Contacts of the helix formed by residues 147 - 166 (chain Z) in PDB entry 3TDD
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 SER 147 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Z PHE* 3.6 5.8 - - - -
145Z TYR 4.1 0.2 + - - -
146Z LEU* 1.3 74.6 - - - +
148Z VAL* 1.3 65.6 + - - +
149Z GLU* 2.8 23.0 + - - +
150Z GLU* 2.9 26.9 + - - +
151Z VAL* 2.9 12.0 + - - +
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Residues in contact with VAL 148 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Z PHE* 3.3 44.4 - - + -
13Z VAL* 4.6 1.1 - - + -
147Z SER* 1.3 71.4 - - - +
149Z GLU* 1.3 80.5 + - + +
151Z VAL* 4.0 0.6 - - - +
152Z ILE* 3.0 41.8 + - + +
177Z ILE* 3.9 22.9 - - + -
179Z THR* 6.0 1.1 - - + -
185Z ARG* 4.3 9.2 - - - +
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Residues in contact with GLU 149 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147Z SER* 2.8 24.5 + - - +
148Z VAL* 1.3 94.8 - - + +
150Z GLU* 1.3 63.5 + - - +
152Z ILE* 3.6 7.2 + - - +
153Z LYS* 3.4 28.4 + - - +
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Residues in contact with GLU 150 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H LYS* 3.3 35.9 - - - +
14Z LYS* 6.2 0.4 - - - +
146Z LEU* 4.0 33.4 - - + -
147Z SER* 2.9 18.0 + - - +
149Z GLU* 1.3 76.0 - - - +
151Z VAL* 1.3 65.7 + - - +
153Z LYS* 3.1 33.3 + - - +
154Z LEU* 3.2 21.1 + - - +
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Residues in contact with VAL 151 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Z ILE* 4.0 30.3 - - + -
11Z PHE* 3.6 24.2 - - + -
13Z VAL* 3.7 30.3 - - + -
145Z TYR* 5.0 2.9 - - + -
146Z LEU* 3.8 24.7 - - + -
147Z SER 2.9 17.8 + - - +
148Z VAL 4.0 4.0 - - - +
150Z GLU* 1.3 76.7 - - - +
152Z ILE* 1.3 63.2 + - - +
154Z LEU* 3.0 11.4 + - - +
155Z VAL* 2.9 21.2 + - + +
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Residues in contact with ILE 152 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Z VAL* 4.8 12.1 - - + -
148Z VAL* 3.0 34.6 + - + +
149Z GLU* 4.0 6.5 - - - +
150Z GLU 3.3 0.2 - - - -
151Z VAL* 1.3 77.2 - - + +
153Z LYS* 1.3 57.4 + - + +
155Z VAL* 3.8 7.5 - - + +
156Z ARG* 3.0 38.9 + - + +
175Z ILE* 4.0 22.9 - - + -
177Z ILE* 4.2 11.2 - - + -
185Z ARG* 4.7 1.1 - - - +
187Z GLU* 3.6 35.0 - - - +
189Z TYR* 4.3 2.9 - - - +
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Residues in contact with LYS 153 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H GLN* 3.5 48.6 + - + +
202H LYS* 4.9 9.4 - - + +
149Z GLU* 3.4 18.3 + - - +
150Z GLU* 3.1 32.9 + - - +
151Z VAL 3.0 0.8 + - - -
152Z ILE* 1.3 75.2 - - - +
154Z LEU* 1.3 63.1 + - + +
156Z ARG* 3.4 2.5 + - - +
157Z ASP* 2.9 34.9 + - - +
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Residues in contact with LEU 154 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H LYS* 4.5 3.4 - - + -
204H TYR* 3.5 31.4 - - + +
6Z ILE* 5.2 5.6 - - + -
137Z PHE* 4.0 8.9 - - + -
