Contacts of the helix formed by residues 147 - 166 (chain H) 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 THR 147 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H PHE* 4.1 2.2 - - - -
9H ASN* 3.4 15.5 - - - +
145H ASP 4.8 2.7 - - - +
146H LEU* 1.3 77.5 - - - +
148H LYS* 1.3 65.5 + - - +
149H GLU* 3.4 14.1 + - - +
150H GLU* 2.9 42.2 + - + +
151H ALA* 2.9 20.8 + - - +
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Residues in contact with LYS 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H PHE* 3.7 36.0 - - + -
9H ASN* 4.4 1.8 + - - +
147H THR* 1.3 73.0 - - - +
149H GLU* 1.3 76.2 + - - +
151H ALA* 3.5 2.1 + - - +
152H ILE* 3.1 49.1 + - + +
177H VAL* 4.0 16.9 - - + +
179H GLU* 3.5 29.7 + - - +
182H LYS* 3.9 17.1 - - - +
185H GLU* 2.8 30.1 + - - +
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Residues in contact with GLU 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H THR* 3.1 13.2 + - - +
148H LYS* 1.3 96.6 + - + +
150H GLU* 1.3 66.3 + - + +
152H ILE* 3.4 9.8 + - + +
153H LYS* 3.1 23.4 + - - +
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Residues in contact with GLU 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H LYS* 2.9 31.1 + - - -
145H ASP 3.9 2.3 - - - +
146H LEU* 3.4 20.7 - - + +
147H THR* 2.9 53.0 + - - +
149H GLU* 1.3 77.6 - - + +
151H ALA* 1.3 57.3 + - - +
153H LYS* 3.3 7.1 + - - +
154H LEU* 2.9 30.2 + - - +
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Residues in contact with ALA 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL* 4.2 10.5 - - + +
8H PHE* 3.6 24.5 - - + -
13H VAL* 3.6 21.0 - - + +
146H LEU* 4.3 8.2 - - + +
147H THR 2.9 15.1 + - - +
148H LYS 3.7 4.3 - - - +
150H GLU* 1.3 75.1 - - - +
152H ILE* 1.3 60.6 + - - +
154H LEU* 3.2 6.1 + - - +
155H ALA* 2.8 32.6 + - - +
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Residues in contact with ILE 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H PHE* 6.2 0.2 - - + -
13H VAL* 4.5 13.5 - - + -
148H LYS* 3.1 35.3 + - + +
149H GLU* 3.4 8.7 + - + +
151H ALA* 1.3 75.8 - - - +
153H LYS* 1.3 57.4 + - - +
155H ALA* 4.2 0.8 - - - +
156H SER* 2.8 31.4 + - - -
175H VAL* 4.4 13.1 - - + +
177H VAL* 3.6 31.4 - - + -
185H GLU* 5.4 0.7 - - - +
187H LEU* 4.9 6.7 - - + -
191H TYR* 3.4 38.6 - - + +
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Residues in contact with LYS 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H GLU 3.1 14.1 + - - +
150H GLU* 3.5 11.0 - - - +
151H ALA 3.1 0.2 - - - -
152H ILE* 1.3 76.0 - - - +
154H LEU* 1.3 55.4 + - - +
156H SER* 3.3 4.6 + - - -
157H ASP* 2.7 76.4 + - - +
191H TYR* 5.7 1.3 - - - -
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Residues in contact with LEU 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL* 4.3 5.2 - - + -
137H VAL* 4.2 15.7 - - + +
138H LEU* 3.9 22.4 - - + -
141H HIS* 3.7 29.8 - - + +
142H TRP* 3.7 35.9 - - + -
146H LEU* 3.8 21.8 - - + -
150H GLU 2.9 16.7 + - - +
151H ALA* 3.2 5.4 + - - +
153H LYS* 1.3 74.0 - - - +
155H ALA* 1.3 65.8 + - - +
157H ASP* 3.1 7.7 + - + +
158H ALA* 2.9 21.5 + - - +
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Residues in contact with ALA 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H VAL* 3.7 22.3 - - + +
6H VAL* 4.1 15.7 - - + +
13H VAL* 4.4 17.7 - - + +
15H ALA* 4.3 11.2 - - + +
151H ALA 2.8 19.6 + - - +
152H ILE 4.2 2.2 - - - +
154H LEU* 1.3 72.9 - - - +
156H SER* 1.3 62.7 + - - +
158H ALA* 3.2 5.0 + - - +
159H ILE* 3.1 29.6 + - - +
175H VAL* 5.8 0.9 - - + -
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Residues in contact with SER 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H ALA* 4.9 1.5 - - - +
152H ILE* 2.8 23.4 + - - -
153H LYS* 3.5 6.5 - - - -
155H ALA* 1.3 79.0 - - - +
157H ASP* 1.3 63.2 + - - +
159H ILE* 3.4 3.3 + - - +
160H GLN* 3.1 28.0 + - - +
173H VAL* 4.0 14.2 - - - +
175H VAL* 5.1 2.0 - - - +
191H TYR* 3.6 19.3 - - - -
192H LEU* 3.1 30.7 - - - +
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Residues in contact with ASP 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1401 LYS* 4.6 17.5 + - - +
137H VAL* 4.1 16.3 - - + +
141H HIS* 5.2 6.9 - - - -
153H LYS* 2.7 61.7 + - - +
154H LEU* 3.1 8.5 + - + +
