Contacts of the helix formed by residues 11 - 20 (chain A) in PDB entry 1LC7
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PHE* 3.6 17.5 - - - -
6A THR* 3.4 35.2 - - - +
8A HIS 3.9 4.2 - - - +
9A GLY* 3.2 3.5 + - - +
10A GLY* 1.3 75.5 + - - +
12A ILE* 1.3 58.9 + - - +
13A ARG 3.3 2.9 - - - -
14A GLU* 2.9 37.0 + - + +
15A PRO* 3.0 22.3 - - - +
30A SER* 4.2 2.0 + - - -
321A LEU* 3.8 17.6 - - - +
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Residues in contact with ILE 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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10A GLY 2.8 15.0 + - - +
11A ASN* 1.3 69.1 - - - +
13A ARG* 1.3 66.5 + - + +
15A PRO* 4.3 1.1 - - - -
16A ALA* 2.9 32.7 + - - +
23A PRO* 4.1 29.8 - - + +
26A LEU* 3.8 12.2 - - + +
28A ASP* 3.3 42.4 - - + +
321A LEU* 4.1 9.0 - - + -
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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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11A ASN 3.3 0.4 - - - -
12A ILE* 1.3 83.4 - - + +
14A GLU* 1.3 91.9 + - - +
16A ALA* 3.8 1.6 - - - +
17A THR* 2.9 49.6 + - - +
23A PRO* 3.8 20.8 - - + +
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Residues in contact with GLU 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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4A PHE* 3.7 25.2 - - + +
5A ASN 4.9 4.9 + - - +
6A THR* 3.7 12.6 + - - -
11A ASN* 2.9 36.3 + - + +
12A ILE 3.3 0.2 - - - -
13A ARG* 1.3 106.5 - - - +
15A PRO* 1.3 61.1 - - - +
17A THR* 3.3 4.3 + - - -
18A VAL* 3.1 24.8 + - + +
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Residues in contact with PRO 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* 4.2 16.4 - - + -
11A ASN* 3.0 17.4 - - - +
14A GLU* 1.3 74.7 - - - +
16A ALA* 1.3 65.0 + - - +
18A VAL* 3.1 18.3 + - + +
19A LEU* 3.3 12.5 + - - +
26A LEU* 3.7 20.0 - - + -
316A LEU* 4.2 6.8 - - + +
321A LEU* 3.9 25.8 - - + -
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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 ILE 2.9 18.2 + - - +
13A ARG 3.8 3.1 - - - +
15A PRO* 1.3 75.9 - - - +
17A THR* 1.3 58.2 + - - +
19A LEU* 3.0 3.6 + - - -
20A GLY 2.9 23.7 + - - -
21A ILE* 3.0 34.7 + - + +
22A SER 3.7 3.1 - - - +
23A PRO* 3.5 26.9 - - + -
26A LEU* 3.5 10.7 - - + +
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Residues in contact with THR 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* 2.9 40.1 + - - +
14A GLU* 3.6 8.1 - - - -
15A PRO 3.2 0.2 - - - -
16A ALA* 1.3 77.6 - - - +
18A VAL* 1.3 61.0 + - + +
20A GLY* 3.3 12.7 + - - +
21A ILE 4.7 2.6 + - - -
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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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4A PHE* 3.8 31.4 - - + +
14A GLU* 3.1 17.2 + - + +
15A PRO* 3.1 11.6 + - + +
17A THR* 1.3 77.8 - - + +
19A LEU* 1.3 65.9 + - + +
316A LEU* 4.5 15.9 - - + -
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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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15A PRO 3.3 10.1 + - - +
16A ALA 3.0 6.5 + - - +
18A VAL* 1.3 83.5 - - + +
20A GLY* 1.3 62.7 + - - +
21A ILE* 3.8 23.3 - - + +
26A LEU* 3.9 16.6 - - + -
316A LEU* 3.4 54.1 - - + +
317A THR* 4.9 3.6 - - - +
319A ARG* 3.8 27.8 + - - +
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Residues in contact with GLY 20 (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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16A ALA 2.9 4.5 + - - -
17A THR* 3.3 12.6 + - - -
18A VAL 3.4 0.2 - - - -
19A LEU* 1.3 80.6 - - - +
21A ILE* 1.3 61.5 + - - +
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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