Contacts of the helix formed by residues 10 - 24 (chain A) in PDB entry 2PWZ
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 GLY 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY 3.4 10.8 + - - -
9A ALA* 1.3 82.1 - - - +
11A GLY* 1.3 60.5 + - - -
12A ILE 3.4 2.5 - - - -
13A GLY 3.9 1.6 - - - -
14A GLN* 3.0 28.7 + - - +
34A ASP* 3.9 3.4 + - - -
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Residues in contact with GLY 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 GLY* 1.3 70.2 - - - +
12A ILE* 1.3 61.5 + - - +
14A GLN* 4.2 4.0 - - - +
15A ALA* 3.3 23.6 + - - +
224A THR* 3.7 24.3 - - - +
225A LEU* 4.9 3.3 - - - +
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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* 3.4 0.4 - - - -
11A GLY* 1.3 73.6 - - - +
13A GLY* 1.3 61.5 + - - +
15A ALA* 3.3 2.6 + - - +
16A LEU* 2.8 34.4 + - + +
76A SER* 3.8 29.2 - - - +
117A ILE* 4.3 12.8 - - + -
223A ALA 4.1 6.1 - - - +
224A THR* 3.7 32.6 - - + +
227A MET* 3.8 32.5 - - + +
228A GLY* 4.1 11.1 - - - +
231A ALA* 5.3 0.7 - - + -
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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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5A VAL* 4.4 3.0 - - - +
7A GLY 3.5 21.9 + - - -
8A ALA* 3.5 12.0 - - - +
10A GLY 3.4 5.2 + - - -
12A ILE* 1.3 79.3 - - - +
14A GLN* 1.3 56.5 + - - +
16A LEU* 3.6 5.2 - - - +
17A ALA* 2.8 32.1 + - - +
76A SER* 3.7 12.3 + - - -
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Residues in contact with GLN 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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8A ALA 3.2 16.6 + - - +
9A ALA* 2.9 20.8 + - - +
10A GLY 3.0 18.6 + - - +
11A GLY* 4.3 3.8 - - - +
13A GLY* 1.3 73.6 - - - +
15A ALA* 1.3 57.9 + - - +
17A ALA* 3.9 4.7 - - - +
18A LEU* 3.0 30.0 + - - +
38A VAL* 5.0 4.4 - - - +
42A VAL* 3.9 25.5 - - + +
217C LYS* 5.5 1.4 + - - -
224C THR* 4.3 6.9 + - - -
225C LEU* 3.7 36.6 - - + +
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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 GLY 3.3 19.7 + - - +
12A ILE 3.6 3.6 - - - +
14A GLN* 1.3 73.0 - - - +
16A LEU* 1.3 59.9 + - - +
18A LEU* 3.6 4.7 + - - +
19A LEU* 3.1 38.1 + - - +
224A THR 4.1 13.0 - - - +
225A LEU* 4.1 13.5 - - + -
228A GLY* 4.1 7.2 - - - -
18C LEU* 4.0 22.6 - - + +
225C LEU* 5.7 0.7 - - - -
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Residues in contact with LEU 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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5A VAL* 3.9 29.4 - - + -
12A ILE* 2.8 22.0 + - + +
13A GLY 3.6 3.6 - - - +
15A ALA* 1.3 71.7 - - - +
17A ALA* 1.3 60.0 + - - +
19A LEU* 3.2 3.6 + - - +
20A LEU* 2.9 55.3 + - + +
74A LEU* 4.1 10.5 - - + -
76A SER* 4.4 5.4 - - - +
117A ILE* 3.9 27.8 - - + -
228A GLY* 4.0 12.4 - - - +
231A ALA* 3.9 8.7 - - + +
232A ALA* 3.7 31.2 - - - +
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Residues in contact with ALA 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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5A VAL* 5.1 1.8 - - + -
8A ALA 5.1 0.4 - - - +
13A GLY 2.8 22.6 + - - +
14A GLN* 3.9 4.7 - - - +
16A LEU* 1.3 74.9 - - - +
18A LEU* 1.3 57.3 + - - +
20A LEU* 3.2 7.2 + - - +
21A LYS* 2.9 31.5 + - - +
30A LEU* 3.8 4.9 - - + +
32A LEU* 3.6 31.9 - - + -
42A VAL* 5.3 0.4 - - + -
46A LEU* 3.6 20.3 - - + +
