Contacts of the helix formed by residues 154 - 169 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU* 4.2 26.9 - - + -
76G LEU* 4.1 27.9 - - + +
77G CYS* 4.2 12.3 - - - -
80G ALA* 3.6 20.2 - - + -
85G LEU* 3.1 21.0 + - - +
86G CYS* 4.0 16.4 - - - -
96G VAL* 3.5 26.5 - - + -
100G GLU* 3.2 42.2 - - + -
153G THR* 1.3 69.4 - - - +
155G VAL* 1.3 63.0 + - + +
156G ASP 2.9 4.9 - - - -
157G PHE* 2.7 38.8 + - + +
158G LEU* 3.1 11.4 + - + +
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Residues in contact with VAL 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G VAL* 3.3 43.5 - - + +
99G LEU* 4.3 18.8 - - + +
100G GLU* 4.3 9.0 - - + +
147G PHE* 4.9 6.1 - - + -
148G VAL* 3.6 18.8 - - + -
153G THR* 3.1 25.6 - - - +
154G PHE* 1.3 90.8 - - + +
156G ASP* 1.3 59.0 + - - +
158G LEU* 3.7 9.3 - - + +
159G ALA* 3.0 27.9 + - - +
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Residues in contact with ASP 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G TRP* 3.3 37.7 - - + +
147G PHE* 3.2 27.0 + - - -
148G VAL 4.7 0.2 + - - -
152G ILE* 3.8 7.9 - - + -
153G THR* 2.8 47.0 + - - +
154G PHE 2.8 0.6 + - - -
155G VAL* 1.3 80.5 - - - +
157G PHE* 1.3 61.9 + - - +
159G ALA* 3.5 1.5 + - - -
160G TYR 3.1 17.7 + - - -
183G PHE* 3.5 17.9 - - + -
187G PHE* 3.4 11.6 - - + -
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Residues in contact with PHE 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ALA* 4.3 16.0 - - + +
18G LEU* 3.6 18.4 - - + +
19G LEU* 3.5 43.5 - - + -
22G TYR* 3.6 32.5 - + + -
76G LEU* 6.0 1.8 - - + -
85G LEU* 3.7 18.2 - - + -
152G ILE* 4.1 15.0 - - + -
153G THR 3.2 20.0 - - - -
154G PHE* 2.7 21.1 + - + +
156G ASP* 1.3 71.4 - - - +
158G LEU* 1.3 64.2 + - - +
160G TYR* 3.5 3.6 + - - +
161G ASP* 3.2 20.3 + - - +
187G PHE* 3.4 30.7 - + + -
193G ILE* 4.1 4.9 - - + -
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Residues in contact with LEU 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ALA* 4.3 12.3 - - + +
73G ASN* 4.1 18.2 - - - +
76G LEU* 4.3 18.4 - - + -
99G LEU 4.4 0.7 - - - +
100G GLU* 4.1 33.9 - - + +
103G ALA* 3.6 21.3 - - + -
104G MET* 4.5 17.9 - - + +
107G SER* 5.1 1.8 - - - +
154G PHE* 3.1 8.8 + - + +
155G VAL* 3.7 14.4 - - - +
157G PHE* 1.3 79.4 - - - +
159G ALA* 1.3 57.7 + - - +
161G ASP* 2.8 26.5 + - + +
162G VAL* 3.0 17.9 + - + +
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Residues in contact with ALA 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G LEU* 4.1 13.7 - - + -
103G ALA* 4.9 1.5 - - - +
137G PHE* 6.1 1.6 - - + -
147G PHE* 3.5 35.2 - - + -
155G VAL 3.0 16.7 + - - +
156G ASP 3.7 4.5 - - - +
157G PHE 3.4 0.2 - - - -
158G LEU* 1.3 78.1 - - - +
160G TYR* 1.3 57.8 + - - +
162G VAL* 3.2 10.4 + - - +
163G LEU* 3.0 34.2 + - + +
183G PHE* 4.1 1.6 - - + -
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Residues in contact with TYR 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G HIS* 4.7 9.2 - - - -
18G LEU* 3.7 18.2 - - + -
156G ASP 3.1 17.9 + - - +
157G PHE 3.7 2.7 - - - +
159G ALA* 1.3 75.6 - - - +
161G ASP* 1.3 53.9 + - - +
163G LEU* 3.3 3.0 + - - +
164G ASP* 2.8 48.5 + - + +
167G ARG* 4.0 8.7 + - - -
183G PHE* 3.8 9.8 - + + -
184G ILE* 4.2 22.4 - - + -
187G PHE* 3.4 46.2 - + + -
188G GLU* 3.2 33.4 + - + -
197G MET* 3.1 29.9 - - + +
202G PHE* 5.5 0.6 - + - -
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Residues in contact with ASP 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ARG* 2.9 29.8 + - - -
11G GLY 4.8 4.3 - - - +
12G LEU* 5.3 4.5 - - - -
14G HIS* 3.3 30.0 - - + +
15G ALA* 4.4 11.6 + - + +
18G LEU* 5.5 0.2 - - + -
107G SER* 5.5 2.4 + - - -
157G PHE 3.2 12.2 + - - +
158G LEU* 2.8 17.9 + - + +
160G TYR* 1.3 75.8 - - - +
162G VAL* 1.3 66.9 + - + +
164G ASP* 3.1 11.2 + - - +
165G LEU* 3.1 30.1 + - - +
