.8 - - + +
81B LEU* 4.2 12.3 - - + -
113B ILE* 4.4 4.5 - - + -
170B VAL 3.1 11.6 + - - +
171B PHE* 3.0 9.5 + - - +
173B MET* 1.3 78.6 - - - +
175B THR* 1.3 58.9 + - - +
177B ALA* 3.1 7.3 - - - +
178B ALA 2.8 23.0 + - - -
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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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46B ILE* 3.4 28.3 - - + +
48B VAL* 3.8 15.9 - - + -
53B VAL* 3.5 37.9 - - + -
55B LEU* 3.7 15.1 - - + +
79B VAL* 5.4 0.2 - - - -
171B PHE 2.9 16.3 + - - -
172B GLU 3.7 3.4 - - - -
174B ALA* 1.3 72.9 - - - +
176B ARG* 1.3 66.9 + - - +
177B ALA 3.0 1.3 - - - -
178B ALA* 3.0 17.0 + - + +
179B LEU* 3.1 15.7 + - + +
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Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 4.6 10.4 - - + +
49B ASP* 4.2 28.6 + - - +
154B PHE* 4.3 14.3 - - + -
169B GLU* 4.5 3.8 + - - +
172B GLU* 2.9 48.1 + - - +
173B MET* 3.4 41.0 - - - +
175B THR* 1.3 73.2 - - - +
177B ALA* 1.3 62.2 + - - +
179B LEU* 3.5 11.0 + - + +
180B GLN* 3.3 19.9 + - - +
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 3.9 14.6 - - + -
111B PRO* 3.8 21.0 - - + +
113B ILE* 4.2 2.9 - - + -
154B PHE* 3.8 31.9 - - + -
173B MET 2.8 13.2 + - - +
174B ALA* 3.1 15.3 - - - +
175B THR 3.0 0.2 - - - -
176B ARG* 1.3 75.1 - - - +
178B ALA* 1.3 64.7 + - - +
180B GLN* 3.4 16.3 + - - +
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Residues in contact with ALA 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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6B LYS* 3.6 49.8 + - + -
55B LEU* 5.2 0.7 - - + -
78B ASP* 3.9 21.2 - - + +
79B VAL* 4.2 9.5 - - + +
174B ALA 2.8 15.6 + - - +
175B THR* 3.0 11.2 + - + +
177B ALA* 1.3 75.4 - - - +
179B LEU* 1.3 64.2 + - + +
180B GLN 3.6 5.5 - - - +
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Residues in contact with LEU 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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4B ILE* 4.4 27.6 - - + -
6B LYS* 4.9 9.3 + - + +
48B VAL* 3.6 31.2 - - + +
49B ASP* 5.8 3.4 - - + +
51B LYS* 4.5 21.1 - - + -
53B VAL* 4.2 18.4 - - + -
175B THR* 3.1 15.5 + - + +
176B ARG* 3.8 9.4 - - + +
178B ALA* 1.3 74.8 - - + +
180B GLN* 1.3 72.0 + - - +
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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
----------------------------------------------------------
111B PRO* 5.6 4.0 - - - +
154B PHE* 4.2 27.2 - - + -
176B ARG 3.3 11.4 + - - +
177B ALA 3.6 14.5 - - - +
178B ALA 3.4 7.6 - - - +
179B LEU* 1.3 87.6 - - - +
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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