Contacts of the helix formed by residues 145 - 162 (chain A) 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 GLY 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 1.3 77.2 - - - +
146A ALA* 1.3 64.2 + - - +
147A GLN* 3.1 17.0 + - - +
148A TYR* 3.0 25.4 + - - +
149A ILE 3.7 0.9 + - - -
171A THR* 4.6 2.6 + - - -
175A GLY 5.1 2.5 - - - -
178A GLN* 4.7 4.3 - - - -
180A ASP* 3.3 24.8 - - - +
181A PHE* 4.5 9.2 - - - -
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN* 3.7 7.4 - - - +
143A ILE* 3.0 17.8 + - + +
144A ILE 3.4 1.4 + - - -
145A GLY* 1.3 77.2 - - - +
147A GLN* 1.3 63.0 + - - +
148A TYR 3.1 0.9 + - - -
149A ILE* 3.4 9.7 + - + +
150A GLN* 3.2 29.3 + - - +
180A ASP* 4.2 10.9 + - - +
91B ASP* 3.8 10.8 - - - +
96B GLN* 3.5 30.7 - - + +
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 3.6 23.1 - - + +
100A PRO 4.3 3.1 - - - +
101A GLY* 4.4 8.7 - - - -
138A LEU* 6.3 0.4 - - + -
141A GLN* 3.6 24.2 + - + +
143A ILE 3.3 5.7 - - - +
144A ILE* 4.6 3.8 - - - +
145A GLY* 3.1 13.4 + - - +
146A ALA* 1.3 81.6 + - - +
148A TYR* 1.3 60.0 + - + +
150A GLN* 4.5 9.2 - - - -
151A ALA* 2.9 29.7 + - - +
169A THR* 3.0 26.8 + - - +
170A TYR 3.1 22.7 + - - +
171A THR* 3.7 18.0 + - - +
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Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLY* 3.0 13.8 + - - +
147A GLN* 1.3 84.0 - - + +
149A ILE* 1.3 65.8 + - - +
151A ALA* 3.2 15.0 + - - +
152A ALA 3.2 9.7 + - - -
169A THR* 3.7 21.3 - - + -
170A TYR 4.1 0.4 - - - -
171A THR* 3.4 38.6 - - + +
180A ASP 3.6 10.1 - - - +
181A PHE* 3.3 41.3 - + - -
184A GLY* 3.7 9.9 - - - -
185A ILE* 3.7 2.5 - - + -
197A PHE* 3.3 38.7 - + + +
198A VAL 3.0 32.1 + - - -
199A VAL* 3.5 6.8 - - - +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ALA* 3.4 15.9 - - + +
148A TYR* 1.3 75.5 - - - +
150A GLN* 1.3 66.1 + - + +
152A ALA* 3.5 5.8 + - - +
153A GLY 3.4 10.6 + - - -
180A ASP* 3.3 37.7 - - - +
183A GLU* 3.8 13.9 - - + -
184A GLY* 3.5 18.4 - - - +
187A PHE* 6.3 0.2 - - + -
60B SER* 3.3 36.6 - - - +
61B GLY* 4.1 11.6 - - - +
64B GLY* 3.1 24.4 - - - +
65B LEU 3.8 1.0 + - - -
91B ASP* 6.0 0.9 - - - +
92B SER* 3.7 13.9 - - - +
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Residues in contact with GLN 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.7 12.8 - - + +
138A LEU* 3.5 23.8 - - + +
141A GLN* 3.7 10.9 + - - +
146A ALA* 3.2 21.1 + - - +
147A GLN* 4.0 2.5 - - - +
149A ILE* 1.3 77.1 - - + +
151A ALA* 1.3 58.8 + - - +
153A GLY* 3.1 3.3 + - - -
154A VAL* 2.9 30.0 + - + +
64B GLY* 3.3 12.3 - - - +
67B ILE* 3.8 36.7 - - + +
68B GLY* 3.5 3.4 - - - +
71B LEU* 5.5 0.2 - - + -
92B SER* 5.8 0.4 + - - -
96B GLN* 3.1 41.6 + - - +
100B ILE* 5.3 2.0 - - - +
103B ARG* 5.1 0.9 + - - +
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 3.7 17.0 - - + -
147A GLN 2.9 20.2 + - - +
148A TYR 3.2 7.2 + - - +
150A GLN* 1.3 73.3 - - - +
152A ALA* 1.3 65.9 + - - +
153A GLY 3.0 2.2 - - - -
154A VAL* 3.1 1.6 + - - +
155A ALA* 2.9 27.1 + - - +
167A ALA* 3.9 6.7 - - + +
169A THR* 3.7 26.9 - - + +
195A ALA* 4.9 3.6 - - + -
197A PHE* 4.1 6.3 - - + -
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Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TYR 3.2 5.8 + - - +
149A ILE 3.7 9.9 - - - +
151A ALA* 1.3 78.6 - - - +
153A GLY* 1.3 60.2 + - - +
155A ALA* 3.9 3.6 + - - +
156A LEU* 3.3 22.2 + - - +
184A GLY* 3.5 26.0 - - - +
187A PHE* 4.0 12.1 - - + -
188A ALA* 3.9 24.0 - - + +
191A PHE* 6.0 0.9 - - - +
193A ALA* 4.4 4.2 - - - +
