Contacts of the helix formed by residues 146 - 160 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PRO* 4.3 5.8 - - - -
127B PRO* 4.8 5.7 + - + +
144B PHE* 3.4 14.8 - - - +
145B GLU* 1.3 81.5 - - + +
147B VAL* 1.3 80.1 + - - +
148B LEU* 3.1 35.7 + - + +
149B GLY* 3.0 21.0 + - - +
150B ALA 3.5 0.3 + - - -
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Residues in contact with VAL 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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100B ALA* 3.8 30.5 - - + -
101B SER* 3.8 17.5 - - - +
102B PRO* 3.9 23.2 - - + +
146B ASP* 1.3 81.3 + - - +
148B LEU* 1.3 67.2 + - + +
150B ALA* 3.2 1.8 + - - +
151B CYS* 2.8 29.1 + - + +
177B GLN* 5.9 0.4 - - - +
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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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146B ASP* 3.1 26.2 - - + +
147B VAL* 1.3 85.2 - - + +
149B GLY* 1.3 56.4 + - - +
151B CYS* 3.5 10.9 + - + +
152B ASN* 3.0 35.8 + - - +
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Residues in contact with GLY 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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125B PHE* 3.3 25.8 - - - +
126B GLY* 4.1 4.7 - - - -
127B PRO* 5.9 0.2 - - - -
144B PHE* 3.7 17.3 - - - -
146B ASP* 3.0 13.5 + - - +
148B LEU* 1.3 76.1 - - - +
150B ALA* 1.3 63.4 + - - +
152B ASN* 3.1 6.4 + - - +
153B ALA* 3.1 18.2 + - - +
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Residues in contact with ALA 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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101B SER 2.9 29.6 - - - +
102B PRO* 3.6 20.4 - - + +
104B VAL* 3.7 12.3 - - + -
144B PHE* 3.5 16.4 - - + -
146B ASP 3.5 1.6 + - - -
147B VAL 3.2 6.6 + - - +
149B GLY* 1.3 73.9 - - - +
151B CYS* 1.3 57.4 + - - +
153B ALA* 3.2 2.9 + - - +
154B VAL* 2.9 33.4 + - - +
173B TYR* 3.9 3.1 - - + -
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Residues in contact with CYS 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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100B ALA* 5.6 1.1 - - + -
147B VAL* 2.8 22.6 + - + +
148B LEU* 3.6 14.6 - - + +
149B GLY 3.3 0.2 - - - -
150B ALA* 1.3 72.7 - - - +
152B ASN* 1.3 57.3 + - - +
154B VAL* 3.8 0.3 - - - +
155B ASN* 2.9 57.3 + - - +
173B TYR* 3.3 23.5 - - + +
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Residues in contact with ASN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 3.6 31.4 + - - +
124B GLU 5.2 0.8 + - - -
125B PHE* 2.9 38.5 + - + +
148B LEU* 3.0 19.7 + - - +
149B GLY 3.1 7.8 + - - +
151B CYS* 1.3 79.1 - - - +
153B ALA* 1.3 56.6 + - - +
155B ASN* 3.5 3.8 + - - +
156B TYR* 2.9 30.0 + - - +
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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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104B VAL* 4.9 0.9 - - + -
122B LEU* 4.6 6.7 - - + -
125B PHE* 3.6 32.5 - - + -
144B PHE* 3.8 23.6 - - + -
149B GLY 3.1 5.2 + - - +
150B ALA 3.2 7.4 + - - +
152B ASN* 1.3 76.0 - - - +
154B VAL* 1.3 58.3 + - - +
156B TYR* 3.4 3.3 + - - +
157B ALA* 3.0 28.8 + - - +
162B ILE* 3.7 5.2 - - + +
171B VAL* 4.8 11.4 - - + -
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Residues in contact with VAL 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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104B VAL* 4.0 11.4 - - + -
150B ALA 2.9 19.5 + - - +
151B CYS 4.0 0.2 - - - +
153B ALA* 1.3 73.0 - - - +
155B ASN* 1.3 66.7 + - - +
157B ALA* 3.3 8.2 + - - +
158B ALA* 3.1 22.0 + - + +
171B VAL* 4.5 5.6 - - + +
172B ASN* 4.0 15.3 - - + -
173B TYR* 3.7 59.9 - - + +
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Residues in contact with ASN 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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136A LYS 5.3 1.1 - - - +
138A ARG* 3.0 33.7 - - - +
151B CYS* 2.9 46.3 + - - +
152B ASN* 4.5 1.0 + - - -
154B VAL* 1.3 77.6 - - - +
156B TYR* 1.3 63.1 + - - +
158B ALA* 3.2 20.8 + - - +
159B ASP* 3.7 10.9 + - - +
173B TYR* 4.5 3.8 + - - -
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Residues in contact with TYR 156 (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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136A LYS 4.7 3.4 - - - -
137A LYS* 3.4 57.0 + - + -
138A ARG* 5.0 0.8 - - - +
139A GLN* 3.4 29.8 + - - -
124B GLU* 4.4 0.2 - - - -
125B PHE* 3.5 20.9 - + + -
152B ASN 2.9 17.8 + - - +
153B ALA 3.5 5.4 - - - +
154B VAL 3.3 0.2 - - - -
155B ASN* 1.3 74.8 - - - +
157B ALA* 1.3 59.2 + - - +
158B ALA 3.3 0.5 + - - -
159B ASP 3.3 1.0 + - - -
160B ASN* 2.9 51.1 + - + +
161B GLN 4.0 8.9 + - - -
162B ILE* 3.5 29.6 - - + -
181B GOL 3.7 20.4 + - - -
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Residues in contact with ALA 157 (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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153B ALA 3.0 16.4 + - - +
154B VAL 3.3 5.8 + - - +
156B TYR* 1.3 75.4 - - - +
158B ALA* 1.3 63.4 + - - +
160B ASN 3.0 20.3 + - - +
162B ILE* 3.9 17.7 - - + +
169B ALA 6.0 0.7 - - - +
170B PHE* 6.1 0.2 - - - -
171B VAL* 3.9 28.3 - - + +
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Residues in contact with ALA 158 (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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154B VAL* 3.1 13.8 + - + +
155B ASN* 3.2 14.8 + - - +
157B ALA* 1.3 77.7 - - - +
159B ASP* 1.3 64.1 - - - +
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Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 3.9 41.5 + - - +
155B ASN 3.7 8.1 + - - +
156B TYR 3.3 2.2 + - - +
158B ALA* 1.3 82.4 - - - +
160B ASN* 1.3 78.0 + - - +
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Residues in contact with ASN 160 (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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136A LYS* 3.2 30.4 + - - +
137A LYS* 3.3 35.7 - - - +
156B TYR* 2.9 43.5 + - + +
157B ALA* 3.0 26.4 - - - +
158B ALA 3.7 0.6 - - - -
159B ASP* 1.3 89.1 - - - +
161B GLN* 1.3 63.3 + - - +
162B ILE 3.7 0.2 + - - -
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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