Contacts of the helix formed by residues 149 - 163 (chain D) in PDB entry 3DVA
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 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D MET* 3.9 6.5 - - - +
147D PRO* 4.3 0.2 - - - +
148D SER* 1.3 95.0 - - - +
150D PRO* 1.3 70.3 - - - +
151D TYR* 4.1 1.9 - - - +
152D ASP* 3.0 29.5 + - - -
153D ALA* 2.9 30.1 + - - +
179D PHE* 4.3 9.4 - - + -
181D GLN* 3.3 17.1 + - - +
198D LYS* 3.8 20.9 - - - -
213D VAL* 6.1 0.7 - - + -
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Residues in contact with PRO 150 (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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3D MET 3.4 27.1 - - - +
4D THR* 3.6 10.5 - - - +
5D MET* 3.6 28.2 - - + +
8D ALA* 3.2 11.9 - - + +
149D THR* 1.3 84.1 - - - +
151D TYR* 1.3 61.6 + - - +
154D LYS* 3.1 20.1 + - - +
179D PHE* 3.6 23.8 - - + +
181D GLN* 3.3 21.3 - - + +
183D VAL* 3.7 14.3 - - + +
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Residues in contact with TYR 151 (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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149D THR* 4.1 1.1 - - - +
150D PRO* 1.3 75.1 - - - +
152D ASP* 1.3 76.6 + - - +
155D GLY 3.3 8.7 + - - -
181D GLN* 3.1 32.0 + - - +
182D GLU 4.5 4.5 - - - +
183D VAL* 3.8 8.2 - - + +
184D PRO* 3.7 26.2 - - + -
188D TYR* 2.7 57.2 + + - -
190D ILE* 3.5 23.4 - - + +
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Residues in contact with ASP 152 (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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147D PRO* 4.1 8.3 - - + -
148D SER* 4.1 6.2 + - - -
149D THR* 3.0 26.9 + - - +
151D TYR* 1.3 88.7 - - - +
153D ALA* 1.3 56.1 + - - +
155D GLY* 3.9 0.2 - - - -
156D LEU* 2.8 56.7 + - + +
190D ILE* 3.8 13.0 - - - +
196D ASP* 4.3 7.8 - - - +
198D LYS* 2.9 30.4 + - - -
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Residues in contact with ALA 153 (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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5D MET* 3.6 24.9 - - + +
9D ILE* 3.9 17.3 - - + -
147D PRO* 3.6 23.0 - - + +
149D THR 2.9 18.9 + - - +
150D PRO 3.7 3.8 - - - +
151D TYR 3.3 0.2 - - - -
152D ASP* 1.3 75.7 - - - +
154D LYS* 1.3 58.2 + - - +
157D LEU* 2.9 34.7 + - - +
169D PHE* 3.5 2.5 - - + -
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Residues in contact with LYS 154 (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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3D MET* 4.6 1.0 - - + +
8D ALA* 3.5 27.5 - - + +
11D ASP* 2.7 29.5 + - + +
12D ALA* 3.7 10.4 - - + +
15D ILE* 4.7 3.8 - - - +
150D PRO 3.1 11.3 + - - +
153D ALA* 1.3 77.9 - - - +
155D GLY* 1.3 64.8 + - - +
158D ILE* 3.0 43.4 + - + +
183D VAL* 3.7 11.2 - - + -
184D PRO 2.8 17.4 + - - -
185D GLU* 3.7 0.8 - - - +
186D GLY 2.6 38.0 + - - +
188D TYR* 3.5 26.9 - - + +
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Residues in contact with GLY 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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151D TYR 3.3 8.1 + - - -
154D LYS* 1.3 80.1 - - - +
156D LEU* 1.3 61.4 + - - +
158D ILE* 3.5 0.5 + - - +
159D SER* 3.1 25.6 + - - -
188D TYR* 3.5 33.1 - - - -
189D THR* 3.8 2.8 - - - -
190D ILE* 3.3 17.4 + - - -
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Residues in contact with LEU 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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145D VAL* 3.8 32.0 - - + +
146D ILE 5.2 0.7 - - - -
147D PRO* 4.1 12.8 - - + -
152D ASP* 2.8 46.3 + - + +
155D GLY* 1.3 69.8 - - - +
157D LEU* 1.3 54.1 + - - +
159D SER* 3.1 6.2 + - - -
160D ALA* 2.7 35.3 + - - +
169D PHE* 3.9 7.0 - - + -
190D ILE* 3.7 33.9 - - + +
