Contacts of the strand formed by residues 8 - 24 (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 ASN 8 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E ILE* 3.8 1.7 - - - +
7E SER* 1.3 110.6 + - - +
9E VAL* 1.3 72.0 + - - +
10E ARG* 4.2 10.5 - - - +
39E ILE* 3.6 0.3 - - - -
40E GLU* 2.8 53.0 + - - +
72E VAL* 4.5 4.9 - - - -
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Residues in contact with VAL 9 (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* 4.2 4.7 - - + -
8E ASN* 1.3 83.4 - - - +
10E ARG* 1.3 65.9 + - - +
37E ILE* 4.5 1.6 - - + -
38E GLU 3.2 8.1 - - - +
39E ILE* 4.1 24.2 - - + -
65E TYR* 3.9 15.7 + - + -
68E ALA* 3.7 46.0 - - + +
69E LYS* 3.9 18.4 - - + +
71E LEU* 4.7 2.2 - - + -
72E VAL* 4.2 13.2 - - + -
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Residues in contact with ARG 10 (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 ASN* 4.2 11.7 - - - +
9E VAL* 1.3 77.8 - - - +
11E VAL* 1.3 65.6 + - - +
12E ARG* 4.1 9.8 + - + +
36E LEU 3.8 0.2 - - - +
37E ILE* 3.5 5.5 - - - +
38E GLU* 2.9 82.1 + - + +
40E GLU* 2.8 38.9 + - - +
46E VAL* 4.2 15.0 - - - +
65E TYR* 4.7 5.2 - - - -
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Residues in contact with VAL 11 (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* 1.3 76.9 - - - +
12E ARG* 1.3 65.1 - - - +
13E PRO* 3.6 13.7 - - + +
35E ASN* 4.4 3.1 - - + -
36E LEU 3.3 9.6 - - - +
37E ILE* 4.3 7.0 - - + -
61E ALA* 3.9 29.4 - - + +
64E LEU* 3.8 21.8 - - + -
65E TYR* 3.5 47.8 - - + +
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Residues in contact with ARG 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 ARG* 4.6 11.4 - - + +
11E VAL* 1.3 80.3 - - - +
13E PRO* 1.3 66.3 - - - +
14E LEU* 3.5 9.0 + - + +
35E ASN* 4.5 0.4 - - - -
36E LEU* 3.1 43.0 + - + +
38E GLU* 3.1 42.9 + - - +
360E LEU* 5.8 2.0 - - - +
362E GLU* 4.0 19.8 + - - -
365E VAL* 3.4 27.2 - - - +
366E ALA* 4.4 5.1 - - - +
369E GLU* 2.8 46.0 + - + +
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Residues in contact with PRO 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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11E VAL* 3.6 9.9 - - + +
12E ARG* 1.3 85.5 - - - +
14E LEU* 1.3 64.4 + - - +
34E VAL 3.7 0.2 - - - +
35E ASN* 3.3 24.9 - - - +
57E GLN* 3.7 7.2 - - + +
61E ALA* 3.9 19.1 - - + -
369E GLU* 3.7 10.1 - - + +
372E TYR* 3.4 49.3 - - + +
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Residues in contact with LEU 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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12E ARG* 3.6 13.0 - - + +
13E PRO* 1.3 75.7 - - - +
15E VAL* 1.3 65.9 + - - +
16E LEU* 4.1 19.7 - - + -
33E ALA* 3.2 3.2 - - - +
34E VAL* 2.8 40.9 + - + +
36E LEU* 3.7 27.4 - - + -
57E GLN* 2.8 18.1 + - - +
335E ILE* 4.2 15.7 - - + -
365E VAL* 3.3 35.0 - - + +
368E GLY 3.7 2.7 - - - -
369E GLU* 3.4 24.9 - - + +
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Residues in contact with VAL 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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14E LEU* 1.3 80.4 - - - +
16E LEU* 1.3 68.3 + - - +
31E SER* 3.6 20.9 - - - +
32E PHE 3.4 6.1 - - - +
33E ALA* 4.5 3.8 - - + -
57E GLN* 3.7 15.3 - - - +
368E GLY* 3.3 6.3 + - - -
371E ARG* 3.0 51.5 + - + +
372E TYR* 3.6 23.1 - - + -
375E SER* 4.6 7.4 - - - +
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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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14E LEU* 4.1 11.0 - - + -
15E VAL* 1.3 87.3 - - - +
17E PRO* 1.3 69.4 - - + +
18E LEU* 4.6 1.0 - - - +
31E SER* 3.1 3.8 - - - -
32E PHE* 2.7 49.1 + - + +
