Contacts of the helix formed by residues 135 - 146 (chain A) in PDB entry 3LAW
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 ALA 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ARG* 4.2 8.0 + - - +
133A GLN 3.7 4.8 + - - +
134A VAL* 1.3 87.9 - - - +
136A THR* 1.3 66.1 + - - +
137A LYS* 3.2 19.9 + - + +
138A ARG* 3.8 16.2 + - + +
139A ALA* 3.8 5.0 + - - +
151A TYR* 5.0 0.3 + - - -
153A GLU* 4.7 0.3 - - - +
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Residues in contact with THR 136 (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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132A ARG* 3.8 6.3 + - - +
134A VAL 3.8 0.6 + - - -
135A ALA* 1.3 73.3 - - - +
137A LYS* 1.3 78.3 + - + +
139A ALA* 3.9 0.9 - - - +
140A GLN* 2.7 64.1 + - - +
151A TYR* 4.4 6.4 - - + -
153A GLU* 2.8 40.4 + - + +
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Residues in contact with LYS 137 (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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135A ALA* 3.0 11.7 - - + +
136A THR* 1.3 105.4 - - + +
138A ARG* 1.3 57.7 + - - +
140A GLN* 3.7 7.8 - - + +
141A ALA* 3.0 26.3 + - - +
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Residues in contact with ARG 138 (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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93A PRO* 5.4 5.5 - - - +
96A PHE* 3.5 35.2 - - + -
97A LYS* 5.1 18.8 - - - +
134A VAL* 4.2 27.1 - - + +
135A ALA* 3.8 11.0 + - + +
137A LYS* 1.3 75.4 - - - +
139A ALA* 1.3 61.0 + - - +
141A ALA* 3.8 9.0 - - - +
142A TRP* 3.2 23.4 + - - +
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Residues in contact with ALA 139 (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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88A PHE* 3.9 7.0 - - + -
96A PHE* 3.2 28.5 - - + -
134A VAL* 4.4 1.3 - - + -
135A ALA 3.8 10.9 + - - +
136A THR 3.6 1.2 + - - +
137A LYS 3.4 0.2 - - - -
138A ARG* 1.3 78.1 - - - +
140A GLN* 1.3 65.3 + - - +
141A ALA 3.3 0.2 - - - -
142A TRP* 3.6 1.0 - - - +
143A CYS* 3.1 32.9 + - - -
151A TYR* 3.8 29.8 - - + +
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Residues in contact with GLN 140 (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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136A THR* 2.7 46.7 + - - +
137A LYS* 3.7 11.2 - - + +
139A ALA* 1.3 76.2 - - - +
141A ALA* 1.3 65.3 + - - +
143A CYS* 3.4 4.0 + - - +
144A TYR* 3.1 23.0 + - - +
151A TYR* 4.5 23.8 + - + +
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Residues in contact with ALA 141 (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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137A LYS 3.0 18.7 + - - +
138A ARG* 3.8 10.1 - - - +
140A GLN* 1.3 75.2 - - - +
142A TRP* 1.3 51.9 + - - +
144A TYR* 2.9 10.1 + - - +
145A SER* 2.7 35.1 + - - -
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Residues in contact with TRP 142 (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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86A LEU* 4.6 8.1 - - + -
96A PHE* 3.7 24.0 - + + -
99A LEU* 3.5 42.2 - - + -
100A ASP* 3.0 52.0 + - - -
103A ARG* 4.8 6.1 - - - -
122A VAL* 4.1 16.2 - - + -
138A ARG 3.2 17.3 + - - +
139A ALA 3.9 2.7 - - - +
140A GLN 3.3 0.6 - - - -
141A ALA* 1.3 79.4 - - - +
143A CYS* 1.3 73.0 + - - +
145A SER* 3.0 27.7 + - - -
146A LYS* 3.4 22.9 + - + +
149A ILE* 4.7 7.2 - - + -
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Residues in contact with CYS 143 (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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122A VAL* 3.6 42.8 - - - -
139A ALA* 3.1 25.8 + - - +
140A GLN* 3.9 3.4 - - - +
142A TRP* 1.3 85.0 - - - +
144A TYR* 1.3 61.2 + - - +
146A LYS 3.6 2.8 - - - +
148A ASN* 3.3 2.9 + - - -
149A ILE* 2.8 57.7 + - + +
151A TYR* 3.9 17.5 - - + -
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Residues in contact with TYR 144 (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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140A GLN 3.1 12.8 + - - +
141A ALA* 2.9 12.2 + - - +
143A CYS* 1.3 75.5 - - - +
145A SER* 1.3 64.7 - - - +
146A LYS 3.0 3.2 + - - -
147A ASN 3.8 0.9 + - - -
148A ASN* 3.2 53.1 + - + +
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Residues in contact with SER 145 (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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141A ALA 2.7 18.2 + - - -
142A TRP* 3.0 21.0 + - - -
144A TYR* 1.3 74.6 - - - +
146A LYS* 1.3 79.8 + - - +
147A ASN* 3.5 4.2 + - - +
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Residues in contact with LYS 146 (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 ASP* 3.3 25.2 + - - +
103A ARG* 3.6 26.6 + - - +
142A TRP* 3.4 35.7 + - + +
143A CYS 3.6 0.6 + - - +
144A TYR 3.0 1.4 - - - -
145A SER* 1.3 97.2 + - - +
147A ASN* 1.3 73.5 + - - +
148A ASN 3.2 1.4 + - - -
149A ILE* 3.5 30.7 - - + +
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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