191D PRO 3.9 9.6 - - - +
192D ILE* 4.7 10.0 - - + +
194D LYS 5.5 3.4 - - - +
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Residues in contact with LEU 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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9D ILE* 3.5 45.1 - - + +
12D ALA* 4.0 9.0 - - + -
13D LEU* 3.8 13.2 - - + -
77D VAL* 5.4 0.2 - - + -
113D THR* 4.0 17.9 - - + -
115D ARG* 4.4 9.2 - - + -
153D ALA 2.9 19.7 + - - +
154D LYS 3.8 2.7 - - - +
156D LEU* 1.3 75.4 - - - +
158D ILE* 1.3 57.0 + - - +
160D ALA* 3.1 1.4 + - - -
161D ILE* 2.8 49.5 + - + +
169D PHE* 3.5 27.5 - - + -
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Residues in contact with ILE 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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12D ALA* 3.8 21.1 - - + +
15D ILE* 4.3 9.9 - - + -
16D GLU* 3.4 24.2 - - - +
154D LYS* 3.0 38.2 + - + +
155D GLY 3.8 0.4 - - - +
157D LEU* 1.3 75.1 - - - +
159D SER* 1.3 62.3 + - - +
161D ILE* 3.4 1.7 + - - +
162D ARG* 3.1 34.5 + - - +
187D GLU* 4.2 10.8 - - + +
188D TYR 3.5 29.4 - - - +
189D THR* 3.6 20.6 - - + -
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Residues in contact with SER 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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155D GLY 3.1 5.3 + - - -
156D LEU 3.4 7.6 - - - -
158D ILE* 1.3 78.1 - - - +
160D ALA* 1.3 56.9 + - - +
162D ARG* 3.4 5.2 + - - +
163D ASP* 2.9 30.8 + - - +
189D THR* 3.4 13.0 - - - -
190D ILE 2.5 42.2 + - - -
191D PRO* 4.5 1.5 - - - +
192D ILE* 4.0 16.3 - - - +
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Residues in contact with ALA 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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113D THR* 2.8 24.9 + - + -
145D VAL* 5.3 0.9 - - + -
156D LEU 2.7 20.5 + - - +
157D LEU* 3.1 9.2 + - - +
159D SER* 1.3 73.4 - - - +
161D ILE* 1.3 62.2 + - - +
163D ASP* 3.4 17.7 + - - +
165D ASP 4.8 0.3 - - - +
167D VAL* 3.6 30.6 - - + +
169D PHE* 4.4 6.3 - - + -
192D ILE* 3.9 13.0 - - + +
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Residues in contact with ILE 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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13D LEU* 3.7 31.0 - - + -
16D GLU* 3.6 46.4 - - + +
23D VAL* 4.0 9.0 - - + -
75D ARG* 3.0 43.6 + - + +
77D VAL* 4.0 21.8 - - + -
111D PRO 4.7 0.9 - - - +
113D THR* 3.2 14.8 + - - +
157D LEU* 2.8 34.7 + - + +
158D ILE 3.9 0.7 - - - +
160D ALA* 1.3 74.0 - - - +
162D ARG* 1.3 55.7 + - - +
163D ASP 3.5 2.4 + - - +
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Residues in contact with ARG 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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15D ILE* 5.3 0.2 - - - +
16D GLU* 3.6 30.6 + - - +
19D ASN* 4.1 23.3 + - - +
75D ARG* 3.0 18.4 + - - +
158D ILE* 3.1 24.5 + - - +
159D SER* 3.9 3.8 - - - +
161D ILE* 1.3 73.9 - - - +
163D ASP* 1.3 65.8 + - - +
164D ASN* 3.3 9.2 + - - +
187D GLU* 2.7 43.5 + - - +
189D THR* 3.9 16.8 - - - +
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Residues in contact with ASP 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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75D ARG* 3.5 6.8 + - - -
111D PRO* 3.9 5.9 - - - +
112D ILE 5.4 0.2 - - - +
143D LYS* 2.9 34.7 + - - +
159D SER 2.9 17.8 + - - +
160D ALA 3.4 12.2 - - - +
161D ILE 3.3 4.4 - - - +
162D ARG* 1.3 78.3 - - - +
164D ASN* 1.3 59.2 + - - +
165D ASP* 2.8 48.0 + - - +
167D VAL* 3.9 13.5 - - + -
192D ILE* 3.6 10.0 - - + +
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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
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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