34E VAL* 4.5 10.3 - - + -
303E THR* 3.4 33.2 - - + -
331E VAL* 4.3 23.2 - - + +
333E GLU 5.4 3.4 - - - +
335E ILE* 4.2 24.0 - - + -
364E LEU 4.7 4.3 - - - +
368E GLY* 3.9 17.9 - - - -
371E ARG* 5.2 1.8 - - - +
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Residues in contact with PRO 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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16E LEU* 1.3 87.9 - - + +
18E LEU* 1.3 63.1 + - - +
30E GLU 3.6 10.8 - - - +
31E SER* 3.7 4.0 - - - -
331E VAL* 3.8 6.9 - - - +
332E GLN* 3.0 41.5 + - + +
333E GLU* 4.5 1.3 + - + +
371E ARG* 3.1 48.0 - - - +
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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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16E LEU 4.6 0.7 - - - +
17E PRO* 1.3 78.6 - - - +
19E LYS* 1.3 65.8 + - - +
20E GLN* 3.1 14.4 + - - +
22E TYR* 3.7 19.7 - - + -
29E ARG* 3.4 26.2 - - + +
30E GLU 3.0 13.9 + - - +
31E SER* 3.5 17.0 - - - +
32E PHE* 3.5 52.5 - - + +
330E LEU* 3.5 18.8 - - + +
331E VAL* 4.4 2.5 - - + -
332E GLN* 3.8 14.1 + - - -
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Residues in contact with LYS 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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18E LEU* 1.3 73.6 - - - +
20E GLN* 1.3 65.8 + - + +
328E TRP* 6.0 3.9 - - - -
329E GLN* 3.1 33.2 + - - +
330E LEU* 3.0 13.4 + - - +
331E VAL 3.5 13.0 - - - +
332E GLN* 3.6 34.5 + - + +
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Residues in contact with GLN 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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18E LEU* 3.1 19.8 - - - +
19E LYS* 1.3 84.3 - - + +
21E PRO* 1.3 90.3 + - + +
22E TYR* 3.3 2.9 + - - +
23E HIS* 6.0 1.6 - - - -
30E GLU* 5.4 1.8 - - - -
144E GLN* 4.8 25.4 - - - +
145E GLY* 5.6 3.2 - - - +
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Residues in contact with PRO 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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20E GLN* 1.3 105.7 + - + +
22E TYR* 1.3 59.9 + - - +
23E HIS* 3.6 20.6 + - + -
28E ILE* 3.3 33.9 - - + -
29E ARG 3.6 6.5 - - - +
30E GLU* 4.2 17.9 - - + +
144E GLN* 5.3 2.6 + - - -
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Residues in contact with TYR 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* 3.7 17.3 - - + -
20E GLN 3.3 1.5 + - - +
21E PRO* 1.3 71.6 - - - +
23E HIS* 1.3 78.0 + - - +
24E TRP* 3.6 5.6 + - + -
28E ILE* 3.5 1.7 - - - -
29E ARG* 2.7 69.5 + - + +
32E PHE* 4.9 4.3 - + - -
142E PHE* 3.6 28.1 - + - -
144E GLN* 3.7 27.6 - - - +
301E PHE* 3.4 37.2 - + - -
330E LEU* 4.4 11.2 - - + -
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Residues in contact with HIS 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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20E GLN* 6.0 1.8 - - - -
21E PRO* 3.6 24.6 + - + -
22E TYR* 1.3 87.3 - - - +
24E TRP* 1.3 62.2 + - - +
27E GLY 3.7 5.8 - - - +
28E ILE* 3.4 33.3 - - + +
146E GLU* 3.5 46.2 + - + +
169E LYS* 4.9 9.2 + - - -
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Residues in contact with TRP 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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89D GLN* 3.4 34.1 - - + -
93D GLY* 3.9 17.9 - - - +
94D HIS* 3.8 19.1 - + - -
22E TYR* 3.7 17.3 - - + -
23E HIS* 1.3 76.0 - - - +
25E SER* 1.3 68.3 + - - +
26E TYR* 3.0 55.0 + + + -
27E GLY* 3.0 44.5 + - - +
28E ILE 3.7 11.3 + - - -
29E ARG* 3.3 37.4 - - + +
169E LYS* 5.9 2.5 - - - +
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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