138Z LEU* 5.1 7.0 - - + -
141Z GLN* 3.9 20.9 - - + +
142Z VAL* 3.7 30.1 - - + -
146Z LEU* 3.7 20.9 - - + -
150Z GLU* 3.6 23.1 - - + +
151Z VAL* 3.0 8.2 + - - +
153Z LYS* 1.3 72.8 - - - +
155Z VAL* 1.3 59.8 + - - +
157Z ASP* 3.8 3.6 - - - +
158Z SER* 2.8 35.6 + - - -
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Residues in contact with VAL 155 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Z LEU* 4.0 16.2 - - + +
6Z ILE* 4.0 21.8 - - + -
13Z VAL* 4.4 12.1 - - + -
15Z ALA* 3.9 19.1 - - + -
151Z VAL* 2.9 25.7 + - + +
152Z ILE* 3.8 8.1 - - - +
154Z LEU* 1.3 75.3 - - - +
156Z ARG* 1.3 64.8 + - - +
158Z SER* 3.0 4.7 + - - -
159Z PHE* 3.0 37.9 + - + -
173Z LEU* 4.1 2.9 - - + -
175Z ILE* 3.8 24.0 - - + -
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Residues in contact with ARG 156 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198H GLU* 3.7 22.6 + - - -
201H GLN* 3.2 39.4 + - + +
152Z ILE* 3.0 27.6 + - + +
153Z LYS 3.7 3.1 - - - +
155Z VAL* 1.3 77.6 - - - +
157Z ASP* 1.3 64.1 + - - +
159Z PHE* 3.3 2.6 + - - +
160Z THR* 3.0 30.1 + - + +
173Z LEU* 4.0 21.3 - - + +
175Z ILE* 4.6 1.6 - - + -
189Z TYR* 3.0 57.8 + - + +
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Residues in contact with ASP 157 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H ARG* 4.5 0.5 + - - -
200H LYS* 3.6 12.5 - - + +
201H GLN* 2.7 32.3 + - - +
202H LYS* 3.5 12.0 + - - +
204H TYR* 2.4 44.4 + - + +
140I SER* 4.9 1.6 - - - +
137Z PHE* 4.6 6.3 - - + -
153Z LYS 2.9 18.0 + - - +
154Z LEU* 3.8 3.8 - - - +
156Z ARG* 1.3 76.3 - - - +
158Z SER* 1.3 62.7 + - - +
160Z THR* 3.1 8.3 + - - -
161Z SER* 3.0 29.0 + - - -
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Residues in contact with SER 158 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I SER* 5.2 0.2 - - - -
4Z LEU* 4.2 7.8 - - - +
134Z ILE* 3.6 25.6 - - - +
137Z PHE* 3.3 27.0 - - - -
138Z LEU* 3.3 13.7 - - - +
154Z LEU 2.8 17.7 + - - -
155Z VAL 3.0 10.1 + - - -
157Z ASP* 1.3 77.1 - - - +
159Z PHE* 1.3 58.4 + - - +
161Z SER* 3.5 4.5 + - - -
162Z ALA* 2.9 28.6 + - - +
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Residues in contact with PHE 159 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Z THR* 3.6 38.8 - - + -
3Z ILE 4.3 1.6 - - - -
4Z LEU* 3.7 36.8 - - + -
15Z ALA* 4.1 1.8 - - + -
16Z GLY* 4.0 7.0 - - - -
17Z ASP* 3.6 23.3 - - + -
134Z ILE* 4.7 4.7 - - + -
155Z VAL* 3.0 30.1 + - + +
156Z ARG 3.9 3.8 - - - +
158Z SER* 1.3 78.4 - - - +
160Z THR* 1.3 56.5 + - - +
162Z ALA* 3.8 4.0 - - + +
163Z THR* 2.6 38.1 + - - -
169Z VAL* 4.3 10.8 - - + +
173Z LEU* 3.8 36.6 - - + -
191Z LEU* 4.3 10.8 - - + -
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Residues in contact with THR 160 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H ARG* 2.8 31.7 + - - +
198H GLU* 3.6 32.3 - - + +
200H LYS* 5.6 0.7 - - - -
156Z ARG* 3.0 19.6 + - + +
157Z ASP* 3.1 16.6 + - - -
159Z PHE* 1.3 74.3 - - - +
