Contacts of the helix formed by residues 10 - 20 (chain A) in PDB entry 5LUQ
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 CYS 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A SER* 1.3 66.6 + - - +
12A LEU* 3.0 28.0 + - - +
13A LEU* 3.3 22.4 + - - +
14A ARG* 3.6 15.5 + - - +
41A GLU* 5.2 1.6 + - - -
54A GLN* 3.5 37.3 - - - +
58A VAL* 5.0 4.9 - - - +
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Residues in contact with SER 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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10A CYS* 1.3 78.5 - - - +
12A LEU* 1.3 57.2 + - - +
13A LEU 3.4 0.2 - - - -
14A ARG* 3.7 11.2 - - - +
15A LEU* 2.9 39.8 + - - +
41A GLU* 2.7 39.7 + - - -
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Residues in contact with LEU 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 CYS 3.0 13.2 - - - +
11A SER* 1.3 75.8 - - - +
13A LEU* 1.3 66.4 + - - +
15A LEU* 4.8 1.3 - - + -
16A GLN* 3.0 28.8 + - - +
37A GLY 4.4 1.1 - - - +
38A LEU* 3.2 30.0 - - + +
41A GLU* 3.4 40.4 - - + +
42A CYS* 3.9 31.9 - - + +
54A GLN* 5.9 4.0 - - + +
55A THR* 5.4 3.1 - - + -
58A VAL* 3.6 34.3 - - + -
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Residues in contact with LEU 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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10A CYS* 3.3 15.3 + - - +
12A LEU* 1.3 76.7 - - - +
14A ARG* 1.3 70.5 + - + +
16A GLN* 3.3 9.9 - - - +
17A GLU* 2.9 32.6 + - - +
57A LEU* 4.1 17.5 - - + -
58A VAL* 3.8 33.7 - - + +
61A ARG* 3.3 51.8 - - - +
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Residues in contact with ARG 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 CYS 3.7 14.6 + - - +
11A SER* 3.7 11.9 - - - +
12A LEU 3.3 0.6 - - - -
13A LEU* 1.3 83.2 - - - +
15A LEU* 1.3 64.0 + - + +
17A GLU* 3.1 22.2 + - - +
18A THR* 2.9 27.9 + - + +
61A ARG* 5.5 1.6 - - - +
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Residues in contact with LEU 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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11A SER* 2.9 35.4 + - - +
12A LEU* 5.2 1.3 - - + -
14A ARG* 1.3 72.8 - - + +
16A GLN* 1.3 59.1 + - - +
18A THR* 2.4 40.0 + - + +
19A LEU* 3.0 12.1 + - + -
34A LEU* 3.4 14.3 - - + +
37A GLY* 4.8 15.9 - - - -
38A LEU* 3.6 17.5 - - + +
41A GLU* 4.9 6.3 - - - +
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Residues in contact with GLN 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 LEU 3.0 26.2 + - - +
13A LEU* 3.3 14.7 - - - +
15A LEU* 1.3 75.8 - - - +
17A GLU* 1.3 57.7 + - + +
20A SER* 2.7 42.1 + - - -
34A LEU* 3.9 3.4 - - - -
38A LEU* 3.4 24.9 - - + +
58A VAL* 3.6 25.8 + - - +
61A ARG* 2.9 39.3 - - - +
62A ASP* 3.7 21.0 - - - +
65A LEU* 4.1 13.4 - - + +
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Residues in contact with GLU 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 LEU 2.9 20.7 + - - +
14A ARG* 3.1 20.3 + - - +
16A GLN* 1.3 80.4 - - + +
18A THR* 1.3 61.6 + - - +
20A SER* 4.1 5.6 - - - -
21A ALA* 4.1 14.8 - - - +
61A ARG* 2.4 41.0 + - - +
65A LEU* 5.1 4.5 - - + -
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Residues in contact with THR 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 ARG* 2.9 17.1 + - + +
15A LEU* 2.4 39.7 + - + +
17A GLU* 1.3 80.3 - - - +
19A LEU* 1.3 70.3 + - - +
20A SER 3.4 0.4 - - - -
22A ALA* 2.7 32.4 + - - +
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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 LEU* 3.0 10.2 + - + -
18A THR* 1.3 87.8 + - - +
20A SER* 1.3 54.0 + - - +
22A ALA* 3.8 15.7 - - + -
23A ASP* 2.6 33.7 + - - +
30A ALA* 3.2 47.4 - - + +
33A GLN* 5.4 5.2 - - + +
34A LEU* 3.5 43.1 - - + +
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Residues in contact with SER 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 GLN* 2.7 24.3 + - - -
17A GLU* 4.1 3.8 - - - -
19A LEU* 1.3 76.8 - - - +
21A ALA* 1.3 71.0 + - - +
23A ASP* 3.1 8.6 - - - +
24A ARG* 2.9 28.0 + - - +
34A LEU* 4.3 5.5 - - - +
65A LEU* 3.2 40.5 - - - +
69A VAL* 3.8 12.1 - - - +
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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