Contacts of the helix formed by residues 10 - 24 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E GLY 3.6 8.6 + - - -
8E ALA 3.5 1.6 - - - -
9E ALA* 1.3 81.0 - - - +
11E GLY* 1.3 65.6 + - - -
12E ILE 3.3 2.5 - - - -
13E GLY 3.8 2.2 - - - -
14E GLN* 3.0 22.8 + - - +
34E ASP* 3.9 3.8 + - - -
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Residues in contact with GLY 11 (chain E).
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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10E GLY* 1.3 72.3 - - - +
12E ILE* 1.3 62.3 + - - +
14E GLN* 4.2 2.3 - - - +
15E ALA* 3.3 23.9 + - - +
224E THR* 3.7 26.6 - - - +
225E LEU* 4.9 3.0 - - - +
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Residues in contact with ILE 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLY* 3.3 0.6 - - - -
11E GLY* 1.3 75.6 - - - +
13E GLY* 1.3 57.6 + - - +
15E ALA* 3.3 2.8 + - - +
16E LEU* 3.0 31.1 + - + +
76E SER* 3.9 26.5 - - - +
117E ILE* 4.3 14.1 - - + -
222E SER* 6.1 0.2 - - - +
223E ALA 3.9 8.7 - - - +
224E THR* 3.7 30.9 - - + +
227E MET* 3.7 32.3 - - + +
228E GLY* 4.0 8.6 - - - +
231E ALA* 5.4 0.7 - - + -
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Residues in contact with GLY 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E VAL* 4.3 7.1 - - - +
7E GLY 3.5 22.3 + - - -
8E ALA* 3.3 10.7 - - - +
10E GLY* 3.4 5.2 + - - -
11E GLY 3.4 0.6 - - - -
12E ILE* 1.3 78.5 - - - +
14E GLN* 1.3 56.3 + - - +
16E LEU* 3.6 5.2 + - - +
17E ALA* 2.9 29.5 + - - +
76E SER* 3.7 12.7 + - - -
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Residues in contact with GLN 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ALA 3.3 15.3 - - - +
9E ALA* 2.8 22.4 + - - +
10E GLY 3.0 16.6 + - - +
11E GLY* 4.2 3.1 - - - +
13E GLY* 1.3 75.0 - - - +
15E ALA* 1.3 61.1 + - - +
17E ALA* 4.0 4.7 - - - -
18E LEU* 3.1 24.4 + - - +
38E VAL* 4.9 4.8 - - - +
42E VAL* 3.9 27.1 - - + +
217G LYS* 5.2 3.0 + - - +
224G THR* 4.4 6.9 + - - -
225G LEU* 3.8 35.1 - - + +
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Residues in contact with ALA 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLY 3.3 18.4 + - - +
12E ILE 3.7 2.9 - - - +
14E GLN* 1.3 73.9 - - - +
16E LEU* 1.3 65.5 + - - +
18E LEU* 3.5 5.9 + - - +
19E LEU* 3.1 30.2 + - - +
224E THR 4.0 14.1 - - - +
225E LEU* 4.0 14.6 - - + -
228E GLY* 4.0 8.5 - - - -
18G LEU* 3.9 22.2 - - + +
225G LEU* 5.6 0.4 - - - -
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Residues in contact with LEU 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E VAL* 4.1 22.2 - - + -
12E ILE* 3.0 17.7 + - + +
13E GLY 3.7 2.7 - - - +
15E ALA* 1.3 76.8 - - - +
17E ALA* 1.3 55.6 + - - +
19E LEU* 3.4 2.9 + - - +
20E LEU* 3.0 47.3 + - + +
74E LEU* 3.8 21.3 - - + -
76E SER* 4.6 6.1 - - - +
117E ILE* 4.1 19.7 - - + -
228E GLY* 3.8 13.8 - - - +
231E ALA* 3.6 8.7 - - + +
232E ALA* 3.3 37.0 - - - +
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Residues in contact with ALA 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E VAL* 5.2 1.5 - - + +
8E ALA 5.1 0.4 - - - +
13E GLY 2.9 20.2 + - - +
14E GLN* 4.0 6.1 - - - +
15E ALA 3.3 0.2 - - - -
16E LEU* 1.3 73.7 - - - +
18E LEU* 1.3 60.8 + - - +
20E LEU* 3.9 7.9 - - - +
21E LYS* 3.0 31.4 + - - +
30E LEU* 3.9 3.6 - - + +
