Contacts of the helix formed by residues 154 - 169 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.2 17.5 - - + -
76D LEU* 4.2 19.3 - - + +
77D CYS* 4.0 19.1 - - - -
80D ALA* 3.5 31.6 - - + -
85D LEU* 3.0 18.0 + - - +
86D CYS* 3.9 22.7 - - + -
96D VAL* 3.3 28.3 - - + -
100D GLU* 3.4 30.1 - - + -
153D THR* 1.3 70.4 - - - +
155D VAL* 1.3 68.6 + - + +
157D PHE* 3.0 35.4 + - - +
158D LEU* 3.6 11.7 + - + +
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ARG 5.0 0.7 - - - +
96D VAL* 3.3 52.7 - - + +
99D LEU* 3.7 22.8 - - + +
100D GLU* 3.9 13.0 - - + +
147D PHE* 4.8 11.0 - - + -
148D VAL* 5.0 1.8 - - + -
153D THR* 2.9 24.8 + - - +
154D PHE* 1.3 88.3 - - + +
156D ASP* 1.3 57.7 + - - +
157D PHE 3.1 0.4 - - - -
158D LEU* 3.4 6.8 + - - +
159D ALA* 3.0 28.9 + - - +
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Residues in contact with ASP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D TRP* 3.1 32.3 - - + +
147D PHE* 3.1 26.2 + - - -
152D ILE* 3.4 11.6 - - + -
153D THR* 2.8 39.5 + - - +
155D VAL* 1.3 79.0 - - - +
157D PHE* 1.3 57.9 + - + +
159D ALA* 4.4 0.4 - - - -
160D TYR* 3.1 26.3 + - - +
183D PHE* 3.1 25.3 - - + -
187D PHE* 3.6 10.4 - - + -
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Residues in contact with PHE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA* 4.4 15.9 - - + +
18D LEU* 3.5 21.9 - - + +
19D LEU* 3.4 49.6 - - + -
22D TYR* 3.5 36.6 - + + -
76D LEU* 5.8 2.0 - - + -
85D LEU* 5.5 2.7 - - + -
152D ILE* 3.7 24.5 - - + -
153D THR 4.0 8.5 - - - -
154D PHE* 3.0 18.7 + - - +
156D ASP* 1.3 78.4 - - - +
158D LEU* 1.3 64.1 + - + +
160D TYR* 3.5 3.6 + - - +
161D ASP* 3.2 22.2 + - - +
187D PHE* 3.4 27.4 - + - -
193D ILE* 4.1 4.3 - - + -
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA* 4.3 14.3 - - + +
73D ASN* 4.2 5.6 - - - +
76D LEU* 3.8 33.4 - - + -
99D LEU* 5.2 0.2 - - + -
100D GLU* 3.8 35.4 - - + +
103D ALA* 4.1 14.4 - - + -
104D MET* 4.2 22.7 - - + -
154D PHE* 3.6 8.7 + - + +
155D VAL* 3.4 15.6 + - - +
157D PHE* 1.3 76.2 - - - +
159D ALA* 1.3 60.3 + - - +
161D ASP* 3.4 7.8 - - + +
162D VAL* 2.8 37.0 + - + +
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Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 4.3 12.1 - - + +
103D ALA* 5.3 1.1 - - - -
137D PHE* 5.5 5.8 - - + -
147D PHE* 4.2 17.5 - - + -
155D VAL 3.0 17.3 + - - +
156D ASP 3.9 1.1 - - - +
158D LEU* 1.3 75.8 - - - +
160D TYR* 1.3 59.5 + - - +
162D VAL* 3.4 6.5 + - - +
163D LEU* 2.8 39.7 + - + +
183D PHE* 3.9 21.8 - - + -
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Residues in contact with TYR 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D HIS* 4.8 9.2 - + - -
18D LEU* 3.6 33.0 - - + -
156D ASP 3.1 19.4 + - - +
157D PHE 3.6 4.3 - - - +
158D LEU 3.3 0.2 - - - -
159D ALA* 1.3 74.5 - - - +
161D ASP* 1.3 56.2 + - - +
163D LEU* 3.8 3.6 - - - +
164D ASP* 2.8 55.1 + - + +
167D ARG* 5.5 0.3 + - - -
183D PHE* 3.9 7.5 - - + -
184D ILE* 3.3 37.5 - - + -
187D PHE* 3.9 37.0 - + + -
188D GLU* 3.9 13.1 + - + +
197D MET* 2.9 34.6 - - + +
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Residues in contact with ASP 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ARG* 2.9 28.2 + - - +
11D GLY 4.5 7.4 - - - +
12D LEU* 5.5 3.1 - - - +
14D HIS* 3.2 26.1 - - + +
15D ALA* 4.2 13.8 + - + +
18D LEU* 5.3 0.9 - - + -
107D SER* 5.3 2.3 + - - -
157D PHE 3.2 11.0 + - - +
158D LEU* 3.4 14.8 - - + +
160D TYR* 1.3 84.4 - - - +
162D VAL* 1.3 67.1 + - + +
164D ASP* 3.0 2.1 + - - +
165D LEU* 2.9 37.5 + - - +
