Contacts of the strand formed by residues 27 - 40 (chain E) in PDB entry 2PGW
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 27 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E HIS* 3.7 5.1 - - - +
24E TRP* 3.0 33.3 + - - +
25E SER 3.5 3.2 + - - -
26E TYR* 1.3 75.3 - - - +
28E ILE* 1.3 63.9 + - - +
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Residues in contact with ILE 28 (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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21E PRO* 3.3 31.4 - - + -
22E TYR 3.5 2.5 - - - +
23E HIS* 3.4 41.1 - - + +
24E TRP* 3.7 7.2 + - - +
26E TYR 3.9 0.7 + - - +
27E GLY* 1.3 77.6 - - - -
29E ARG* 1.3 63.1 + - - +
30E GLU* 3.8 18.1 + - + +
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Residues in contact with ARG 29 (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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93D GLY 3.1 25.0 + - - -
94D HIS* 4.5 17.6 + - - -
18E LEU* 3.4 6.7 - - + +
21E PRO* 3.6 0.9 - - - +
22E TYR* 2.7 55.8 + - + +
24E TRP* 3.3 41.6 - - + +
28E ILE* 1.3 73.1 - - - +
30E GLU* 1.3 60.9 + - - +
31E SER 3.3 24.5 - - - +
32E PHE* 3.8 15.9 - - - +
301E PHE* 3.3 45.1 - - - +
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Residues in contact with GLU 30 (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 PRO* 3.6 4.9 - - - +
18E LEU* 3.0 26.9 + - - +
20E GLN 5.4 0.7 - - - -
21E PRO* 4.2 19.3 - - + +
28E ILE* 3.8 19.2 + - + -
29E ARG* 1.3 77.7 - - - +
31E SER* 1.3 62.9 + - - +
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Residues in contact with SER 31 (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 VAL* 3.6 22.5 - - - +
16E LEU 3.1 24.9 - - - -
17E PRO* 3.7 4.3 - - - -
18E LEU* 3.5 9.0 - - - +
29E ARG* 3.3 20.8 - - - +
30E GLU* 1.3 80.5 - - - +
32E PHE* 1.3 65.7 + - - +
371E ARG* 5.8 0.2 - - - -
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Residues in contact with PHE 32 (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 VAL* 3.4 3.3 - - - -
16E LEU* 2.7 45.2 + - + +
18E LEU* 3.5 35.9 - - + +
22E TYR* 4.9 5.4 - + - -
29E ARG* 3.8 15.9 - - - -
31E SER* 1.3 84.6 + - - +
33E ALA* 1.3 60.0 + - - +
34E VAL* 5.5 1.6 - - + -
300E SER 5.4 0.2 - - - -
301E PHE* 3.4 66.9 - + + +
302E THR* 4.1 13.7 - - - +
303E THR* 6.4 0.7 - - + -
327E MSE 4.9 2.2 - - - -
330E LEU* 4.2 25.8 - - + -
331E VAL* 4.3 8.5 - - + -
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Residues in contact with ALA 33 (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 LEU 3.2 14.4 - - - +
15E VAL* 4.5 5.6 - - + -
16E LEU* 5.8 0.2 - - - -
32E PHE* 1.3 75.8 - - - +
34E VAL* 1.3 68.4 + - - +
52E THR* 4.8 1.6 - - - -
53E VAL* 3.5 29.0 + - + +
57E GLN* 3.5 21.8 - - + +
301E PHE 4.5 3.8 + - - +
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Residues in contact with VAL 34 (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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12E ARG 3.9 0.2 - - - +
14E LEU* 2.8 55.5 + - + +
16E LEU* 4.5 4.5 - - + -
32E PHE* 5.5 1.8 - - + -
33E ALA* 1.3 81.7 - - - +
35E ASN* 1.3 64.7 + - - +
36E LEU* 4.4 3.4 - - + -
50E GLU* 3.8 25.6 - - + +
51E CYS 3.4 11.7 - - - +
52E THR* 5.3 0.2 - - - -
53E VAL* 3.7 0.9 - - - -
57E GLN* 3.2 2.7 + - - -
