Contacts of the helix formed by residues 148 - 159 (chain B) in PDB entry 2CLS
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 SER 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B ARG* 3.4 13.0 + - - +
146B PRO 3.3 3.6 + - - -
147B ILE* 1.3 77.5 - - - +
149B TYR* 1.3 65.8 + - - +
150B GLU* 3.4 12.1 + - - +
151B GLN* 3.1 39.2 + - - +
152B GLY* 2.9 19.6 + - - -
164B TYR* 4.8 0.3 + - - -
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Residues in contact with TYR 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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130B ARG* 3.4 8.9 - - - +
148B SER* 1.3 73.7 - - - +
150B GLU* 1.3 71.1 + - + +
152B GLY* 3.2 2.6 + - - -
153B CYS* 3.1 47.2 + - - -
164B TYR* 3.7 28.3 + + - -
165B LEU* 5.7 0.9 - - - -
166B GLU* 3.7 38.8 - - + +
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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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148B SER* 3.2 10.0 + - - +
149B TYR* 1.3 86.0 - - + +
151B GLN* 1.3 61.3 + - + +
153B CYS* 3.2 9.6 + - - +
154B ALA* 3.1 20.3 + - - +
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Residues in contact with GLN 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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145B ALA 5.0 0.9 - - - +
146B PRO 3.7 5.3 + - - +
147B ILE* 3.4 24.3 - - + +
148B SER* 3.1 37.7 + - - +
150B GLU* 1.3 74.1 - - + +
152B GLY* 1.3 67.8 + - - +
154B ALA* 3.2 8.4 + - - +
155B ILE* 2.9 35.7 + - + +
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Residues in contact with GLY 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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92B PHE* 4.7 1.1 - - - -
122B LEU* 3.7 2.4 - - - +
147B ILE* 3.9 7.9 - - - +
148B SER 2.9 11.7 + - - -
149B TYR 3.2 4.9 + - - -
151B GLN* 1.3 76.0 - - - +
153B CYS* 1.3 57.4 + - - +
155B ILE* 3.4 5.3 + - - -
156B ALA* 3.1 28.4 + - - +
164B TYR* 3.5 36.2 - - - +
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Residues in contact with CYS 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 TYR* 3.1 55.1 + - - -
150B GLU* 3.6 8.3 - - - +
151B GLN 3.2 0.4 - - - -
152B GLY* 1.3 76.1 - - - +
154B ALA* 1.3 61.7 + - - +
156B ALA* 3.6 3.9 + - - +
157B LYS* 3.2 20.6 + - - +
164B TYR* 4.0 14.1 - - - -
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Residues in contact with ALA 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 3.1 12.4 + - - +
151B GLN* 3.2 10.5 + - - +
153B CYS* 1.3 73.6 - - - +
155B ILE* 1.3 65.2 + - + +
157B LYS* 3.3 9.7 + - - +
158B GLN* 3.1 30.7 + - - +
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Residues in contact with ILE 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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92B PHE* 4.8 3.1 - - + -
100B VAL* 3.5 39.5 - - + +
104B LEU* 3.9 10.8 - - + -
122B LEU* 3.7 10.1 - - + -
147B ILE* 4.2 17.3 - - + -
151B GLN* 2.9 32.9 + - + +
152B GLY* 3.8 5.6 - - - +
154B ALA* 1.3 72.1 - - + +
156B ALA* 1.3 57.4 + - - +
158B GLN* 3.2 19.4 + - + +
159B LEU* 2.9 53.0 + - + +
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Residues in contact with ALA 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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122B LEU* 3.5 13.1 - - + +
152B GLY 3.1 17.7 + - - +
153B CYS* 3.6 6.7 - - - +
155B ILE* 1.3 75.1 - - - +
157B LYS* 1.3 61.7 + - - +
159B LEU* 3.4 1.0 + - - -
160B GLY 3.1 3.6 + - - -
161B ALA* 2.8 48.7 + - + +
163B ILE* 4.1 6.7 - - - +
164B TYR* 3.9 18.6 - - + +
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Residues in contact with LYS 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 CYS 3.2 10.8 + - - +
154B ALA* 3.3 13.0 + - - +
156B ALA* 1.3 79.4 - - - +
158B GLN* 1.3 61.1 + - + +
160B GLY* 3.3 12.5 + - - -
161B ALA 5.1 2.5 - - - -
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Residues in contact with GLN 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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100B VAL* 5.9 0.8 + - - +
101B ASP* 4.6 13.7 + - - +
154B ALA* 3.1 23.8 + - - +
155B ILE* 3.4 25.4 - - + +
157B LYS* 1.3 76.5 - - + +
159B LEU* 1.3 67.9 + - + +
160B GLY 3.4 0.6 + - - -
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Residues in contact with LEU 159 (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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90B LEU* 4.3 7.9 - - + -
100B VAL 5.4 1.6 - - - +
101B ASP 5.4 0.7 - - - +
104B LEU* 3.6 44.6 - - + +
105B LYS* 4.1 12.8 - - + +
108B ARG* 2.9 43.9 + - + +
120B VAL* 6.2 0.2 - - + -
122B LEU* 4.1 15.3 - - + -
155B ILE* 2.9 40.6 + - + +
156B ALA* 4.2 3.6 - - - +
158B GLN* 1.3 84.2 - - + +
160B GLY* 1.3 59.6 + - - +
161B ALA* 3.3 4.8 + - + +
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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