161Z SER* 1.3 64.2 + - - +
163Z THR* 3.5 7.4 + - - -
164Z GLU* 3.2 27.7 + - - +
191Z LEU* 3.9 16.2 - - + -
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Residues in contact with SER 161 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H ARG* 3.0 19.5 + - - +
200H LYS* 5.0 0.7 - - - +
136I GLY* 4.8 4.9 - - - -
139I GLU* 3.5 27.0 + - - +
140I SER* 2.6 27.8 + - - -
133Z LEU* 5.5 0.7 - - - -
157Z ASP 3.0 15.6 + - - -
158Z SER* 3.7 5.2 - - - -
160Z THR* 1.3 75.7 + - - +
162Z ALA* 1.3 66.3 + - - +
164Z GLU* 2.9 18.7 + - - +
165Z ARG* 3.3 6.2 + - - +
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Residues in contact with ALA 162 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Z THR* 5.7 0.2 - - + -
130Z ALA* 3.7 26.5 - - + -
133Z LEU* 4.3 13.7 - - + -
134Z ILE* 4.3 11.9 - - + +
158Z SER 2.9 18.8 + - - +
159Z PHE* 3.8 7.2 - - + +
161Z SER* 1.3 75.5 - - - +
163Z THR* 1.3 58.2 + - - +
165Z ARG 3.2 1.0 + - - -
166Z HIS* 2.8 33.8 + - - +
169Z VAL* 4.2 10.5 - - + -
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Residues in contact with THR 163 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ARG* 5.3 5.2 + - - -
26H VAL* 5.7 0.5 - - - +
159Z PHE 2.6 26.3 + - - -
160Z THR* 3.7 9.0 - - - -
161Z SER 3.2 0.2 - - - -
162Z ALA* 1.3 76.9 - - - +
164Z GLU* 1.3 60.1 + - - +
166Z HIS 3.8 10.6 - - - +
169Z VAL* 3.5 32.9 + - - +
170Z GLY* 3.9 8.5 - - - -
191Z LEU* 3.8 14.9 - - - +
192Z LYS* 3.9 37.6 - - + +
194Z ASP* 5.2 5.9 - - - +
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Residues in contact with GLU 164 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ARG* 5.8 0.7 + - - -
26H VAL* 3.6 20.7 - - - +
29H LYS* 3.2 34.4 + - - +
197H ARG* 3.0 30.7 - - + +
139I GLU* 3.6 25.4 - - + +
160Z THR 3.2 15.6 + - - +
161Z SER 2.9 9.9 + - - +
163Z THR* 1.3 78.6 - - - +
165Z ARG* 1.3 62.7 + - - +
166Z HIS 3.7 0.2 - - - -
192Z LYS* 2.9 44.3 + - - +
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Residues in contact with ARG 165 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H ILE* 3.3 12.6 - - + +
26H VAL* 2.8 51.3 + - - +
27H ALA 3.0 23.0 + - - -
28H ASP* 4.2 3.0 - - - +
29H LYS* 3.2 29.9 - - - +
123I ASP* 4.4 8.1 + - - -
124I PHE* 3.4 26.5 + - - -
135I PHE* 3.2 37.7 - - + +
139I GLU* 2.8 31.2 + - + +
133Z LEU* 3.8 21.3 - - + -
161Z SER 3.3 1.5 + - - +
162Z ALA 3.2 2.2 + - - -
164Z GLU* 1.3 81.9 - - - +
166Z HIS* 1.3 57.8 + - - +
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Residues in contact with HIS 166 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H PRO* 3.5 29.5 - - + +
25H ILE* 3.8 15.4 - - + +
26H VAL* 4.7 1.3 - - - -
129Z ALA* 3.4 43.6 + - + +
130Z ALA* 4.1 9.8 + - + -
133Z LEU* 4.5 4.8 - - + +
162Z ALA 2.8 14.3 + - - +
163Z THR 3.8 7.1 - - - +
164Z GLU 3.7 0.8 - - - -
165Z ARG* 1.3 78.8 - - - +
167Z ILE* 1.3 65.2 + - - +
168Z GLN* 3.1 46.3 + - + +
169Z VAL* 3.2 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