Contacts of the helix formed by residues 12 - 22 (chain A) in PDB entry 2ZUQ
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 ARG 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLY* 1.3 71.7 - - - -
13A GLY* 1.3 52.1 + - - +
16A LEU* 2.7 59.4 + - + +
62A ALA* 4.0 18.4 - - - +
63A ILE* 5.0 5.8 - - - +
64A ALA 5.3 0.9 - - - +
65A PRO* 3.7 28.9 - - + +
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Residues in contact with GLY 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 GLY* 3.3 1.6 - - - -
12A ARG* 1.3 75.7 - - - +
14A ALA* 1.3 54.0 + - - +
15A TRP 2.5 16.7 + - - -
16A LEU* 3.1 1.3 + - - -
17A LEU* 2.8 33.0 + - - +
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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 GLN* 3.9 32.5 - - + +
11A GLY 4.2 3.9 - - - +
13A GLY* 1.3 70.3 - - - +
15A TRP* 1.3 68.2 + - + +
17A LEU* 5.1 4.7 - - - -
18A MET* 4.1 24.4 - - + +
77A TRP* 5.2 1.2 - - - -
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Residues in contact with TRP 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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10A GLN* 3.7 18.9 - - + +
11A GLY 3.2 18.2 - - - +
13A GLY 2.5 5.5 + - - -
14A ALA* 1.3 81.8 + - - +
16A LEU* 1.3 49.4 + - - +
17A LEU 2.9 4.3 - - - -
18A MET* 2.7 12.2 + - - +
19A ALA* 2.6 35.0 + - - -
57A ALA 3.5 14.1 - - - -
58A ALA* 3.2 40.5 - - - +
61A GLY* 3.1 24.7 + - - -
62A ALA* 3.4 7.9 - - + +
70A ARG* 3.4 22.7 - - + +
73A ALA* 3.6 20.2 - - + -
74A MET* 4.2 25.8 - - + -
77A TRP* 3.5 37.2 - + - -
161A VAL* 6.0 3.4 - - + -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ARG* 2.7 46.5 + - + +
13A GLY* 4.4 1.6 - - - +
15A TRP* 1.3 73.9 - - - +
17A LEU* 1.3 55.0 + - - +
19A ALA* 3.9 14.8 - - + -
20A PHE* 3.2 25.4 + - + +
59A LEU* 5.8 0.4 - - + -
62A ALA* 3.6 15.4 - - + +
63A ILE* 4.5 18.2 - - + -
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Residues in contact with LEU 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 GLY* 2.8 19.5 + - - +
14A ALA* 5.1 2.2 - - - -
15A TRP 2.8 0.6 + - - -
16A LEU* 1.3 77.3 - - - +
18A MET* 1.3 68.7 + - + +
20A PHE* 3.1 13.9 + - + +
21A THR* 2.7 36.1 + - - -
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Residues in contact with MET 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* 4.1 20.6 - - + +
15A TRP* 2.7 12.6 + - - +
17A LEU* 1.3 94.3 - - + +
19A ALA* 1.3 64.1 + - - +
21A THR* 2.8 34.2 + - + +
22A ALA* 3.0 10.2 + - - +
54A VAL* 5.6 0.9 - - - +
58A ALA* 3.9 2.6 - - - +
77A TRP* 3.0 44.1 - - + -
153A TYR* 4.6 5.3 + - + -
156A VAL* 5.1 12.1 - - + -
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Residues in contact with ALA 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 TRP 2.6 17.1 + - - +
16A LEU* 3.9 18.2 - - + +
18A MET* 1.3 72.7 - - - +
20A PHE* 1.3 60.3 + - - +
22A ALA 3.8 0.9 + - - -
23A LEU* 3.8 8.4 + - - +
55A LEU* 3.2 27.8 - - + +
58A ALA* 3.3 7.0 - - - +
59A LEU* 3.5 39.5 - - + +
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Residues in contact with PHE 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 LEU* 3.2 20.4 + - + +
17A LEU* 3.1 12.7 + - + +
19A ALA* 1.3 74.1 - - - +
21A THR* 1.3 63.3 + - - +
22A ALA 3.1 0.4 - - - -
23A LEU* 2.9 38.5 + - + +
24A ALA* 3.0 20.9 + - + -
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Residues in contact with THR 21 (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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17A LEU* 2.7 19.7 + - - -
18A MET* 2.8 42.3 + - + +
20A PHE* 1.3 76.0 - - - +
22A ALA* 1.3 55.5 + - - +
24A ALA* 3.3 29.7 + - - +
25A LEU* 3.7 9.9 - - - +
153A TYR* 3.0 25.6 + - + +
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Residues in contact with ALA 22 (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 MET 3.0 11.4 + - - +
20A PHE 3.1 0.2 - - - -
21A THR* 1.3 75.1 - - - +
23A LEU* 1.3 57.9 + - - +
24A ALA 3.2 0.7 - - - -
25A LEU* 3.7 1.3 + - - -
26A GLU* 3.1 30.5 + - - +
51A LEU* 3.9 31.5 - - + +
54A VAL* 4.6 4.0 - - + -
55A LEU* 3.3 33.9 - - + +
153A TYR* 4.1 6.7 - - - +
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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