Contacts of the helix formed by residues 147 - 164 (chain M) in PDB entry 1VYH
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 ASN 147 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142M ARG 3.2 18.9 + - - +
143M GLY* 4.0 3.8 - - - -
145M LYS 2.8 20.5 - - - +
146M PRO* 1.3 74.9 - - - +
148M PRO* 1.3 69.6 - - + +
149M LEU* 2.8 53.7 + - - +
150M ARG* 3.0 24.3 + - - +
151M GLN* 3.4 13.6 + - - +
20N GLY 4.1 11.2 + - - +
21N ASP* 3.8 22.0 - - - +
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Residues in contact with PRO 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147M ASN* 1.3 86.6 - - + -
149M LEU* 1.3 62.6 + - + +
151M GLN* 3.2 17.8 - - + +
152M LYS* 3.0 24.1 + - - +
20N GLY* 4.5 15.3 - - - +
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Residues in contact with LEU 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M THR 5.6 0.2 - - - +
107M HIS* 4.0 12.3 - - + +
142M ARG* 3.1 45.5 - - + +
147M ASN* 2.8 17.0 + - - +
148M PRO* 1.3 77.6 - - + +
150M ARG* 1.3 66.9 + - - +
151M GLN 2.9 1.8 - - - -
152M LYS* 2.9 39.3 + - + +
153M ASN* 3.0 24.1 + - - +
19N GLN 3.6 22.0 - - - +
20N GLY* 4.6 2.2 - - - -
21N ASP* 3.6 23.1 - - + +
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Residues in contact with ARG 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141M PRO* 3.9 28.1 - - + +
142M ARG* 3.4 19.3 + - - +
143M GLY 2.8 25.5 + - - -
144M GLU 2.9 21.8 + - - -
145M LYS 3.3 3.2 - - - -
146M PRO* 3.4 29.0 - - + +
147M ASN* 3.0 18.7 + - - +
149M LEU* 1.3 78.5 - - - +
151M GLN* 1.3 59.7 + - - +
153M ASN* 4.3 2.6 - - - +
154M ALA* 3.3 21.7 + - - +
180M VAL* 3.2 21.0 - - - +
184M GLY* 2.6 24.7 + - - -
186M ILE* 3.4 10.6 - - - +
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Residues in contact with GLN 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147M ASN* 3.4 18.0 + - - +
148M PRO* 3.2 16.8 - - + +
150M ARG* 1.3 78.3 - - - +
152M LYS* 1.3 66.0 + - - +
154M ALA* 3.1 8.4 - - - +
155M LYS* 3.0 40.9 + - - +
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Residues in contact with LYS 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M GLY 5.7 2.0 - - - -
104M THR 6.0 0.2 + - - -
106M ASN* 3.7 19.5 + - - -
107M HIS* 3.8 15.8 - - - +
108M GLU 4.9 0.4 - - - +
109M ASN 3.3 26.0 + - - +
110M THR* 4.8 0.7 - - - -
111M ALA* 3.8 26.0 - - + +
114M VAL* 4.8 6.5 - - - -
148M PRO 3.0 9.9 + - - +
149M LEU* 2.9 33.7 + - + +
151M GLN* 1.3 79.2 - - - +
153M ASN* 1.3 71.8 + - - +
155M LYS* 3.0 19.9 + - - +
156M VAL* 3.0 15.4 + - + +
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Residues in contact with ASN 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M GLY 5.4 0.3 - - - +
104M THR* 3.4 28.4 + - - +
139M LEU* 3.7 30.7 - - + +
140M LEU 2.9 28.1 + - - +
141M PRO* 5.5 0.2 - - + -
142M ARG* 4.2 7.9 - - - +
149M LEU* 3.0 18.6 + - - +
150M ARG* 4.3 4.5 - - - +
152M LYS* 1.3 83.3 - - - +
154M ALA* 1.3 64.5 + - - +
156M VAL* 3.1 11.4 + - - +
157M ASN* 3.0 29.8 + - - +
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Residues in contact with ALA 154 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150M ARG 3.3 15.9 + - - +
151M GLN* 3.1 14.3 + - + +
153M ASN* 1.3 76.2 - - - +
155M LYS* 1.3 63.4 + - - +
157M ASN* 3.0 13.0 + - - +
158M GLN* 2.9 21.7 + - - +
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Residues in contact with LYS 155 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M ALA* 3.5 17.7 - - + +
112M GLU* 4.0 18.8 - - - +
151M GLN* 3.0 35.3 + - - +
152M LYS* 3.0 13.7 + - - +
154M ALA* 1.3 75.1 - - - +
156M VAL* 1.3 68.3 + - - +
158M GLN* 2.9 15.8 + - + +
159M LEU* 2.9 34.4 + - + +