32E LEU* 3.7 29.4 - - + -
42E VAL* 5.3 0.4 - - + -
46E LEU* 3.7 22.0 - - + +
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Residues in contact with LEU 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E GLN 3.1 18.8 + - - +
15E ALA* 3.6 5.4 - - - +
17E ALA* 1.3 76.4 - - - +
19E LEU* 1.3 60.7 + - + +
21E LYS* 3.7 1.2 - - - +
22E THR* 3.0 26.0 + - + +
46E LEU* 3.7 23.0 - - + +
49E ILE* 4.0 11.7 - - + -
15G ALA* 3.8 39.9 - - + +
18G LEU* 4.5 11.2 - - + -
19G LEU* 4.1 19.5 - - + -
225G LEU* 3.7 24.2 - - + +
229G GLN* 4.5 13.7 - - + +
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Residues in contact with LEU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ALA 3.1 17.5 + - - +
16E LEU 3.9 1.1 - - - +
18E LEU* 1.3 75.1 - - + +
20E LEU* 1.3 58.9 + - - +
22E THR* 3.3 3.1 + - - -
23E GLN* 2.9 54.3 + - - +
228E GLY 3.9 3.6 - - - +
229E GLN* 3.4 57.2 - - - +
232E ALA* 3.7 17.0 - - + -
236E LEU* 5.7 0.2 - - - -
18G LEU* 4.1 16.6 - - + -
19G LEU* 4.1 24.7 - - + -
22G THR* 5.6 3.6 - - - +
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Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E VAL* 4.2 11.9 - - + -
5E VAL* 3.9 20.9 - - + -
16E LEU* 3.0 47.6 + - + +
17E ALA* 3.9 0.7 - - - +
19E LEU* 1.3 73.9 - - - +
21E LYS* 1.3 62.5 + - - +
23E GLN* 5.0 0.4 - - - -
24E LEU* 2.8 54.2 + - + +
30E LEU* 3.7 18.8 - - + -
53E VAL* 4.4 0.2 - - - +
74E LEU* 4.3 3.6 - - + -
232E ALA* 4.4 8.7 - - + +
235E GLY* 5.1 5.4 - - - -
236E LEU* 4.2 30.7 - - + +
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Residues in contact with LYS 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ALA 3.0 20.1 + - - +
18E LEU 3.7 4.5 - - - +
20E LEU* 1.3 78.5 - - - +
22E THR* 1.3 55.8 + - + +
30E LEU* 3.6 9.4 - - + +
46E LEU* 3.0 45.5 - - + +
47E SER* 4.3 4.3 + - - +
49E ILE* 3.6 20.7 + - + -
51E THR* 2.7 54.1 + - - +
53E VAL* 2.4 50.0 + - + +
55E ILE* 4.2 16.4 - - + +
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Residues in contact with THR 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E LEU* 3.0 19.8 + - + +
19E LEU* 3.3 11.6 + - - +
21E LYS* 1.3 75.7 - - - +
23E GLN* 1.3 69.0 + - - +
24E LEU 3.9 1.6 - - - +
49E ILE* 3.8 29.4 - - + -
51E THR* 4.1 17.0 - - + +
19G LEU* 5.0 4.5 - - - +
23G GLN* 5.8 2.0 + - - -
229G GLN* 3.3 28.1 + - - +
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Residues in contact with GLN 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 2.9 45.3 + - - +
22E THR* 1.3 88.3 + - - +
24E LEU* 1.3 67.4 + - - +
25E PRO* 3.5 2.3 - - - +
229E GLN* 5.1 9.0 + - - +
232E ALA* 5.7 0.9 - - - +
236E LEU* 3.7 33.8 - - + +
22G THR* 6.0 0.2 + - - -
23G GLN* 5.3 8.3 - - - +
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Residues in contact with LEU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 6.3 0.2 - - + -
3E VAL* 4.1 31.6 - - + -
20E LEU* 2.8 51.2 + - + +
21E LYS 4.5 0.2 + - - -
22E THR 3.9 1.8 - - - +
23E GLN* 1.3 77.3 + - - +
25E PRO* 1.3 77.6 - - + +
26E SER 3.8 0.3 + - - -
28E SER* 3.7 23.3 - - - +
29E GLU 4.4 5.4 - - - +
30E LEU* 4.4 4.3 - - + -
51E THR* 5.8 0.5 - - - -
53E VAL* 3.7 23.1 - - + +
236E LEU* 3.7 17.9 - - + +
239E VAL* 4.2 14.1 - - + -
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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