Contacts of the helix formed by residues 154 - 169 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.2 21.1 - - + -
73C ASN* 5.1 1.6 - - - -
76C LEU* 3.8 36.5 - - + +
77C CYS* 4.4 23.8 - - - -
80C ALA* 3.8 18.8 - - + -
85C LEU* 3.0 35.2 + - + +
86C CYS* 4.4 8.5 - - + -
96C VAL* 3.5 31.2 - - + -
100C GLU* 4.3 20.6 - - + -
153C THR* 1.3 70.8 - - - +
155C VAL* 1.3 69.0 + - + +
157C PHE* 2.8 37.9 + - - +
158C LEU* 3.5 6.9 + - + +
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Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C VAL* 3.2 45.1 - - + +
99C LEU* 3.7 23.1 - - + +
100C GLU* 4.2 9.4 - - - +
148C VAL* 3.5 17.9 - - + -
153C THR* 3.2 21.8 - - - +
154C PHE* 1.3 89.1 - - + +
156C ASP* 1.3 62.3 + - - +
158C LEU* 3.2 10.0 + - - +
159C ALA* 2.9 30.2 + - - +
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Residues in contact with ASP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C TRP* 3.5 32.3 - - + +
147C PHE* 3.1 29.1 + - - -
148C VAL 5.0 0.5 + - - -
151C LYS 4.1 0.2 - - - +
152C ILE* 3.9 3.0 - - + -
153C THR* 3.2 37.1 + - - +
154C PHE 3.0 0.8 + - - -
155C VAL* 1.3 78.1 - - - +
157C PHE* 1.3 59.1 + - + +
159C ALA* 4.0 2.7 - - - -
160C TYR* 3.1 28.4 + - - +
183C PHE* 3.5 22.1 - - + -
187C PHE* 3.7 12.4 - - + -
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Residues in contact with PHE 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA* 4.6 13.1 - - + +
18C LEU* 3.6 46.0 - - + +
19C LEU* 3.7 19.1 - - + -
22C TYR* 3.5 40.6 - + + -
76C LEU* 5.6 2.5 - - + -
85C LEU* 4.9 0.4 - - + -
152C ILE* 4.1 17.0 - - + -
153C THR 3.4 19.1 - - - -
154C PHE* 2.8 26.3 + - + +
156C ASP* 1.3 77.5 - - - +
158C LEU* 1.3 63.8 + - + +
160C TYR* 3.5 3.6 + - - +
161C ASP* 3.2 22.3 + - - +
187C PHE* 3.3 30.5 - + - -
193C ILE* 4.6 4.3 - - + -
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA* 3.9 14.4 - - + -
73C ASN* 3.9 14.4 - - - +
76C LEU* 3.7 33.0 - - + -
99C LEU 6.0 0.7 - - - -
100C GLU* 4.1 30.3 - - + +
103C ALA* 4.4 12.3 - - + -
104C MET* 4.1 19.7 - - + +
154C PHE* 3.5 8.0 + - + +
155C VAL* 3.2 15.3 + - - +
157C PHE* 1.3 78.6 - - - +
159C ALA* 1.3 57.3 + - - +
161C ASP* 3.0 11.2 + - + +
162C VAL* 2.8 35.9 + - + +
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Residues in contact with ALA 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 5.2 8.5 - - + -
103C ALA* 4.8 4.9 - - + +
137C PHE* 6.0 4.5 - - + -
147C PHE* 3.5 38.1 - - + -
155C VAL 2.9 17.3 + - - +
156C ASP 4.1 2.9 - - - +
158C LEU* 1.3 76.9 - - - +
160C TYR* 1.3 56.3 + - - +
162C VAL* 3.2 8.0 + - - +
163C LEU* 2.9 38.9 + - + +
183C PHE* 4.4 0.4 - - + -
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Residues in contact with TYR 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C HIS* 4.3 17.7 - - - -
18C LEU* 4.0 13.9 - - + -
156C ASP 3.1 20.5 + - - +
157C PHE 3.8 2.9 - - - +
159C ALA* 1.3 74.5 - - - +
161C ASP* 1.3 58.5 + - - +
163C LEU* 4.8 2.2 - - - -
164C ASP* 2.8 56.4 + - + +
183C PHE* 4.1 11.6 - - + -
184C ILE* 3.6 26.1 - - + +
187C PHE* 3.2 39.0 - + + -
188C GLU* 3.1 41.2 + - + -
197C MET* 3.6 19.2 - - + +
202C PHE* 5.4 2.4 - - - -
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Residues in contact with ASP 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ARG* 2.8 31.7 + - - -
11C GLY 4.6 9.2 - - - +
14C HIS* 3.0 27.9 - - + +
15C ALA* 4.8 9.4 + - + +
18C LEU* 5.0 0.4 - - + -
107C SER* 5.2 4.9 + - - -
157C PHE 3.2 10.3 + - - +
158C LEU* 3.0 13.4 + - - +
160C TYR* 1.3 83.1 - - + +
162C VAL* 1.3 68.0 + - - +
164C ASP* 3.9 2.2 - - - +
165C LEU* 3.1 33.2 + - - +