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Residues in contact with VAL 156 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111M ALA* 3.8 20.6 - - - +
114M VAL* 3.6 27.4 - - + -
115M ALA* 4.5 5.3 - - - +
118M ILE* 4.1 9.6 - - + -
139M LEU* 3.8 25.4 - - + -
152M LYS* 3.0 20.4 + - + +
153M ASN* 3.1 10.5 + - - +
155M LYS* 1.3 75.2 - - - +
157M ASN* 1.3 67.1 + - - +
159M LEU* 3.2 5.6 + - - +
160M LEU* 2.9 47.4 + - + +
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Residues in contact with ASN 157 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M GLY* 3.7 7.2 - - - -
139M LEU* 2.9 45.0 + - - +
153M ASN 3.0 13.4 + - - +
154M ALA* 3.0 11.8 + - - +
156M VAL* 1.3 78.8 - - - +
158M GLN* 1.3 62.1 + - - +
160M LEU* 3.2 8.2 + - - +
161M LYS* 2.9 24.6 + - - +
172M LEU* 4.1 6.6 - - + +
174M ASP* 2.7 35.5 + - - +
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Residues in contact with GLN 158 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154M ALA 2.9 9.9 + - - +
155M LYS* 2.9 22.6 + - + +
157M ASN* 1.3 77.5 - - - +
159M LEU* 1.3 70.3 + - + +
161M LYS* 3.1 19.3 + - - +
162M VAL* 3.4 11.1 + - - +
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Residues in contact with LEU 159 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M ALA 4.5 2.2 - - - +
112M GLU* 3.7 45.8 - - + +
115M ALA* 4.0 17.7 - - + -
119M GLU* 5.3 1.6 - - - +
155M LYS* 2.9 21.9 + - + +
156M VAL 3.7 5.8 - - - +
158M GLN* 1.3 84.3 - - + +
160M LEU* 1.3 57.1 + - - +
162M VAL* 3.3 13.6 + - + +
163M SER* 2.9 32.6 + - - -
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Residues in contact with LEU 160 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M ALA* 4.0 25.1 - - + +
118M ILE* 3.6 45.1 - - + -
119M GLU* 4.4 3.1 - - + -
136M VAL* 4.4 13.2 - - + -
138M GLY* 5.4 3.1 - - - -
139M LEU* 5.9 0.4 - - + +
156M VAL* 2.9 29.1 + - + +
157M ASN* 3.7 8.1 - - - +
158M GLN 3.2 0.2 - - - -
159M LEU* 1.3 72.2 - - - +
161M LYS* 1.3 66.3 + - - +
162M VAL 3.0 1.8 - - - -
163M SER* 3.6 10.5 - - - +
164M LEU* 2.9 42.4 + - + +
172M LEU* 4.3 16.4 - - + -
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Residues in contact with LYS 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157M ASN 2.9 13.1 + - - +
158M GLN* 3.1 15.6 + - - +
160M LEU* 1.3 75.7 - - - +
162M VAL* 1.3 59.0 + - + +
165M PRO* 3.1 24.7 - - - +
172M LEU* 3.6 22.8 - - + +
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Residues in contact with VAL 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158M GLN 3.4 6.8 + - - +
159M LEU* 3.3 19.4 + - + +
160M LEU 3.0 0.4 - - - -
161M LYS* 1.3 84.1 - - + +
163M SER* 1.3 69.3 + - - +
164M LEU 3.5 0.2 - - - -
165M PRO* 3.6 8.5 - - - +
166M LYS* 4.3 20.9 + - - +
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Residues in contact with SER 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M GLU* 3.3 37.7 + - - +
159M LEU 2.9 20.8 + - - -
160M LEU* 3.6 9.7 - - - +
162M VAL* 1.3 79.2 - - - +
164M LEU* 1.3 62.7 + - - +
165M PRO 3.7 0.2 - - - -
166M LYS* 3.7 17.3 - - - +
167M LEU* 3.4 24.2 - - - +
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Residues in contact with LEU 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118M ILE* 5.0 1.3 - - + -
119M GLU* 5.4 6.3 - - + -
122M VAL* 4.1 17.0 - - + -
136M VAL* 4.0 29.2 - - + -
160M LEU* 2.9 36.2 + - + +
163M SER* 1.3 82.4 + - - +
165M PRO* 1.3 55.3 - - + +
166M LYS 2.2 26.3 - - - +
167M LEU* 3.6 11.1 - - + +
170M VAL* 3.7 46.3 - - + +
171M GLN* 4.7 1.6 - - - -
172M LEU* 4.1 26.2 - - + +
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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