156H SER* 1.3 72.5 - - - +
158H ALA* 1.3 60.3 + - - +
160H GLN* 3.1 21.7 + - - +
161H ALA* 2.9 26.0 + - - +
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Residues in contact with ALA 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H THR* 4.2 0.3 - - - +
4H VAL* 3.8 19.3 - - + -
134H ALA* 3.4 29.4 - - + +
137H VAL* 3.9 13.9 - - + +
138H LEU* 4.0 13.5 - - + -
154H LEU 2.9 12.5 + - - +
155H ALA 3.5 9.2 - - - +
157H ASP* 1.3 78.1 - - - +
159H ILE* 1.3 61.4 + - - +
161H ALA* 3.2 16.8 + - - +
162H GLY 3.4 3.8 + - - -
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Residues in contact with ILE 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H THR* 3.4 28.3 - - + +
4H VAL* 3.7 21.1 - - + +
15H ALA* 3.5 36.1 - - + +
16H ALA 3.6 22.2 - - - +
17H ASP* 3.6 11.9 - - + +
155H ALA 3.1 14.4 + - - +
156H SER 3.8 6.7 - - - +
157H ASP 3.3 0.2 - - - -
158H ALA* 1.3 75.3 - - - +
160H GLN* 1.3 59.4 + - - +
162H GLY* 3.1 3.6 + - - -
163H ILE* 2.9 27.2 + - + +
173H VAL* 3.8 20.0 - - + -
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Residues in contact with GLN 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H SER* 3.1 14.2 + - - +
157H ASP* 3.1 25.4 + - - +
159H ILE* 1.3 75.1 - - - +
161H ALA* 1.3 66.2 + - - +
163H ILE* 4.2 9.6 - - + -
164H TRP* 3.0 58.5 + - + +
173H VAL* 4.5 13.5 - - + -
192H LEU* 3.5 24.3 - - - +
194H PRO* 5.1 8.6 - - + +
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Residues in contact with ALA 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361 PRO* 4.8 4.0 - - + +
1401 LYS* 5.9 2.7 - - + -
133H ALA* 3.3 30.3 - - + +
137H VAL* 3.6 20.9 - - + -
157H ASP 2.9 6.6 + - - +
158H ALA 3.3 11.4 - - - +
160H GLN* 1.3 74.6 - - - +
162H GLY* 1.3 58.3 + - - +
164H TRP* 5.1 1.1 - - - -
165H ASN* 2.9 43.1 + - - +
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Residues in contact with GLY 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H THR* 3.7 17.3 - - - -
130H GLY* 4.3 2.0 - - - -
133H ALA* 3.8 12.9 - - - +
158H ALA 3.4 3.6 + - - -
159H ILE 3.1 7.8 + - - -
161H ALA* 1.3 80.0 - - - +
163H ILE* 1.3 60.2 + - - +
166H ASP* 2.7 39.0 + - - +
169H SER* 3.6 7.5 - - - -
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Residues in contact with ILE 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ASP* 4.0 16.6 - - + -
159H ILE* 2.9 21.3 + - + +
160H GLN* 3.1 11.6 + - + +
162H GLY* 1.3 78.4 - - - +
164H TRP* 1.3 68.2 + - + +
166H ASP 3.6 0.3 - - - +
169H SER* 3.2 9.7 - - - +
170H GLY* 3.6 14.4 - - - +
171H SER 3.8 9.2 - - - +
172H ASN 3.5 24.9 - - - +
173H VAL* 3.6 21.3 - - + -
194H PRO* 5.1 2.7 - - + -
195H ASN* 3.6 25.4 - - - +
194Z ASP* 2.9 34.3 - - + +
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Residues in contact with TRP 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H GLN* 3.0 48.8 + - + +
161H ALA* 5.1 0.9 - - - -
163H ILE* 1.3 82.5 - - + +
165H ASN* 1.3 66.3 + - - +
166H ASP 3.9 0.3 + - - -
194H PRO* 3.6 34.5 - - + -
195H ASN* 3.2 37.5 - - - -
26Z ILE* 4.0 6.8 - - - +
29Z ARG* 2.9 27.9 + - - +
193Z ARG* 3.2 37.3 - - + +
194Z ASP* 3.8 13.3 - - + +
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Residues in contact with ASN 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361 PRO* 3.5 39.0 - - + +
1391 ARG* 3.0 49.8 + - - +
133H ALA* 4.4 3.6 - - + -
161H ALA* 2.9 27.7 + - - +
164H TRP* 1.3 84.8 - - - +
166H ASP* 1.3 59.8 + - - +
24Z TYR 3.8 8.7 - - - +
25Z SER* 4.5 2.4 + - - -
26Z ILE* 4.4 16.6 + - - +
29Z ARG* 4.0 8.1 - - - +
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Residues in contact with ASP 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H SER* 2.5 39.9 + - - +
130H GLY* 3.4 16.6 + - - -
133H ALA* 5.3 2.5 - - + -
161H ALA 4.2 0.2 + - - -
162H GLY* 2.7 23.5 + - - +
163H ILE 3.6 4.0 - - - +
164H TRP 5.2 0.7 - - - -
165H ASN* 1.3 74.0 - - - +
167H LEU* 1.3 58.5 + - - +
168H GLY 3.0 13.5 + - - -
169H SER* 2.7 49.4 + - - +
24Z TYR* 3.6 19.0 - - - +
194Z ASP* 3.6 1.9 - - - +
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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
------------------------------------------------------------
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