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Residues in contact with VAL 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G ALA* 3.5 39.9 - - + +
106G VAL* 3.5 21.3 - - + -
107G SER* 3.8 13.0 - - - +
134G MET* 5.5 1.8 - - + -
137G PHE* 4.2 17.9 - - + -
158G LEU* 3.0 16.5 + - + +
159G ALA* 3.4 10.3 - - - +
161G ASP* 1.3 79.5 - - + +
163G LEU* 1.3 66.5 + - + +
165G LEU* 4.1 6.8 + - - +
166G HIS* 2.8 38.3 + - + +
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Residues in contact with LEU 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G MET* 3.4 30.1 - - + -
137G PHE* 5.0 6.5 - - + -
147G PHE* 5.1 4.5 - - + -
159G ALA* 3.0 19.7 + - + +
160G TYR* 3.8 3.6 - - - +
162G VAL* 1.3 78.9 - - + +
164G ASP* 1.3 68.0 + - - +
166G HIS* 3.8 4.1 - - - +
167G ARG* 3.1 25.6 + - - +
174G LEU* 3.7 13.7 - - + +
180G LEU* 4.3 24.7 - - + +
183G PHE* 3.7 22.9 - - + -
184G ILE* 3.3 33.9 - - + -
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Residues in contact with ASP 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ARG* 3.0 28.0 + - - +
14G HIS* 4.4 5.5 + - - +
160G TYR* 2.8 34.2 + - + +
161G ASP* 3.1 8.5 + - - +
163G LEU* 1.3 79.7 - - - +
165G LEU* 1.3 63.3 + - - +
167G ARG* 2.6 54.7 + - - +
168G ILE* 3.4 21.9 + - - +
202G PHE* 6.1 0.5 - - - -
204G PRO* 4.9 3.3 - - - +
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Residues in contact with LEU 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ARG* 3.1 35.0 - - - +
107G SER* 5.5 11.7 - - - +
110G LEU* 3.6 28.7 - - + -
161G ASP* 3.1 35.4 - - - +
162G VAL* 4.2 9.0 - - - +
164G ASP* 1.3 76.7 - - - +
166G HIS* 1.3 59.8 + - + +
168G ILE* 3.4 12.0 + - - +
169G PHE* 3.0 27.6 + - - +
207G LEU* 3.9 19.3 - - + -
208G TYR* 3.9 12.3 - - + +
214G TRP* 4.5 4.6 - - + -
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Residues in contact with HIS 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G VAL* 4.7 10.1 - - + -
107G SER* 5.9 0.9 - - - -
110G LEU* 3.9 25.6 - - + +
126G TYR* 2.9 35.5 + + - -
130G LEU* 3.5 33.0 - - + +
133G MET* 4.8 1.9 - - - -
134G MET* 5.1 9.9 - - + -
162G VAL* 2.8 39.3 + - + +
163G LEU* 3.5 7.4 + - - +
164G ASP 3.1 1.2 - - - -
165G LEU* 1.3 80.3 - - + +
167G ARG* 1.3 58.0 + - - +
169G PHE* 3.4 6.3 - + + +
170G GLU* 2.8 31.7 + - - +
173G CYS* 3.6 13.8 - - - -
174G LEU* 5.5 0.2 - - + -
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Residues in contact with ARG 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G TYR* 4.0 9.9 + - - -
163G LEU 3.1 9.5 + - - +
164G ASP* 2.6 58.3 + - - +
166G HIS* 1.3 76.1 - - - +
168G ILE* 1.3 64.2 + - + +
170G GLU 4.0 7.4 - - - -
171G PRO* 2.9 36.4 - - + +
173G CYS* 4.2 1.5 - - - -
174G LEU* 4.0 25.1 - - + -
181G LYS* 6.1 5.1 - - - +
184G ILE* 4.3 15.2 - - - +
188G GLU* 3.2 26.8 + - - -
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Residues in contact with ILE 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G ASP* 3.4 33.0 - - - +
165G LEU* 3.4 7.6 + - - +
166G HIS 3.2 0.4 - - - -
167G ARG* 1.3 82.5 - - + +
169G PHE* 1.3 68.2 + - - +
171G PRO* 4.1 5.0 - - - +
204G PRO 5.5 2.7 - - - +
205G LYS* 4.8 18.4 - - + +
207G LEU* 4.4 21.8 - - + -
214G TRP* 4.9 11.9 - - + -
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Residues in contact with PHE 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G LEU* 3.6 33.0 - - + -
113G VAL* 5.6 4.0 - - + -
114G CYS* 3.7 17.0 - - - -
119G PHE* 4.3 6.7 - + - -
123G LYS* 3.6 44.9 + - + -
126G TYR* 4.8 12.6 - + + -
127G LEU* 4.3 11.4 - - + -
130G LEU* 5.3 5.4 - - + -
165G LEU 3.0 16.9 + - - +
166G HIS* 3.4 11.9 - + + +
168G ILE* 1.3 81.2 - - - +
170G GLU* 1.3 68.6 + - + +
171G PRO* 3.5 4.3 - - - +
214G TRP* 3.5 39.0 - + - +
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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