Contacts of the helix formed by residues 144 - 165 (chain D) in PDB entry 2VXX
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 ASP 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D LEU* 3.7 26.8 - - + +
25D THR* 4.3 2.6 - - + +
29D ILE* 3.5 31.5 - - + +
83D ARG* 2.9 25.2 + - - -
87D LEU* 3.8 6.9 - - - +
139D ALA* 3.0 14.9 + - + +
142D LEU 3.5 2.2 - - - -
143D GLY* 1.3 72.9 - - - +
145D ARG* 1.3 62.6 + - - +
146D ALA* 3.6 1.7 + - - +
147D THR* 2.6 29.7 + - - -
148D ALA* 3.3 15.4 + - - +
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Residues in contact with ARG 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D GLU* 5.1 17.4 + - + +
143D GLY* 3.1 16.5 + - - +
144D ASP* 1.3 73.6 + - - +
146D ALA* 1.3 58.4 + - - +
148D ALA* 3.5 7.2 + - - +
149D TYR* 3.1 27.0 + - - +
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Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ARG* 3.5 25.4 - - - +
144D ASP* 3.3 1.6 + - - +
145D ARG* 1.3 76.7 - - - +
147D THR* 1.3 60.0 + - - +
149D TYR* 3.4 9.6 + - + +
150D LEU* 2.9 30.0 + - - +
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Residues in contact with THR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE* 4.1 7.9 - - + -
33D MET* 3.8 14.1 - - + -
83D ARG* 3.1 22.6 + - - +
87D LEU* 3.9 6.4 - - - +
139D ALA* 3.8 11.0 - - + -
144D ASP* 2.6 34.7 + - - -
146D ALA* 1.3 76.5 - - - +
148D ALA* 1.3 58.3 + - - +
150D LEU* 3.2 5.8 + - + +
151D TYR* 2.8 58.7 + - + +
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ALA* 3.7 26.6 - - + +
139D ALA* 3.8 5.1 - - - +
140D GLU* 3.8 24.5 - - + +
144D ASP 3.3 11.2 + - - +
145D ARG* 3.7 9.4 - - - +
146D ALA 3.4 0.2 - - - -
147D THR* 1.3 78.7 - - - +
149D TYR* 1.3 58.2 + - - +
151D TYR* 3.5 1.6 + - - +
152D ASP* 3.0 38.9 + - - +
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Residues in contact with TYR 149 (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 ARG 3.1 17.8 + - - +
146D ALA* 3.5 10.3 - - + +
148D ALA* 1.3 75.3 - - - +
150D LEU* 1.3 65.9 + - + +
152D ASP* 3.2 11.1 + - + +
153D GLN* 2.9 56.5 + - + +
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Residues in contact with LEU 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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33D MET* 5.5 2.2 - - + -
79D ALA* 4.1 24.9 - - + +
80D LEU* 4.0 22.7 - - + -
83D ARG* 4.2 25.8 - - + +
146D ALA 2.9 17.7 + - - +
147D THR* 3.7 5.2 - - - +
149D TYR* 1.3 82.3 - - + +
151D TYR* 1.3 59.1 + - + +
153D GLN* 3.2 21.8 + - - +
154D ILE* 2.9 45.2 + - + +
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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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29D ILE* 4.0 4.9 + - + -
32D GLY 4.1 0.7 - - - -
33D MET* 3.2 46.4 + - + +
36D LEU* 3.5 20.3 - - + +
80D LEU* 3.8 29.4 - - + -
132D LEU* 3.6 23.0 - - + +
135D GLN* 3.6 23.1 - - + +
136D ALA* 3.6 32.8 - - + -
139D ALA* 5.0 0.2 - - + -
147D THR* 2.8 35.2 + - + +
148D ALA 3.7 4.5 - - - +
150D LEU* 1.3 77.9 - - + +
152D ASP* 1.3 52.0 + - - +
154D ILE* 3.2 5.0 + - + +
155D LEU* 2.6 36.8 + - - +
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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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136D ALA* 3.7 16.5 - - - +
140D GLU* 5.7 0.5 - - - +
148D ALA* 3.0 24.1 + - - +
149D TYR* 3.2 11.6 + - + +
151D TYR* 1.3 71.2 - - - +
153D GLN* 1.3 66.1 + - - +
155D LEU* 3.2 14.6 + - - +
156D LEU* 3.0 25.5 + - - +
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Residues in contact with GLN 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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149D TYR* 2.9 45.6 + - + +
150D LEU* 3.3 24.4 - - - +
152D ASP* 1.3 77.2 - - - +
154D ILE* 1.3 62.6 + - + +
156D LEU* 3.5 14.4 + - - +
157D LYS* 3.6 17.6 + - + +
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Residues in contact with ILE 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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40D PHE* 3.5 32.8 - - + -
76D HIS* 3.6 39.5 - - + +
79D ALA* 4.6 2.5 - - + -
80D LEU* 3.8 35.0 - - + -
132D LEU* 4.0 7.2 - - + -
150D LEU* 2.9 35.1 + - + +
151D TYR* 3.6 10.5 - - + +
153D GLN* 1.3 75.1 - - + +
155D LEU* 1.3 64.5 + - - +
157D LYS* 3.3 3.8 + - - +
158D THR* 2.8 28.0 + - - +
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ILE* 4.1 23.8 - - + -
132D LEU* 3.9 27.6 - - + -
133D ARG* 3.8 23.3 - - + +
136D ALA* 6.3 0.7 - - + -
151D TYR 2.6 20.7 + - - +
152D ASP* 3.4 17.5 - - - +
154D ILE* 1.3 72.5 - - - +
156D LEU* 1.3 56.7 + - - +
158D THR 3.1 0.3 + - - -
159D GLU* 2.8 66.0 + - + +
