Contacts of the helix formed by residues 146 - 160 (chain A) in PDB entry 3R27
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A PRO* 4.3 4.7 - - - -
127A PRO* 4.8 5.8 + - + +
144A PHE* 3.0 17.8 - - - +
145A GLU* 1.3 82.5 - - + +
147A VAL* 1.3 82.0 + - - +
148A LEU* 3.1 34.6 + - + +
149A GLY* 3.1 16.1 + - - +
150A ALA 3.5 0.3 + - - -
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Residues in contact with VAL 147 (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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100A ALA* 3.8 25.6 - - + +
101A SER* 3.7 24.5 - - - +
102A PRO* 3.9 22.6 - - + +
146A ASP* 1.3 81.0 + - - +
148A LEU* 1.3 69.0 + - + +
150A ALA* 3.2 3.0 + - - +
151A CYS* 2.8 28.0 + - + +
173A TYR* 5.3 0.2 - - + -
177A GLN* 5.7 0.4 - - - +
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Residues in contact with LEU 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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146A ASP* 3.1 23.3 + - + +
147A VAL* 1.3 84.0 - - + +
149A GLY* 1.3 61.1 + - - +
151A CYS* 3.5 10.7 - - + +
152A ASN* 3.0 35.8 + - - +
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Residues in contact with GLY 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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125A PHE* 3.3 26.1 - - - +
126A GLY* 4.2 5.2 - - - -
127A PRO* 5.9 0.2 - - - -
144A PHE* 3.8 18.4 - - - -
146A ASP* 3.1 13.6 + - - +
148A LEU* 1.3 78.4 - - - +
150A ALA* 1.3 60.6 + - - +
152A ASN* 3.2 6.8 + - - +
153A ALA* 3.2 17.0 + - - +
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Residues in contact with ALA 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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101A SER 2.9 29.6 - - - +
102A PRO* 3.6 21.3 - - + +
104A VAL* 3.7 8.5 - - + -
144A PHE* 3.5 16.5 - - + -
146A ASP 3.5 3.8 + - - -
147A VAL 3.2 6.4 + - - +
149A GLY* 1.3 73.5 - - - +
151A CYS* 1.3 58.0 + - - +
153A ALA* 3.3 3.6 + - - +
154A VAL* 3.1 33.6 + - - +
173A TYR* 3.9 3.1 - - + -
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Residues in contact with CYS 151 (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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100A ALA* 5.6 1.3 - - + -
147A VAL* 2.8 17.3 + - + +
148A LEU* 3.5 14.8 - - + +
149A GLY 3.3 0.2 - - - -
150A ALA* 1.3 73.2 - - - +
152A ASN* 1.3 66.2 + - - +
154A VAL* 3.3 0.9 + - - +
155A ASN* 2.9 48.8 + - - +
173A TYR* 3.3 23.9 - - + +
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Residues in contact with ASN 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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124A GLU 5.0 1.4 + - - -
125A PHE* 2.8 40.2 + - + +
148A LEU* 3.0 18.9 + - - +
149A GLY 3.4 8.1 - - - +
151A CYS* 1.3 77.5 - - - +
153A ALA* 1.3 57.6 + - - +
155A ASN* 3.5 12.8 + - - +
156A TYR* 3.0 29.1 + - - +
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Residues in contact with ALA 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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104A VAL* 4.9 0.9 - - + -
122A LEU* 4.6 8.1 - - + -
125A PHE* 3.6 32.2 - - + -
144A PHE* 3.9 22.0 - - + -
149A GLY 3.2 2.6 + - - -
150A ALA 3.7 7.2 - - - +
151A CYS 3.3 0.2 - - - -
152A ASN* 1.3 79.4 - - - +
154A VAL* 1.3 56.6 + - - +
156A TYR* 3.4 3.1 + - - +
157A ALA* 3.0 28.6 + - - +
162A ILE* 3.8 5.3 - - + +
171A VAL* 4.7 11.2 - - + -
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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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104A VAL* 3.9 10.1 - - + -
150A ALA 3.1 17.3 + - - +
153A ALA* 1.3 71.7 - - - +
155A ASN* 1.3 66.9 + - - +
157A ALA* 3.2 8.1 + - - +
158A ALA* 3.0 23.6 + - + +
171A VAL* 4.6 8.7 - - + +
172A ASN* 4.0 17.5 - - - +
173A TYR* 3.6 57.9 - - + +
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A CYS* 2.9 47.5 + - - +
152A ASN* 3.5 13.2 + - - +
154A VAL* 1.3 75.4 - - - +
156A TYR* 1.3 64.1 + - - +
158A ALA* 3.1 21.0 + - - +
159A ASP* 3.6 8.8 + - - +
173A TYR* 4.7 3.1 + - - -
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Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLU* 4.3 8.3 - - - -
125A PHE* 3.5 28.0 - + + -
152A ASN 3.0 9.4 + - - +
153A ALA 3.5 8.5 - - - +
154A VAL 3.3 0.2 - - - -
155A ASN* 1.3 72.0 - - - +
157A ALA* 1.3 58.4 + - - +
158A ALA 3.2 0.5 + - - -
159A ASP 3.2 1.4 + - - -
160A ASN* 2.8 69.1 + - + +
161A GLN 3.9 3.8 + - - -
162A ILE* 3.6 21.1 - - + -
181A GOL 3.4 41.7 + - - -
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Residues in contact with ALA 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 ALA 3.0 16.7 + - - +
154A VAL 3.2 5.6 + - - +
156A TYR* 1.3 78.7 - - - +
158A ALA* 1.3 61.4 + - - +
159A ASP 3.4 0.2 - - - -
160A ASN 3.0 21.1 - - - +
162A ILE* 4.1 9.2 - - + +
169A ALA 6.0 0.9 - - - +
170A PHE* 6.0 0.4 - - - -
171A VAL* 3.9 36.6 - - + +
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Residues in contact with ALA 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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154A VAL* 3.0 13.7 + - + +
155A ASN* 3.3 14.6 - - - +
156A TYR 3.1 0.6 - - - -
157A ALA* 1.3 79.2 - - - +
159A ASP* 1.3 65.7 + - - +
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Residues in contact with ASP 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 ASN 3.6 6.0 + - - +
156A TYR 3.2 2.0 + - - +
158A ALA* 1.3 83.3 - - - +
160A ASN* 1.3 78.2 + - - +
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Residues in contact with ASN 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 TYR* 2.8 57.8 + - + +
157A ALA* 3.0 27.1 + - - +
158A ALA 3.6 0.2 - - - -
159A ASP* 1.3 96.5 - - - +
161A GLN* 1.3 62.7 + - - +
162A ILE 3.7 0.7 + - - -
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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