Contacts of the helix formed by residues 154 - 169 (chain B) in PDB entry 4GTU
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 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.1 17.3 - - + -
73B ASN* 5.4 1.8 - - - -
76B LEU* 3.9 26.3 - - + +
77B CYS* 4.1 24.2 - - - -
80B ALA* 4.0 20.9 - - + -
85B LEU* 2.9 34.2 + - - +
86B CYS* 4.3 13.5 - - - -
96B VAL* 3.2 36.1 - - + -
100B GLU* 4.6 14.4 - - + -
153B THR* 1.3 72.7 - - - +
155B VAL* 1.3 69.8 + - + +
157B PHE* 2.9 36.5 + - - +
158B LEU* 3.4 16.0 + - + +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.4 50.7 - - + +
99B LEU* 4.0 22.8 - - + +
100B GLU* 4.1 13.0 - - - +
147B PHE* 5.4 0.2 - - + -
148B VAL* 4.8 5.8 - - + -
153B THR* 2.9 27.6 - - - +
154B PHE* 1.3 90.9 - - + +
156B ASP* 1.3 59.0 + - - +
158B LEU* 3.1 11.2 + - + +
159B ALA* 2.8 29.2 + - - +
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TRP* 3.3 25.1 - - + +
147B PHE* 3.0 32.1 + - - +
148B VAL* 4.4 1.1 - - - +
151B LYS 3.9 0.5 - - - +
152B ILE* 3.3 23.1 - - + -
153B THR* 3.0 32.3 + - - +
155B VAL* 1.3 78.3 - - - +
157B PHE* 1.3 58.7 + - - +
159B ALA* 3.9 3.1 - - - -
160B TYR* 3.4 7.3 + - - +
183B PHE* 3.2 36.7 - - + -
187B PHE* 3.6 9.3 - - + -
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 4.4 15.0 - - + +
18B LEU* 3.8 18.1 - - + +
19B LEU* 3.7 39.9 - - + -
22B TYR* 3.4 46.0 - + + -
76B LEU* 5.3 3.1 - - + -
85B LEU* 4.5 2.2 - - + -
152B ILE* 4.0 11.2 - - + -
153B THR 3.3 21.1 - - - -
154B PHE* 2.9 16.9 + - - +
156B ASP* 1.3 77.7 - - - +
158B LEU* 1.3 62.3 + - - +
160B TYR* 3.2 12.3 + - - +
161B ASP* 3.2 16.7 + - - +
187B PHE* 3.1 37.7 - + - -
193B ILE* 5.4 0.9 - - + -
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 4.6 11.6 - - + +
73B ASN* 4.6 4.9 - - - +
76B LEU* 3.9 30.1 - - + -
99B LEU* 4.9 0.9 - - + +
100B GLU* 4.0 32.1 - - - +
103B ALA* 3.9 17.3 - - + +
104B MET* 3.9 26.9 - - - -
107B SER* 6.0 1.3 - - - +
154B PHE* 3.4 17.8 + - + +
155B VAL* 3.1 13.4 + - + +
157B PHE* 1.3 78.9 - - - +
159B ALA* 1.3 61.8 + - - +
161B ASP* 4.0 7.0 - - - +
162B VAL* 3.2 26.9 + - - +
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.8 5.8 - - + -
103B ALA* 5.5 2.2 - - - -
147B PHE* 3.8 42.0 - - + -
155B VAL 2.8 15.7 + - - +
156B ASP 4.0 2.0 - - - +
158B LEU* 1.3 76.9 - - - +
160B TYR* 1.3 61.6 + - - +
162B VAL* 3.3 9.0 - - - +
163B LEU* 2.8 32.8 + - + +
183B PHE* 3.9 7.2 - - + -
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Residues in contact with TYR 160 (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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10B ARG* 6.0 0.2 - - - -
14B HIS* 5.2 7.9 - + - -
18B LEU* 4.2 20.0 - - + -
156B ASP 3.4 7.3 + - - +
157B PHE 3.2 9.2 + - - +
159B ALA* 1.3 78.3 - - - +
161B ASP* 1.3 64.7 + - - +
163B LEU* 3.0 7.9 + - - +
164B ASP* 2.9 51.0 + - + +
183B PHE* 3.7 8.5 - + + -
184B ILE* 3.3 31.1 - - + +
187B PHE* 3.3 51.6 - + + -
188B GLU* 2.9 24.9 + - + +
193B ILE* 6.3 0.2 - - + -
197B MET* 3.7 15.1 - - + +
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG* 3.1 36.6 + - - +
11B GLY 5.4 0.4 - - - -
12B LEU* 6.1 0.7 - - - -
14B HIS* 3.7 16.3 - - + +
15B ALA* 4.6 17.6 + - + +
18B LEU* 4.9 8.5 - - + -
107B SER* 5.0 4.5 + - - -
157B PHE 3.2 13.1 + - - +
158B LEU* 4.0 6.9 - - - +
160B TYR* 1.3 87.2 - - + +
162B VAL* 1.3 59.2 + - - +
164B ASP* 3.1 4.4 + - - +
165B LEU* 3.0 40.0 + - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA* 4.1 6.7 - - + +
106B VAL* 3.3 25.4 - - + -
107B SER* 3.3 30.7 - - - +
137B PHE* 4.1 26.5 - - + -
158B LEU 3.2 15.0 + - - +
159B ALA* 3.3 16.4 - - - +