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Residues in contact with VAL 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ALA* 3.6 28.7 - - + +
106D VAL* 4.0 31.4 - - + -
107D SER* 3.8 12.1 - - - +
134D MET* 5.7 0.9 - - + -
137D PHE* 4.2 18.4 - - + -
158D LEU* 2.8 27.0 + - + +
159D ALA* 3.7 5.2 - - - +
161D ASP* 1.3 77.3 - - + +
163D LEU* 1.3 63.4 + - + +
165D LEU* 3.4 9.4 + - - +
166D HIS* 3.1 36.2 + - + +
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Residues in contact with LEU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D MET* 3.6 28.3 - - + -
137D PHE* 4.4 15.3 - - + -
147D PHE* 4.7 7.0 - - + -
159D ALA* 2.8 33.6 + - + +
160D TYR 3.8 2.7 - - - +
162D VAL* 1.3 72.3 - - + +
164D ASP* 1.3 58.2 + - - +
166D HIS* 3.3 4.2 + - - +
167D ARG* 2.9 29.7 + - - +
174D LEU* 4.1 9.9 - - + +
180D LEU* 4.2 22.2 - - + +
183D PHE* 3.4 35.4 - - + -
184D ILE* 3.9 23.8 - - + -
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Residues in contact with ASP 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ARG* 2.9 31.2 + - - +
160D TYR* 2.8 39.7 + - + +
161D ASP* 3.4 4.3 - - - +
163D LEU* 1.3 77.6 - - - +
165D LEU* 1.3 62.9 + - - +
167D ARG* 3.0 34.3 + - - +
168D ILE* 3.0 43.0 + - - +
184D ILE* 5.3 1.5 - - - +
207D LEU* 5.7 0.7 - - - +
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ARG* 3.5 29.4 - - - +
107D SER* 5.1 14.1 - - - +
110D LEU* 4.1 18.6 - - + +
161D ASP* 2.9 34.0 + - - +
162D VAL* 3.6 11.0 - - - +
164D ASP* 1.3 76.6 - - - +
166D HIS* 1.3 62.5 + - + +
168D ILE* 3.5 5.9 + - - +
169D PHE* 3.2 22.9 + - - +
207D LEU* 3.8 31.2 - - + -
208D TYR* 4.6 16.4 - - + +
214D TRP* 4.5 2.8 - - - -
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Residues in contact with HIS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL* 3.4 32.7 - - + +
107D SER* 5.7 0.7 - - - -
110D LEU* 4.2 20.8 - - + +
126D TYR* 2.7 31.1 + + - -
130D LEU* 3.3 31.1 - - + +
134D MET* 4.4 14.8 - - + +
162D VAL* 3.1 29.7 + - + +
163D LEU 3.9 3.1 - - - +
165D LEU* 1.3 79.2 - - + +
167D ARG* 1.3 56.0 - - - +
168D ILE 3.3 0.2 - - - -
169D PHE* 4.4 5.8 - + - -
170D GLU* 2.8 35.7 + - - +
173D CYS* 3.5 14.2 - - + -
174D LEU* 5.3 0.4 - - + -
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Residues in contact with ARG 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D TYR* 5.5 0.8 + - - -
163D LEU 2.9 15.0 + - - +
164D ASP* 3.0 35.0 + - - +
166D HIS* 1.3 77.2 - - - +
168D ILE* 1.3 69.1 + - + +
170D GLU 3.9 5.4 - - - -
171D PRO* 3.1 30.1 - - + +
174D LEU* 3.9 27.7 - - + +
181D LYS* 5.6 4.9 + - - +
184D ILE* 4.0 24.4 - - - +
188D GLU* 3.5 20.2 + - - -
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Residues in contact with ILE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ASP* 3.0 44.0 + - - +
165D LEU* 3.9 4.3 - - - +
167D ARG* 1.3 92.7 - - + +
169D PHE* 1.3 66.4 + - - +
171D PRO* 3.8 7.6 - - - +
205D LYS* 5.7 13.5 - - - +
207D LEU* 4.5 19.1 - - + -
214D TRP* 4.3 15.0 - - + -
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Residues in contact with PHE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D LEU* 3.6 29.8 - - + -
113D VAL* 5.0 5.8 - - + -
114D CYS* 5.0 0.9 - - - -
119D PHE* 3.9 17.3 - + - -
123D LYS* 3.4 57.0 + - + -
126D TYR* 5.0 11.0 - + - -
127D LEU* 6.3 1.8 - - + -
130D LEU* 5.9 2.5 - - + -
165D LEU 3.2 16.5 + - - +
166D HIS* 4.2 7.9 - + + +
168D ILE* 1.3 81.9 - - - +
170D GLU* 1.3 66.9 + - + +
171D PRO* 3.7 4.8 - - - +
214D TRP* 3.2 46.9 - + + -
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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