Contacts of the helix formed by residues 8 - 19 (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 LYS 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ALA* 3.4 6.6 - - - +
7A GLU* 1.3 89.9 - - + +
9A PRO* 1.3 79.4 - - + +
10A SER* 3.3 20.9 - - - +
11A LEU* 3.2 21.7 + - + +
12A GLY 3.0 16.3 + - - -
40A TRP* 3.8 5.2 - - - +
41A CYS 3.5 1.3 - - - +
42A ILE* 6.0 0.4 - - - -
43A GLY 6.0 1.3 - - - +
103A ASP* 2.9 38.6 + - - -
317A GLN* 5.3 1.9 - - - +
320A TYR* 4.8 9.3 + - - -
321A GLU* 3.5 25.4 + - - +
328A TYR* 4.8 3.8 - - - -
330A ARG* 5.5 5.0 - - - +
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Residues in contact with PRO 9 (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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8A LYS* 1.3 89.3 - - + +
10A SER* 1.3 58.7 + - - +
12A GLY* 2.9 1.6 + - - -
13A ARG* 2.7 57.2 + - - +
40A TRP* 3.2 49.2 - - + +
41A CYS 3.9 3.6 - - - +
42A ILE* 4.4 10.3 - - + -
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Residues in contact with SER 10 (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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8A LYS* 3.2 11.7 - - - +
9A PRO* 1.3 77.4 - - - +
11A LEU* 1.3 66.3 + - - +
13A ARG* 2.9 29.1 + - - +
14A ALA* 3.2 18.9 + - - +
137A LEU* 5.3 4.8 - - - +
321A GLU* 2.7 41.9 + - - +
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Residues in contact with LEU 11 (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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6A ALA* 3.9 13.5 - - + -
7A GLU* 4.0 5.4 - - + +
8A LYS* 3.2 23.8 + - + +
9A PRO 3.2 0.2 - - - -
10A SER* 1.3 81.1 + - - +
12A GLY* 1.3 63.2 + - - +
14A ALA* 3.1 9.7 + - + +
15A ILE* 3.0 26.8 + - + +
101A ALA* 3.1 30.1 - - + +
102A GLY 5.0 0.4 - - - -
103A ASP* 4.6 14.1 - - - +
134A ILE* 4.1 38.8 - - + +
137A LEU* 4.4 16.6 - - + -
142A VAL* 5.9 0.2 - - + -
320A TYR* 5.3 2.7 - - - +
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Residues in contact with GLY 12 (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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6A ALA* 3.7 9.8 - - - +
8A LYS 3.0 9.1 + - - -
9A PRO 2.9 7.8 + - - -
11A LEU* 1.3 77.0 - - - +
13A ARG* 1.3 60.3 + - - +
15A ILE* 3.2 2.1 + - - -
16A ALA* 2.9 21.2 + - - +
30A ILE* 5.6 1.3 - - - -
38A VAL* 3.5 29.4 - - - +
40A TRP* 4.7 9.6 - - - -
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Residues in contact with ARG 13 (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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9A PRO* 2.7 55.7 + - - +
10A SER* 2.9 30.3 - - - +
12A GLY* 1.3 76.3 - - - +
14A ALA* 1.3 57.8 + - - +
16A ALA* 3.2 6.0 + - - +
17A ASP* 2.8 31.9 + - - +
30A ILE* 6.0 6.5 - - + -
40A TRP* 5.5 9.1 - - - -
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Residues in contact with ALA 14 (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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10A SER 3.2 9.7 + - - +
11A LEU* 3.1 15.5 + - + +
13A ARG* 1.3 80.5 - - - +
15A ILE* 1.3 63.7 + - - +
17A ASP* 3.5 15.6 + - - +
18A VAL* 3.6 12.1 + - - +
137A LEU* 4.3 23.3 - - + +
139A PRO* 5.8 0.7 - - - +
142A VAL* 4.1 20.3 - - + +
324A LYS* 5.5 7.9 - - - +
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Residues in contact with ILE 15 (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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4A PHE* 3.9 37.0 - - + -
6A ALA* 4.3 6.7 - - + -
11A LEU* 3.0 30.0 + - + +
12A GLY 3.7 4.9 - - - +
13A ARG 3.2 0.2 - - - -
14A ALA* 1.3 74.3 - - - +
16A ALA* 1.3 58.5 + - - +
18A VAL* 2.7 21.9 + - + +
19A LEU* 2.7 37.1 - - + +
38A VAL* 4.1 6.3 - - + -
101A ALA* 3.9 27.8 - - + -
132A CYS* 5.6 0.9 - - - -
134A ILE* 4.6 9.9 - - + -
142A VAL* 4.0 16.6 - - + -
146A ILE* 4.6 2.5 - - + -
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Residues in contact with ALA 16 (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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12A GLY 2.9 12.7 + - - +
13A ARG* 3.2 6.3 + - - +
15A ILE* 1.3 76.4 - - - +
17A ASP* 1.3 62.2 + - - +
19A LEU* 2.8 23.3 + - - +
23A HIS* 2.8 28.1 - - + +
30A ILE* 3.3 41.7 - - + -
32A CYS* 4.9 0.9 - - - -
38A VAL* 4.1 2.0 - - + +
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Residues in contact with ASP 17 (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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13A ARG 2.8 17.0 + - - +
14A ALA* 3.5 10.3 - - - +
15A ILE 3.1 0.2 + - - -
16A ALA* 1.3 78.1 - - - +
18A VAL* 1.3 60.3 + - + +
19A LEU 3.6 5.4 - - - +
23A HIS* 3.7 15.2 + - - -
139A PRO* 4.7 17.3 - - + +
324A LYS* 5.6 3.5 + - - -
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Residues in contact with VAL 18 (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 3.8 6.3 - - - +
15A ILE* 2.7 24.4 + - - +
17A ASP* 1.3 75.3 - - + +
19A LEU* 1.4 72.3 + - + +
20A PRO* 3.9 4.0 - - - +
139A PRO* 3.6 36.6 - - + +
142A VAL* 3.7 25.6 - - + -
143A GLU* 3.7 26.2 - - + +
146A ILE* 4.4 14.1 - - + -
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Residues in contact with LEU 19 (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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4A PHE* 4.4 2.7 - - + -
15A ILE* 2.7 53.8 + - + +
16A ALA* 2.8 14.9 + - - +
17A ASP 3.6 1.7 - - - +
18A VAL* 1.4 84.8 - - + +
20A PRO* 1.3 71.6 - - + +
23A HIS* 2.8 19.6 + - - -
32A CYS* 3.4 28.0 - - + -
36A GLN* 2.7 38.8 - - + +
38A VAL* 4.0 6.3 - - + -
146A ILE* 4.0 16.8 - - + -
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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