Contacts of the helix formed by residues 135 - 146 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C ARG* 3.9 4.0 - - - +
133C GLN 4.2 1.0 - - - -
134C VAL* 1.3 76.8 - - - +
136C THR* 1.3 66.4 + - - +
137C LYS* 4.1 6.5 - - + +
138C ARG* 3.1 23.7 + - + +
139C ALA* 3.0 22.7 + - - +
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Residues in contact with THR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ARG* 3.5 10.9 + - - +
135C ALA* 1.3 71.9 - - - +
137C LYS* 1.3 58.7 + - + +
139C ALA* 3.2 1.9 + - - +
140C GLN* 2.7 59.9 + - - +
151C TYR* 3.9 5.8 - - + -
153C GLU* 3.0 36.3 + - + +
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Residues in contact with LYS 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ALA* 3.1 6.0 - - + +
136C THR* 1.3 82.1 - - + +
138C ARG* 1.3 56.1 + - - +
140C GLN* 3.8 16.8 + - + +
141C ALA* 3.0 28.2 + - - +
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Residues in contact with ARG 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C PRO* 5.6 4.4 + - - +
96C PHE* 3.5 46.0 - - + -
97C LYS* 4.2 23.9 - - - +
134C VAL* 4.6 11.0 - - + +
135C ALA* 3.1 22.9 + - + +
137C LYS* 1.3 77.1 - - - +
139C ALA* 1.3 63.0 + - - +
140C GLN 3.3 0.2 - - - -
141C ALA* 4.1 5.0 - - + +
142C TRP* 3.4 15.4 + - - +
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Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PHE* 3.9 7.9 - - + -
96C PHE* 3.3 22.3 - - + -
122C VAL* 5.8 0.2 - - + -
134C VAL* 5.0 1.1 - - + -
135C ALA 3.0 10.5 + - - +
136C THR 3.7 2.2 - - - +
138C ARG* 1.3 75.8 - - - +
140C GLN* 1.3 64.9 + - - +
142C TRP* 3.6 2.3 + - - +
143C CYS* 3.3 28.8 + - - -
151C TYR* 3.2 41.7 - - + +
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Residues in contact with GLN 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C THR* 2.7 38.1 + - - +
137C LYS* 3.8 17.5 + - + +
139C ALA* 1.3 78.2 - - - +
141C ALA* 1.3 63.2 + - - +
143C CYS* 3.6 4.3 + - + +
144C TYR* 3.1 23.7 + - - +
151C TYR* 4.3 24.5 + - + +
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LYS 3.0 20.7 + - - +
138C ARG* 4.1 7.4 - - + +
139C ALA 3.4 0.2 - - - -
140C GLN* 1.3 76.6 - - - +
142C TRP* 1.3 62.5 + - - +
144C TYR* 3.5 7.0 + - - +
145C SER* 3.1 21.0 + - - -
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Residues in contact with TRP 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C LEU* 4.7 7.9 - - + -
96C PHE* 3.8 23.6 - + + -
99C LEU* 3.5 33.4 - - + -
100C ASP* 3.5 43.5 + - - +
103C ARG* 4.8 7.4 - - - -
122C VAL* 3.9 23.1 - - + -
138C ARG 3.4 14.9 + - - +
139C ALA 3.8 2.7 - - - +
140C GLN 3.3 0.4 - - - -
141C ALA* 1.3 74.9 - - - +
143C CYS* 1.3 78.5 + - - +
144C TYR 3.0 0.9 - - - -
145C SER* 2.7 39.0 + - - -
146C LYS* 3.1 28.0 + - + +
149C ILE* 4.4 9.0 - - + -
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Residues in contact with CYS 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C VAL* 3.5 44.0 - - - -
139C ALA 3.3 18.3 + - - +
140C GLN* 3.8 4.9 - - + +
142C TRP* 1.3 85.8 - - - +
144C TYR* 1.3 61.4 + - - +
146C LYS 3.3 8.1 + - - +
148C ASN 3.5 1.4 + - - -
149C ILE* 3.2 47.9 + - + +
151C TYR* 3.9 18.8 - - + -
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Residues in contact with TYR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C GLN 3.1 14.5 + - - +
141C ALA* 3.6 7.9 - - - +
142C TRP 3.0 1.0 - - - -
143C CYS* 1.3 77.2 - - - +
145C SER* 1.3 67.5 + - - +
146C LYS 3.3 0.3 + - - -
147C ASN* 3.6 1.0 + - - -
148C ASN* 3.3 51.1 + - + +
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C ALA 3.1 12.4 + - - -
142C TRP* 2.7 25.3 + - - -
144C TYR* 1.3 75.9 - - - +
146C LYS* 1.3 75.5 + - - +
147C ASN* 3.3 5.5 + - - -
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Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ASP* 2.7 36.8 + - - -
103C ARG* 3.8 33.2 + - - +
142C TRP* 3.1 39.0 + - + +
143C CYS 3.3 5.6 + - - +
144C TYR 3.2 0.6 - - - -
145C SER* 1.3 89.5 - - - +
147C ASN* 1.3 74.6 + - - +
148C ASN 3.4 1.1 - - - -
149C ILE* 3.5 24.6 - - + +
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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