197A PHE* 4.6 1.9 - - + -
65B LEU* 3.8 8.2 - - + +
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE 3.4 4.0 + - - -
150A GLN 3.1 7.3 + - - -
151A ALA 3.0 0.8 - - - -
152A ALA* 1.3 78.4 - - - +
154A VAL* 1.3 63.9 + - - +
156A LEU* 3.4 3.6 + - - +
157A GLY 3.1 17.0 + - - -
65B LEU* 3.6 33.8 - - - +
68B GLY* 3.5 8.2 - - - -
69B LEU* 3.5 10.2 + - - +
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE* 3.8 31.6 - - + -
99A LEU* 4.0 14.6 - - + -
150A GLN 2.9 18.7 + - - +
151A ALA 3.1 5.1 + - - +
153A GLY* 1.3 75.4 - - - +
155A ALA* 1.3 64.4 + - - +
157A GLY* 3.0 12.0 + - - -
158A LEU* 3.0 14.9 + - + +
167A ALA* 3.8 15.0 - - + -
68B GLY* 3.6 22.4 - - - +
71B LEU* 3.8 20.0 - - + -
72B GLN* 3.5 14.8 - - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA 2.9 15.1 + - - +
152A ALA 4.1 1.6 - - - +
154A VAL* 1.3 77.1 - - - +
156A LEU* 1.3 62.7 + - - +
158A LEU* 3.2 6.2 + - - +
159A LYS 3.0 18.0 + - - -
167A ALA* 3.7 8.2 - - + +
193A ALA* 3.8 9.4 - - + -
194A PRO* 3.3 48.1 - - - +
195A ALA* 3.7 12.1 - - + -
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ALA 3.3 16.0 + - - +
153A GLY 3.6 5.6 - - - +
154A VAL 3.2 0.4 - - - -
155A ALA* 1.3 78.7 - - - +
157A GLY* 1.3 57.7 + - - +
159A LYS* 3.1 20.4 + - + +
160A MET* 2.9 49.4 + - + +
191A PHE* 4.2 35.0 - - + +
193A ALA* 4.0 6.4 - - + +
53B PHE* 4.5 10.3 - - + -
65B LEU* 3.8 31.6 - - + -
69B LEU* 4.0 16.2 - - + -
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLY 3.1 8.0 + - - -
154A VAL 3.0 8.2 + - - -
156A LEU* 1.3 78.0 - - - +
158A LEU* 1.3 60.4 + - - +
160A MET 3.4 0.3 + - - -
161A ARG* 3.0 28.4 + - - +
69B LEU* 3.7 9.3 - - - +
72B GLN* 3.8 16.4 - - - -
74B PHE* 3.6 21.9 - - - -
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLU 4.8 6.5 - - - +
97A PHE* 4.8 3.8 - - + +
154A VAL* 3.0 25.7 + - + +
155A ALA* 3.2 10.1 + - - +
157A GLY* 1.3 76.0 - - - +
159A LYS* 1.3 61.2 + - - +
161A ARG 3.3 1.2 + - - -
162A GLY 3.1 3.6 + - - -
163A LYS* 2.9 59.8 + - + +
165A ALA* 3.8 25.8 - - + +
166A VAL* 3.6 33.7 - - - +
167A ALA 3.9 3.1 - - - +
194A PRO* 4.6 1.1 - - + -
72B GLN* 3.4 29.1 - - - +
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ALA 3.0 14.1 + - - +
156A LEU* 3.3 19.9 - - + +
158A LEU* 1.3 76.0 - - - +
160A MET* 1.3 60.3 + - + +
162A GLY* 2.9 20.6 + - - -
163A LYS 5.1 3.1 - - - +
191A PHE 2.9 26.7 + - - +
192A LYS* 2.9 31.5 + - - +
193A ALA* 4.5 0.4 - - - -
194A PRO* 3.9 15.7 - - + +
255A GLY* 5.4 9.2 + - - -
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Residues in contact with MET 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 2.9 36.3 + - + +
157A GLY 3.9 0.2 - - - +
159A LYS* 1.3 77.1 - - + +
161A ARG* 1.3 61.7 + - - +
162A GLY* 3.4 0.7 + - - -
24B LEU* 3.8 25.1 - - + -
50B ASP* 3.2 37.2 - - + +
51B ARG* 5.8 0.4 - - + -
53B PHE* 5.0 5.2 - - + -
69B LEU* 4.0 24.0 - - - -
74B PHE* 3.7 19.3 - - + -
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLY 3.0 22.4 + - - +
158A LEU 3.7 0.2 - - - +
159A LYS 3.2 0.4 - - - -
160A MET* 1.3 75.0 - - - +
162A GLY* 1.3 61.0 + - - +
163A LYS* 3.3 36.5 + - + +
22B ASN* 2.9 28.9 + - - +
72B GLN* 3.1 27.6 + - - +
73B GLY* 3.3 18.4 + - - -
74B PHE* 3.3 24.6 - - + +
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Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LYS* 2.9 16.4 + - - -
160A MET 3.1 1.9 - - - -
161A ARG* 1.3 80.2 - - - +
163A LYS* 1.3 63.5 + - - +
164A LYS* 3.7 19.6 + - - +
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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