Contacts of the helix formed by residues 10 - 24 (chain A) in PDB entry 2HZD
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 SER 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL 3.6 2.6 + - - -
9A TRP* 1.3 79.5 - - - +
11A PRO* 1.3 75.8 - - - +
12A ASP* 3.2 19.1 + - - +
13A ILE* 3.3 31.9 + - - +
14A GLU* 3.7 6.8 + - - +
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Residues in contact with PRO 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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9A TRP 3.5 3.6 - - - +
10A SER* 1.3 88.2 - - - +
12A ASP* 1.3 62.8 + - - +
13A ILE 3.2 1.1 - - - -
14A GLU* 3.5 8.6 + - + +
15A GLN* 3.0 37.8 + - + +
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Residues in contact with ASP 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 SER* 3.2 12.0 + - - +
11A PRO* 1.3 84.5 - - - +
13A ILE* 1.3 58.8 + - + +
15A GLN* 3.7 8.5 - - - +
16A SER* 2.5 37.8 + - - -
54A ARG* 5.1 5.2 - - - +
55A THR* 4.9 15.4 - - + +
57A LYS* 5.9 0.7 - - + -
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Residues in contact with ILE 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 TRP* 4.6 19.1 - - + +
10A SER* 3.6 31.6 - - - +
11A PRO 3.2 0.4 - - - -
12A ASP* 1.3 79.5 - - + +
14A GLU* 1.3 64.6 + - + +
15A GLN 3.1 1.8 - - - -
16A SER* 3.3 6.5 + - - -
17A PHE* 3.2 34.1 + - + -
51A ILE* 5.8 2.0 - - + -
55A THR* 5.7 0.2 - - + -
57A LYS* 3.2 42.2 - - + -
58A THR* 3.1 31.0 - - + -
60A THR* 5.4 0.7 - - - +
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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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9A TRP* 5.3 15.7 - - + +
10A SER 3.7 9.3 + - - +
11A PRO* 3.5 10.0 + - + +
13A ILE* 1.3 80.8 - - + +
15A GLN* 1.3 61.0 + - + +
17A PHE* 3.4 21.3 + - - +
18A GLN* 3.5 8.1 + - - +
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Residues in contact with GLN 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 PRO* 3.0 24.4 + - + +
12A ASP* 3.7 10.8 - - - +
13A ILE 3.1 0.2 - - - -
14A GLU* 1.3 75.8 - - - +
16A SER* 1.3 64.5 - - - +
17A PHE 3.0 2.0 + - - -
18A GLN* 3.2 27.5 + - - +
19A GLU* 3.2 13.6 + - - +
54A ARG* 5.1 0.7 - - - -
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Residues in contact with SER 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 ASP 2.5 24.4 + - - -
13A ILE* 3.3 5.7 + - - +
15A GLN* 1.3 76.2 - - - +
17A PHE* 1.3 60.7 + - - +
19A GLU* 3.4 4.6 + - - +
20A ALA* 3.2 18.9 + - - +
50A TYR* 4.5 2.4 - - - -
51A ILE* 3.1 31.2 - - - +
54A ARG* 2.8 44.4 - - - +
55A THR* 5.6 1.0 - - - +
57A LYS* 6.0 1.2 - - - +
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Residues in contact with PHE 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 ILE* 3.2 27.1 + - + +
14A GLU* 3.4 15.9 - - - +
15A GLN 3.0 0.4 - - - -
16A SER* 1.3 75.7 - - - +
18A GLN* 1.3 60.0 + - - +
20A ALA* 3.2 5.5 + - - +
21A LEU* 2.9 33.2 + - + +
51A ILE* 4.1 15.9 - - + -
58A THR* 5.7 0.4 - - + -
60A THR* 2.9 30.1 - - - -
63A GLN* 3.2 45.1 - - + -
64A VAL* 3.0 35.2 - - + +
67A HIS* 4.2 23.6 - - + +
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Residues in contact with GLN 18 (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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14A GLU 3.5 7.8 + - - +
15A GLN* 3.2 22.2 + - - +
17A PHE* 1.3 78.4 - - - +
19A GLU* 1.3 52.6 + - - +
21A LEU* 3.9 6.5 - - + +
22A SER* 2.5 52.8 + - - -
67A HIS* 5.7 5.8 - - + -
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Residues in contact with GLU 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 GLN 3.2 10.3 + - - +
16A SER* 3.6 11.0 - - - +
17A PHE 3.2 0.2 - - - -
18A GLN* 1.3 81.7 - - - +
20A ALA* 1.3 55.7 + - - +
22A SER* 4.4 5.5 - - - -
23A ILE* 3.1 35.4 + - - +
50A TYR* 2.5 41.7 + - + +
54A ARG* 4.0 15.2 + - - +
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Residues in contact with ALA 20 (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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16A SER 3.2 14.9 + - - +
17A PHE* 3.7 5.6 - - - +
19A GLU* 1.3 76.5 - - - +
21A LEU* 1.3 59.6 + - - +
23A ILE* 4.1 6.7 - - - -
24A TYR* 2.9 34.8 + - - +
47A ILE* 3.5 39.4 - - + +
50A TYR* 4.1 12.8 - - + -
51A ILE* 5.1 2.0 - - + -
64A VAL* 4.6 4.9 - - + -
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Residues in contact with LEU 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 PHE* 2.9 18.0 + - + +
18A GLN* 3.9 6.3 - - + +
20A ALA* 1.3 77.0 - - - +
22A SER* 1.3 63.9 + - - +
24A TYR 3.2 20.6 - - - +
25A PRO* 3.6 7.4 - - - +
64A VAL* 3.5 25.1 - - + +
67A HIS* 3.5 35.2 - - + +
68A ILE* 3.2 49.8 - - + +
71A LEU* 4.2 21.1 - - + +
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Residues in contact with SER 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 GLN* 2.5 35.5 + - - +
19A GLU* 4.2 7.4 - - - -
21A LEU* 1.3 75.5 - - - +
23A ILE* 1.3 61.4 + - - +
25A PRO* 4.1 11.3 - - - +
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Residues in contact with ILE 23 (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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19A GLU* 3.1 32.6 + - - +
20A ALA* 3.6 4.0 - - - +
22A SER* 1.3 80.7 - - - +
24A TYR* 1.3 109.0 + - + +
25A PRO* 3.2 9.4 - - - +
29A ARG* 5.0 11.1 + - - -
50A TYR* 4.0 19.1 - - + +
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Residues in contact with TYR 24 (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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20A ALA 2.9 15.5 + - - +
21A LEU* 3.2 18.7 - - - +
23A ILE* 1.3 111.7 - - + +
25A PRO* 1.3 64.6 - - - +
43A ARG* 5.2 14.7 + - - +
46A LEU* 3.1 56.5 + - + +
47A ILE* 3.5 28.5 - - + -
50A TYR* 4.1 17.4 - + + -
68A ILE* 4.5 9.4 - - + +
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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