Contacts of the helix formed by residues 146 - 155 (chain B) in PDB entry 6VW1
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 PRO 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B LEU* 5.0 6.7 - - + -
144B LEU 3.8 1.6 - - - -
145B GLU* 1.3 107.0 - - + +
147B GLY* 1.3 60.4 + - - +
148B LEU 3.7 0.2 - - - -
149B ASN* 3.7 1.2 + - - +
150B GLU* 2.9 32.1 + - + +
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Residues in contact with GLY 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 4.4 23.3 - - - +
143B LEU 3.6 8.9 + - - +
146B PRO* 1.3 79.5 - - - +
148B LEU* 1.3 66.1 + - - +
150B GLU* 3.0 8.3 + - - +
151B ILE* 3.0 26.3 + - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B VAL* 3.6 33.9 - - + +
142B LEU* 4.6 6.9 - - + +
143B LEU* 3.3 14.2 + - - +
144B LEU* 3.9 13.2 - - - +
147B GLY* 1.3 73.2 - - - +
149B ASN* 1.3 57.3 + - - +
151B ILE* 3.3 9.8 + - + +
152B MET* 2.9 34.2 + - - +
163B TRP* 3.9 13.0 - - + -
164B ALA* 3.7 24.5 - - + +
168B TRP* 4.0 33.0 - - + -
270B MET* 4.0 19.1 - - + -
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Residues in contact with ASN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 3.0 48.0 + - - +
145B GLU* 3.0 28.7 + - - +
146B PRO 4.1 2.5 - - - +
147B GLY 3.2 0.2 - - - -
148B LEU* 1.3 75.2 - - - +
150B GLU* 1.3 58.7 + - - +
152B MET* 3.4 4.0 + - - +
153B ALA* 2.9 32.4 + - - +
269B ASP* 5.4 3.5 - - - +
270B MET* 4.2 15.2 + - - +
271B TRP* 4.6 8.0 - - - -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B PRO* 2.9 21.8 + - + +
147B GLY* 3.0 7.0 + - - +
149B ASN* 1.3 77.6 - - - +
151B ILE* 1.3 68.4 + - - +
153B ALA* 4.5 1.8 - - - -
154B ASN* 2.7 59.4 + - - +
155B SER 4.1 0.3 + - - -
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 4.2 13.5 - - + -
147B GLY 3.0 16.0 + - - +
148B LEU* 3.5 18.6 - - + +
149B ASN 3.2 0.2 - - - -
150B GLU* 1.3 82.2 - - - +
152B MET* 1.3 60.9 + - - +
155B SER* 2.9 40.9 + - - +
160B GLU* 3.7 42.6 - - + +
161B ARG* 3.6 5.3 + - - -
163B TRP* 4.1 25.4 - - + -
164B ALA* 4.0 15.3 - - + -
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Residues in contact with MET 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LEU 2.9 20.3 + - - +
149B ASN* 4.0 4.5 - - - +
151B ILE* 1.3 74.4 - - - +
153B ALA* 1.3 56.4 + - - +
161B ARG* 2.8 55.7 + - - +
164B ALA* 4.0 12.6 - - + -
165B TRP* 4.1 14.4 - - + -
265B HIS* 3.3 37.0 - - + +
268B GLY* 3.0 12.4 - - - +
269B ASP* 3.2 33.2 - - - +
270B MET* 3.7 24.9 - - + +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ASN 2.9 18.3 + - - +
150B GLU* 3.9 3.6 - - - +
152B MET* 1.3 79.5 - - - +
154B ASN* 1.3 73.5 + - - +
161B ARG* 4.4 3.2 + - - -
268B GLY* 3.3 8.7 - - - +
269B ASP* 5.8 0.4 - - - -
277B ASN* 3.4 41.7 - - - +
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Residues in contact with ASN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLU* 2.7 48.1 + - - +
153B ALA* 1.3 88.6 - - - +
155B SER* 1.3 66.9 + - - +
156B LEU* 3.5 10.2 + - - +
277B ASN* 5.9 0.3 - - - -
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Residues in contact with SER 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLU 4.1 0.4 + - - -
151B ILE* 2.9 27.2 + - - -
154B ASN* 1.3 78.6 - - - +
156B LEU* 1.3 60.0 + - - +
157B ASP* 3.1 21.4 + - - +
160B GLU* 2.6 30.7 + - - -
161B ARG* 2.9 34.4 + - - +
252B TYR* 3.6 2.9 + - - -
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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
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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