Contacts of the helix formed by residues 138 - 148 (chain A) in PDB entry 1LMU
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 ASN 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ASP* 3.1 10.1 + - - +
137A LEU* 1.3 78.9 - - - +
139A PRO* 1.3 76.6 - - + +
140A GLN* 2.9 27.9 - - + +
141A ALA* 3.1 5.0 + - - +
142A VAL* 3.1 17.5 + - - +
324A LYS* 3.2 30.5 + - - +
387A THR* 2.9 35.6 - - - +
389A ARG* 3.8 26.0 + - - +
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Residues in contact with PRO 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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14A ALA 5.8 0.9 - - - +
17A ASP* 4.7 17.5 - - + +
18A VAL* 3.6 17.9 - - + +
137A LEU 3.6 5.8 - - - +
138A ASN* 1.3 90.2 - - + +
140A GLN* 1.3 67.9 + - - +
142A VAL* 3.3 2.1 + - + +
143A GLU* 3.0 33.0 + - - +
324A LYS* 4.6 13.7 - - + +
389A ARG* 6.2 0.4 - - - +
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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 ASP* 4.8 3.8 + - - -
138A ASN* 2.9 35.5 - - - +
139A PRO* 1.3 77.9 - - - +
141A ALA* 1.3 65.4 + - + +
143A GLU* 3.3 14.3 + - - +
144A ARG* 3.0 29.2 + - - +
387A THR* 5.0 0.4 - - - +
388A ALA* 4.9 13.5 - - - +
389A ARG* 5.6 0.8 - - - +
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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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134A ILE* 5.9 0.2 - - - -
136A ASP* 3.3 45.1 - - + +
138A ASN 3.1 7.8 + - - +
140A GLN* 1.3 83.6 - - + +
142A VAL* 1.3 60.6 + - - +
144A ARG* 3.1 9.9 + - - +
145A ALA* 2.8 28.0 + - - +
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Residues in contact with VAL 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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14A ALA* 4.3 17.5 - - + +
15A ILE* 4.0 24.2 - - + -
18A VAL* 3.7 31.4 - - + -
134A ILE* 4.5 15.7 - - + -
136A ASP 3.8 10.8 - - - +
137A LEU* 3.7 13.5 - - - +
138A ASN 3.1 16.1 + - - +
139A PRO* 3.8 1.8 - - + +
140A GLN 3.3 0.2 - - - -
141A ALA* 1.3 75.3 - - - +
143A GLU* 1.3 64.8 + - - +
145A ALA* 3.0 7.5 + - - +
146A ILE* 2.9 22.9 + - + +
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Residues in contact with GLU 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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18A VAL* 3.7 27.7 - - + +
139A PRO* 3.0 22.7 + - - +
140A GLN* 3.5 12.6 - - - +
141A ALA 3.2 0.2 - - - -
142A VAL* 1.3 76.4 - - - +
144A ARG* 1.3 61.1 + - - +
146A ILE* 2.8 31.3 - - + +
147A ASP* 3.1 6.9 + - - +
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Residues in contact with ARG 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* 3.0 20.2 + - - +
141A ALA* 3.3 12.7 - - - +
143A GLU* 1.3 78.6 - - - +
145A ALA* 1.3 62.9 + - - +
147A ASP* 3.1 11.9 + - - +
148A ARG* 3.0 57.2 - - - +
339A GLU* 4.4 20.7 + - - +
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Residues in contact with ALA 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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132A CYS* 3.9 15.6 - - - -
133A LEU 3.4 26.3 + - - +
134A ILE* 4.0 12.1 - - + -
141A ALA 2.8 12.9 + - - +
142A VAL 3.0 8.3 + - - +
144A ARG* 1.3 76.4 - - - +
146A ILE* 1.3 61.3 + - - +
148A ARG* 3.1 24.6 + - - +
149A LEU* 3.7 5.7 - - - +
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Residues in contact with ILE 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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2A ARG* 3.3 23.6 + - - +
4A PHE* 3.3 33.0 - - + -
15A ILE* 4.6 3.6 - - + -
18A VAL* 4.4 15.0 - - + -
19A LEU* 4.0 19.7 - - + -
132A CYS* 4.1 5.1 - - - -
142A VAL* 2.9 11.7 + - + +
143A GLU* 2.8 27.4 - - + +
145A ALA* 1.3 76.1 - - - +
147A ASP* 1.3 63.9 + - - +
149A LEU* 3.2 26.1 - - + +
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Residues in contact with ASP 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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143A GLU 3.1 7.8 + - - +
144A ARG* 3.1 15.1 + - - +
146A ILE* 1.3 86.8 - - + +
148A ARG* 1.4 79.7 + - - +
149A LEU* 3.5 4.0 + - - +
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Residues in contact with ARG 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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131A ARG 4.4 1.6 - - - +
132A CYS* 5.4 1.0 - - - -
133A LEU* 5.5 2.8 + - - +
144A ARG* 3.0 58.5 - - - +
145A ALA* 3.1 15.6 + - - +
147A ASP* 1.4 99.0 + - - +
149A LEU* 1.3 61.9 + - - +
150A ARG* 3.7 10.0 + - + +
339A GLU* 5.1 10.7 + - - -
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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