Contacts of the helix formed by residues 9 - 22 (chain A) in PDB entry 5Y1Z
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 HIS 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A SER 3.3 0.6 + - - -
8A GLY* 1.3 85.8 + - - +
10A ARG* 1.3 66.3 + - - +
11A LEU 3.2 2.7 - - - -
12A GLU* 3.2 15.3 + - + +
13A LEU* 3.0 26.5 + - + +
35A GLU* 3.0 41.0 + - - -
40A ASP* 5.3 3.7 - - + +
41A LEU 3.8 16.4 + - - +
42A LYS* 4.2 13.9 - - + +
43A LEU 5.3 1.8 - - - +
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Residues in contact with ARG 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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6A PHE* 3.1 24.8 + - - +
7A SER* 3.1 12.0 + - - +
8A GLY 3.3 0.8 - - - -
9A HIS* 1.3 76.8 - - - +
11A LEU* 1.3 64.0 + - - +
13A LEU* 3.1 8.8 + - - +
14A LEU* 3.0 27.9 + - + +
108A PHE* 3.7 11.9 - - + -
285C LEU* 3.7 15.4 - - + +
288C PHE* 3.4 48.7 - - + -
291C TRP* 5.2 0.6 - - - +
307C PHE* 3.8 24.5 - - - -
310C GLN* 3.7 31.3 + - - +
312C ASP* 2.5 43.9 + - - -
314C ALA* 5.8 0.2 - - - +
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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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9A HIS 3.2 0.6 - - - -
10A ARG* 1.3 78.7 - - - +
12A GLU* 1.3 57.9 + - - +
14A LEU* 3.5 1.0 + - + -
15A ALA* 2.9 35.1 + - + +
287C GLY 3.3 27.8 + - - +
288C PHE* 3.8 20.2 - - + +
289C PRO* 4.6 6.3 - - + -
335C THR* 3.3 33.7 - - + -
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Residues in contact with GLU 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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9A HIS* 3.2 21.8 + - + +
11A LEU* 1.3 78.9 - - - +
13A LEU* 1.3 63.5 + - - +
15A ALA* 3.2 6.2 + - - +
16A ALA* 3.0 24.3 + - - +
43A LEU* 4.5 23.0 - - + +
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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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6A PHE* 4.1 36.8 - - + +
9A HIS* 3.0 23.5 + - + +
10A ARG* 3.1 14.1 + - - +
12A GLU* 1.3 76.9 - - - +
14A LEU* 1.3 63.0 + - - +
17A TYR* 3.1 8.0 + - - +
32A TYR* 2.8 46.4 + - + -
41A LEU* 3.8 17.0 - - + +
42A LYS* 3.6 37.0 - - - -
43A LEU* 3.6 3.8 - - - +
108A PHE* 4.2 12.1 - - + -
109A PHE* 3.8 2.9 - - + -
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Residues in contact with LEU 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 ARG* 3.0 12.5 + - + +
11A LEU 4.3 2.0 - - - +
13A LEU* 1.3 76.7 - - - +
15A ALA* 1.3 58.6 + - - +
17A TYR* 3.8 23.2 - - + +
18A GLU* 2.8 31.8 + - - +
108A PHE* 3.5 41.7 - - + +
109A PHE* 4.6 1.6 - - + -
288C PHE* 3.6 34.8 - - + -
310C GLN* 3.9 24.5 - - + +
335C THR* 5.4 3.6 - - + +
338C ILE* 3.6 25.8 - - + +
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Residues in contact with ALA 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 LEU* 2.9 26.8 + - + +
12A GLU* 3.2 7.4 + - - +
14A LEU* 1.3 75.0 - - - +
16A ALA* 1.3 64.8 + - - +
18A GLU* 3.5 9.8 + - - +
19A GLU* 3.0 27.1 + - - +
335C THR* 5.7 4.9 - - + +
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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 GLU 3.0 15.2 + - - +
15A ALA* 1.3 78.1 - - - +
17A TYR* 1.3 63.1 + - - +
19A GLU* 3.1 9.8 + - - +
20A VAL* 3.0 24.6 + - - +
30A ALA* 3.8 15.5 - - + -
32A TYR* 3.5 14.1 - - - +
43A LEU* 3.9 22.2 - - + -
46A SER* 4.7 8.1 - - - +
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Residues in contact with TYR 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 3.1 13.0 + - - +
14A LEU* 3.8 22.2 - - + +
15A ALA 3.3 0.2 - - - -
16A ALA* 1.3 76.2 - - - +
18A GLU* 1.3 59.4 + - - +
20A VAL* 3.0 9.2 + - - +
21A ILE* 2.9 49.6 + - + +
32A TYR* 3.2 14.7 + - - +
67A PHE* 3.4 40.4 - + + -
108A PHE 5.2 0.7 - - - -
109A PHE* 3.6 27.6 - + + -
110A GLN* 2.5 42.5 + - + +
310C GLN* 5.5 2.7 - - - -
338C ILE* 3.8 24.9 - - + +
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Residues in contact with GLU 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 LEU 2.8 18.2 + - - +
15A ALA* 3.9 6.9 - - - +
17A TYR* 1.3 80.8 - - - +
19A GLU* 1.3 63.4 + - - +
21A ILE* 3.2 6.7 + - + +
22A ARG* 3.0 26.7 + - + +
334C LYS 4.9 0.9 - - - +
335C THR* 3.7 27.1 - - - -
336C LYS 4.0 0.6 + - - -
337C SER* 3.0 45.0 + - - +
338C ILE* 3.7 15.6 + - + -
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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 ALA 3.0 16.8 + - - +
16A ALA* 3.1 12.1 + - - +
18A GLU* 1.3 78.7 - - - +
20A VAL* 1.3 62.2 + - - +
21A ILE 3.5 0.2 + - - -
22A ARG* 3.5 4.7 + - - +
25A SER* 2.9 51.0 + - - -
26A ALA 5.0 0.3 + - - -
27A ALA* 3.5 33.8 + - + +
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Residues in contact with VAL 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 3.0 17.4 + - - +
17A TYR 3.0 7.4 + - - +
19A GLU* 1.3 78.0 - - + +
21A ILE* 1.3 63.8 + - - +
22A ARG 3.9 4.0 - - - +
27A ALA* 3.9 11.8 - - + +
28A ASP* 3.9 8.1 - - - +
29A TRP 3.6 37.2 - - - +
30A ALA* 3.7 8.7 - - + +
46A SER* 6.1 0.2 - - - -
67A PHE* 3.5 31.2 - - + +
69A SER* 3.7 35.5 + - - +
80A TYR* 4.2 1.1 + - + -
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Residues in contact with ILE 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 TYR* 2.9 44.8 + - + +
18A GLU* 3.2 7.1 + - + +
20A VAL* 1.3 76.4 - - - +
22A ARG* 1.3 65.4 + - - +
23A GLU* 3.3 3.8 + - - +
67A PHE* 3.7 21.1 - - + -
78A PRO* 5.6 1.9 - - - +
80A TYR* 3.4 46.3 + - + +
110A GLN 4.9 2.0 - - - +
337C SER* 5.8 3.8 - - - +
338C ILE* 6.2 0.2 - - + -
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Residues in contact with ARG 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 GLU* 3.0 19.1 + - + +
19A GLU* 3.7 7.6 - - - +
20A VAL 3.4 4.1 - - - +
21A ILE* 1.3 78.0 - - - +
23A GLU* 1.3 65.0 + - - +
24A GLU* 3.5 4.4 + - + +
25A SER* 3.3 34.7 + - - +
27A ALA 5.0 0.5 - - - +
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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