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Residues in contact with VAL 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ALA* 3.5 35.7 - - + +
106C VAL* 3.5 26.7 - - + -
107C SER* 4.5 13.0 - - - +
137C PHE* 4.2 17.3 - - + -
158C LEU* 2.8 20.8 + - + +
159C ALA* 3.5 9.0 - - - +
161C ASP* 1.3 80.9 - - + +
163C LEU* 1.3 63.9 + - + +
165C LEU* 3.9 5.1 + - - +
166C HIS* 3.2 36.1 + - + +
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Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C MET* 3.4 31.0 - - + -
137C PHE* 3.8 26.2 - - + -
147C PHE* 4.5 6.7 - - + -
159C ALA* 2.9 22.5 + - + +
160C TYR 4.2 2.0 - - - +
162C VAL* 1.3 78.0 - - + +
164C ASP* 1.3 65.7 + - - +
166C HIS* 3.1 16.9 + - - +
167C ARG* 3.2 14.8 + - - +
174C LEU* 4.3 13.6 - - + +
180C LEU* 3.9 29.4 - - + -
183C PHE* 4.1 24.7 - - + -
184C ILE* 4.2 9.9 - - + -
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Residues in contact with ASP 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ARG* 3.3 27.2 + - - +
14C HIS* 5.2 0.7 + - - -
160C TYR* 2.8 45.1 + - + +
161C ASP 3.3 4.0 + - - +
163C LEU* 1.3 70.3 - - - +
165C LEU* 1.3 66.8 + - - +
167C ARG* 2.7 65.0 + - - +
168C ILE* 3.5 12.9 + - - +
184C ILE* 4.0 2.2 - - + +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ARG* 3.4 37.2 - - - +
107C SER* 4.8 11.7 - - - +
110C LEU* 4.1 14.4 - - + -
161C ASP* 3.1 25.6 + - - +
162C VAL* 4.2 5.8 - - - +
164C ASP* 1.3 75.3 - - - +
166C HIS* 1.3 58.3 + - - +
168C ILE* 2.9 25.8 + - + +
169C PHE* 3.0 13.4 + - - +
207C LEU* 4.1 33.8 - - + +
208C TYR* 4.0 24.7 - - + +
214C TRP* 5.3 1.8 - - + -
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Residues in contact with HIS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL* 4.1 15.2 - - + +
107C SER* 5.7 0.7 - - - -
110C LEU* 3.2 34.9 - - + +
126C TYR* 2.6 27.5 + + - -
130C LEU* 3.5 28.0 - - + +
134C MET* 3.6 17.3 - - + -
162C VAL* 3.2 20.8 + - + +
163C LEU* 3.1 13.6 + - - +
164C ASP 3.1 0.4 - - - -
165C LEU* 1.3 76.4 - - - +
167C ARG* 1.3 51.7 + - - +
169C PHE* 3.5 6.4 - + + +
170C GLU* 2.7 38.9 + - - +
173C CYS* 4.5 13.0 - - - -
174C LEU* 5.0 0.2 - - + -
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Residues in contact with ARG 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C TYR* 4.7 0.2 + - - -
163C LEU 3.2 7.8 + - - +
164C ASP* 2.7 67.1 + - - +
166C HIS* 1.3 75.2 - - - +
168C ILE* 1.3 61.2 + - + +
170C GLU 4.2 0.2 - - - -
171C PRO* 3.1 43.4 - - + +
173C CYS* 5.3 1.1 - - - -
174C LEU* 4.7 12.0 - - + +
181C LYS* 5.8 4.8 - - - +
184C ILE* 3.3 41.3 - - - +
188C GLU* 3.5 22.6 + - - -
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Residues in contact with ILE 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG* 4.9 4.0 - - - +
164C ASP* 3.5 27.8 - - - +
165C LEU* 2.9 12.4 + - - +
167C ARG* 1.3 82.2 - - + +
169C PHE* 1.3 66.0 + - - +
171C PRO* 4.2 4.3 - - - +
204C PRO 5.4 0.2 - - - +
205C LYS* 5.9 6.1 - - - +
207C LEU* 3.9 43.7 - - + -
214C TRP* 4.1 12.1 - - + -
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Residues in contact with PHE 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 3.7 30.7 - - + -
113C VAL* 4.7 2.0 - - + -
114C CYS* 4.0 5.2 - - - -
119C PHE* 3.6 37.0 - + - -
123C LYS* 3.9 23.6 - - + -
126C TYR* 4.2 18.8 - + - -
127C LEU* 3.6 29.2 - - + -
130C LEU* 5.7 1.6 - - + -
165C LEU 3.0 11.3 + - - +
166C HIS* 3.5 13.0 - + + +
168C ILE* 1.3 80.5 - - - +
170C GLU* 1.3 63.3 + - + +
171C PRO* 3.8 3.9 - - - +
214C TRP* 3.6 32.4 - + + -
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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