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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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152D ASP 3.0 12.2 + - - +
153D GLN* 3.7 11.9 - - - +
154D ILE 3.3 0.2 - - - -
155D LEU* 1.3 76.9 - - - +
157D LYS* 1.3 70.5 + - + +
159D GLU* 4.0 13.1 - - + +
160D GLU* 3.2 24.2 + - - +
163D TYR* 6.2 0.2 - - - +
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Residues in contact with LYS 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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72D GLN* 3.3 31.5 - - + +
76D HIS* 3.9 17.3 - - - +
153D GLN* 3.6 12.7 + - + +
154D ILE 3.3 6.8 + - - +
155D LEU 3.3 0.4 - - - -
156D LEU* 1.3 83.5 - - + +
158D THR* 1.3 60.2 + - - +
160D GLU* 3.3 21.7 + - - +
161D ARG* 2.9 35.2 + - - +
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Residues in contact with THR 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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40D PHE* 3.8 3.8 - - - -
76D HIS* 3.9 0.5 - - - -
125D GLU* 3.3 25.5 - - - +
128D ILE* 4.4 6.3 - - + -
129D ILE* 3.6 22.4 - - + -
132D LEU* 3.8 13.2 - - + +
154D ILE* 2.8 31.9 + - - +
155D LEU* 3.1 4.0 + - - -
157D LYS* 1.3 74.7 - - - +
159D GLU* 1.3 59.2 + - - +
161D ARG* 3.1 24.7 + - - +
162D ALA* 3.0 27.0 + - - +
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Residues in contact with GLU 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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129D ILE* 3.9 19.3 - - + -
133D ARG* 2.8 33.6 + - - +
155D LEU* 2.8 44.3 + - + +
156D LEU* 4.0 14.3 - - + +
158D THR* 1.3 74.1 - - - +
160D GLU* 1.3 58.2 + - - +
162D ALA* 3.2 2.6 + - - +
163D TYR* 2.9 44.3 + - + +
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Residues in contact with GLU 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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72D GLN* 5.0 2.3 + - - -
156D LEU* 3.2 16.8 + - - +
157D LYS* 3.4 33.3 + - - +
158D THR 3.2 0.2 - - - -
159D GLU* 1.3 80.1 - - - +
161D ARG* 1.3 60.8 + - + +
163D TYR* 3.6 23.3 + - - +
164D HIS* 2.6 55.7 + - + -
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Residues in contact with ARG 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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40D PHE* 3.7 12.3 - - - -
43D LEU* 4.7 0.2 - - - +
47D TYR* 4.4 2.5 - - - +
65D PHE* 4.4 3.0 - - + -
69D CYS* 4.0 36.3 - - - +
72D GLN* 3.2 33.3 + - - +
73D VAL* 3.8 13.3 - - - +
76D HIS* 3.0 31.7 + - - -
125D GLU* 2.6 45.0 + - - +
157D LYS 2.9 18.7 + - - +
158D THR* 3.1 25.6 + - - +
159D GLU 3.3 0.2 - - - -
160D GLU* 1.3 74.8 - - + +
162D ALA* 1.3 64.1 + - - +
164D HIS* 3.2 8.5 + - - +
165D ILE* 3.0 28.5 + - - +
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Residues in contact with ALA 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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122D LEU* 3.5 27.2 - - + +
125D GLU* 4.0 13.2 - - + +
126D GLN* 5.3 1.6 - - + -
129D ILE* 3.8 21.3 - - + -
158D THR 3.0 13.6 + - - +
159D GLU* 3.5 8.3 - - - +
161D ARG* 1.3 75.6 - - - +
163D TYR* 1.3 57.9 + - + +
165D ILE* 3.2 9.1 + - - +
166D GLY* 3.0 21.8 + - - -
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Residues in contact with TYR 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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156D LEU* 5.7 0.4 - - - +
159D GLU* 2.9 35.2 + - + -
160D GLU* 3.7 22.5 + - - +
162D ALA* 1.3 74.2 - - - +
164D HIS* 1.3 89.7 + + - +
165D ILE 3.3 0.2 - - - -
166D GLY* 3.7 3.9 - - - +
167D HIS* 3.1 48.5 + + + +
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Residues in contact with HIS 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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65D PHE* 4.1 24.2 - + + -
160D GLU* 2.6 56.7 + - + +
161D ARG* 3.2 6.5 + - - +
163D TYR* 1.3 92.7 - + - +
165D ILE* 1.3 63.2 + - - +
167D HIS* 3.4 15.6 + + - +
168D PHE* 3.3 24.9 + - - -
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Residues in contact with ILE 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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47D TYR* 3.3 28.5 - - + +
65D PHE* 3.8 20.2 - - + -
118D LEU* 3.3 33.0 - - + +
121D ASP* 3.8 19.3 - - + -
122D LEU* 3.7 21.8 - - + +
125D GLU* 4.2 5.8 - - + -
161D ARG 3.0 19.2 + - - +
162D ALA* 3.2 6.9 + - - +
164D HIS* 1.3 73.0 - - - +
166D GLY* 1.3 65.6 + - - +
168D PHE* 3.1 13.0 + - - +
169D LEU* 3.0 28.4 + - + +
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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
------------------------------------------------------------
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