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Residues in contact with LEU 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 GLN 3.0 18.6 + - - +
15A ALA* 3.8 3.6 - - - +
17A ALA* 1.3 76.8 - - - +
19A LEU* 1.3 63.5 + - + +
21A LYS* 3.7 2.4 + - - +
22A THR* 3.3 20.3 + - - -
46A LEU* 3.7 26.3 - - + +
49A ILE* 3.8 4.3 - - + -
15C ALA* 3.9 31.0 - - + +
18C LEU* 4.5 11.2 - - + -
19C LEU* 4.1 26.7 - - + -
225C LEU* 3.7 26.9 - - + +
229C GLN* 3.6 20.6 - - - +
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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 ALA 3.1 22.1 + - - +
16A LEU 3.2 3.8 + - - +
18A LEU* 1.3 78.0 - - - +
20A LEU* 1.3 59.8 + - - +
22A THR* 3.4 5.0 + - - +
23A GLN* 3.0 50.9 + - - +
228A GLY 3.8 4.7 - - - +
229A GLN* 3.6 50.3 - - + +
232A ALA* 3.9 14.8 - - + -
18C LEU* 4.2 21.1 - - + -
19C LEU* 4.1 25.8 - - + -
22C THR* 5.2 4.3 - - - +
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Residues in contact with LEU 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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3A VAL* 4.3 11.7 - - + -
5A VAL* 4.2 16.8 - - + -
16A LEU* 2.9 36.8 + - + +
17A ALA* 3.8 4.3 - - - +
19A LEU* 1.3 76.3 - - - +
21A LYS* 1.3 61.2 + - - +
23A GLN* 4.4 0.7 - - - +
24A LEU* 2.9 51.8 + - + +
30A LEU* 4.0 17.0 - - + -
74A LEU* 4.3 6.3 - - + -
232A ALA* 3.9 30.5 - - + +
235A GLY 5.5 0.9 - - - -
236A LEU* 4.2 22.4 - - + +
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Residues in contact with LYS 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 ALA 2.9 17.7 + - - +
18A LEU 3.8 7.0 - - - +
20A LEU* 1.3 77.2 - - - +
22A THR* 1.3 55.0 + - - +
30A LEU* 3.7 14.5 - - + +
46A LEU* 3.3 46.0 - - + +
47A SER* 4.2 5.3 + - - +
49A ILE* 3.0 28.3 + - + +
51A THR* 2.6 47.0 + - - +
53A VAL* 2.9 39.6 + - + +
55A ILE* 3.9 13.7 - - + -
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Residues in contact with THR 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 LEU 3.3 14.4 + - - +
19A LEU* 3.4 7.8 + - - -
20A LEU 3.2 0.2 - - - -
21A LYS* 1.3 77.0 - - - +
23A GLN* 1.3 68.0 + - - +
24A LEU 3.8 4.2 - - - +
49A ILE* 3.8 22.4 - - + -
51A THR* 4.0 17.8 - - + +
53A VAL* 5.8 0.2 - - - -
19C LEU* 5.1 5.7 - - - +
23C GLN* 5.8 1.8 + - - -
229C GLN* 3.3 36.5 + - - +
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Residues in contact with GLN 23 (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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19A LEU* 3.0 44.4 + - - +
22A THR* 1.3 85.5 + - - +
24A LEU* 1.3 67.5 + - - +
25A PRO* 3.5 2.3 - - - +
229A GLN* 5.1 10.2 + - - +
232A ALA* 5.8 1.0 - - - +
236A LEU* 3.4 37.7 - - + +
19C LEU* 6.1 0.2 - - - +
22C THR* 5.8 1.6 + - - -
23C GLN* 6.0 1.4 - - - +
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Residues in contact with LEU 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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1A MET* 6.2 0.2 - - + -
3A VAL* 3.9 25.1 - - + -
20A LEU* 2.9 50.5 + - + +
21A LYS 4.9 0.2 - - - -
22A THR 3.8 4.2 - - - +
23A GLN* 1.3 76.1 - - - +
25A PRO* 1.3 75.6 - - + +
26A SER* 3.6 1.0 + - - -
28A SER* 3.8 20.4 - - - +
29A GLU 4.1 11.9 - - - +
30A LEU* 4.3 7.2 - - + -
53A VAL* 3.9 30.3 - - + +
235A GLY 5.5 1.1 - - - +
236A LEU* 3.8 14.9 - - + +
239A VAL* 4.0 17.3 - - + -
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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