161B ASP* 1.3 78.8 - - - +
163B LEU* 1.3 64.9 + - + +
165B LEU* 3.7 12.8 - - + +
166B HIS* 3.4 30.4 + - + +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B MET* 4.5 10.5 - - + -
137B PHE* 3.9 31.4 - - + -
147B PHE* 4.5 11.4 - - + -
159B ALA* 2.8 25.3 + - - +
160B TYR 3.0 7.9 + - - +
162B VAL* 1.3 76.9 - - + +
164B ASP* 1.3 58.5 + - - +
165B LEU 3.4 0.2 + - - -
166B HIS* 3.5 5.2 + - - +
167B ARG* 3.0 27.8 + - - +
174B LEU* 4.4 10.6 - - + +
180B LEU* 4.4 23.8 - - + +
183B PHE* 3.7 29.2 - - + -
184B ILE* 3.6 22.9 - - + -
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Residues in contact with ASP 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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10B ARG* 3.9 16.1 + - - +
160B TYR* 2.9 37.5 + - + +
161B ASP 3.1 6.7 + - - +
163B LEU* 1.3 74.5 - - - +
165B LEU* 1.3 65.8 + - - +
167B ARG* 3.0 38.3 + - - +
168B ILE* 3.2 42.3 + - - +
184B ILE* 4.5 1.5 - - + +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG* 3.1 38.1 - - - +
107B SER* 4.6 13.7 - - - +
110B LEU* 4.2 20.6 - - + +
161B ASP* 3.0 27.8 + - - +
162B VAL* 3.7 24.0 - - + +
163B LEU 3.2 0.2 - - - -
164B ASP* 1.3 80.1 - - - +
166B HIS* 1.3 58.7 + - - +
168B ILE* 3.4 3.8 + - - +
169B PHE* 3.0 26.6 + - - +
207B LEU* 4.4 19.9 - - + +
208B TYR* 5.4 8.5 - - + +
214B TRP* 4.7 4.3 - - - -
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Residues in contact with HIS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 4.6 16.8 - - + -
110B LEU* 3.5 25.1 - - + +
126B TYR* 2.6 41.5 + + - -
130B LEU* 4.0 14.3 - - + +
133B MET* 3.9 8.5 - - - -
134B MET* 3.3 33.1 - - + +
162B VAL* 3.4 16.3 + - + +
163B LEU 3.5 6.8 + - - +
164B ASP 3.4 0.2 - - - -
165B LEU* 1.3 76.5 - - - +
167B ARG* 1.3 57.8 + - - +
169B PHE* 3.5 7.3 - + - +
170B GLU* 2.7 37.4 + - - +
173B CYS* 3.8 11.4 - - - -
174B LEU* 5.8 0.2 - - + -
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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
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160B TYR* 4.5 0.2 + - - -
163B LEU 3.0 17.5 + - - +
164B ASP* 3.0 37.5 + - - +
166B HIS* 1.3 78.6 - - - +
168B ILE* 1.3 62.7 + - + +
171B PRO* 2.9 33.9 - - + +
173B CYS* 4.1 2.9 - - - -
174B LEU* 3.7 23.8 - - + +
184B ILE* 2.9 42.6 + - - +
188B GLU* 3.8 13.1 + - - -
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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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10B ARG* 5.4 3.1 - - - +
164B ASP* 3.2 32.7 + - - +
165B LEU* 4.0 3.4 - - - +
166B HIS 3.2 0.2 - - - -
167B ARG* 1.3 84.5 - - + +
169B PHE* 1.3 68.0 + - - +
170B GLU 3.3 0.2 - - - -
171B PRO* 4.0 5.9 - - - +
204B PRO* 6.5 0.4 - - + -
205B LYS* 4.5 31.2 - - + +
207B LEU* 5.1 15.9 - - + -
214B TRP* 4.6 13.1 - - + -
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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
----------------------------------------------------------
110B LEU* 3.9 27.6 - - + -
113B VAL* 5.6 3.8 - - + -
114B CYS* 5.2 0.7 - - - -
119B PHE* 3.9 30.1 - + - -
123B LYS* 4.0 28.2 + - + -
126B TYR* 4.2 12.8 - + + -
127B LEU* 4.0 28.0 - - + -
130B LEU* 5.2 1.6 - - + -
165B LEU 3.0 17.3 + - - +
166B HIS* 3.5 12.8 - + + +
168B ILE* 1.3 80.7 - - - +
170B GLU* 1.3 65.7 + - + +
171B PRO* 4.0 2.1 - - - +
214B TRP* 3.3 47.3 - + + -
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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
------------------------------------------------------------
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