301E PHE 4.2 2.2 - - - +
302E THR* 3.9 38.4 - - + -
303E THR* 4.1 12.1 - - + -
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Residues in contact with ASN 35 (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 VAL* 4.4 5.4 - - + -
12E ARG 3.9 3.6 - - - -
13E PRO* 3.3 12.0 - - - +
34E VAL* 1.3 70.5 - - - +
36E LEU* 1.3 65.7 + - - +
50E GLU* 3.4 2.0 - - - -
51E CYS* 2.9 36.2 + - + +
52E THR 4.8 1.6 + - - -
53E VAL* 3.5 10.9 - - - +
57E GLN* 3.1 37.3 + - - +
60E THR* 3.3 26.1 + - - -
61E ALA* 3.3 18.8 - - - +
64E LEU* 3.6 21.6 - - + +
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Residues in contact with LEU 36 (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 ARG 4.4 0.2 - - - -
11E VAL* 3.3 9.5 - - - +
12E ARG* 3.1 52.4 + - + +
14E LEU* 3.7 27.4 - - + -
34E VAL* 4.4 3.1 - - + -
35E ASN* 1.3 76.4 - - - +
37E ILE* 1.3 60.2 + - - +
38E GLU* 4.2 2.7 - - + +
48E ILE* 4.9 5.2 - - + -
49E GLY 3.5 4.0 - - - +
50E GLU* 3.6 19.5 - - + +
64E LEU* 4.0 0.3 - - - +
305E ILE* 3.5 28.0 - - + -
335E ILE* 4.1 7.0 - - + -
360E LEU* 4.4 17.7 - - + -
365E VAL* 3.9 19.3 - - + -
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Residues in contact with ILE 37 (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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9E VAL* 4.5 0.4 - - + -
10E ARG 3.5 13.2 - - - +
11E VAL* 4.3 9.6 - - + -
36E LEU* 1.3 76.4 - - - +
38E GLU* 1.3 71.9 + - - +
39E ILE* 4.1 19.7 - - + -
47E GLY 3.7 1.2 - - - +
48E ILE* 3.5 2.8 - - - -
49E GLY 3.0 34.4 + - - +
50E GLU* 3.9 2.9 - - - +
64E LEU* 4.0 20.4 - - + -
68E ALA* 3.7 29.8 - - + -
108E GLY* 3.4 33.4 - - - +
109E ILE* 4.7 4.3 - - + -
112E ALA* 3.8 2.1 - - + +
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Residues in contact with GLU 38 (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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9E VAL* 3.2 5.9 - - - +
10E ARG* 2.9 80.0 + - + +
12E ARG* 3.1 39.5 + - + -
36E LEU* 5.0 4.6 - - + +
37E ILE* 1.3 77.6 - - - +
39E ILE* 1.3 62.2 + - - +
40E GLU 4.0 0.8 + - - -
46E VAL* 3.9 9.2 - - + -
47E GLY 3.4 4.9 - - - +
48E ILE* 4.1 28.7 - - + +
360E LEU* 5.1 1.7 - - - +
362E GLU* 5.7 0.3 - - - +
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Residues in contact with ILE 39 (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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6E ILE* 3.6 43.5 - - + -
8E ASN 3.6 2.7 - - - -
9E VAL* 4.1 11.4 - - + -
37E ILE* 4.1 16.4 - - + -
38E GLU* 1.3 76.8 - - - +
40E GLU* 1.3 59.2 + - - +
46E VAL* 3.4 2.4 - - - -
47E GLY 2.9 37.4 + - - +
71E LEU* 3.8 23.6 - - + -
109E ILE* 3.9 4.3 - - + +
112E ALA* 3.7 23.8 - - + +
113E MSE 3.8 17.0 - - + +
116E LEU* 3.8 15.0 - - + +
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Residues in contact with GLU 40 (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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6E ILE* 3.4 5.2 - - - +
7E SER* 2.8 27.9 + - - +
8E ASN* 2.8 35.3 + - + +
10E ARG* 2.8 36.1 + - - +
38E GLU 4.0 1.0 - - - -
39E ILE* 1.3 73.1 - - - +
41E ALA* 1.3 73.0 + - - +
44E GLY* 3.8 18.9 - - - +
45E THR 3.4 5.4 - - - +
46E VAL* 3.8 18.0 - - + +
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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