Contacts of the strand formed by residues 27 - 41 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F HIS* 3.7 3.1 - - - +
24F TRP* 3.1 31.5 + - - +
25F SER 3.6 1.0 - - - -
26F TYR* 1.3 78.8 - - - +
28F ILE* 1.3 70.0 + - - +
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Residues in contact with ILE 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F PRO* 3.3 32.8 - - + -
22F TYR 3.2 9.2 - - - +
23F HIS* 3.4 35.7 - - + +
24F TRP* 3.6 6.8 + - - +
26F TYR 4.3 0.2 + - - -
27F GLY* 1.3 81.7 - - - +
29F ARG* 1.3 67.3 + - - +
30F GLU* 3.8 11.9 + - + +
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Residues in contact with ARG 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B GLY 3.5 12.0 + - - -
94B HIS* 4.0 24.1 + - - -
18F LEU* 3.4 8.9 - - + +
21F PRO* 3.8 1.7 - - - +
22F TYR* 2.7 61.6 + - + +
24F TRP* 3.2 50.1 - - + +
28F ILE* 1.3 71.7 - - - +
30F GLU* 1.3 60.9 + - - +
31F SER 3.4 13.9 - - - +
32F PHE* 4.4 10.9 - - - -
301F PHE* 3.1 47.3 - - - +
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Residues in contact with GLU 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F PRO* 3.8 2.9 - - - +
18F LEU* 3.1 25.8 + - - +
20F GLN 4.7 1.0 - - - -
21F PRO* 3.6 33.4 - - - +
28F ILE* 3.8 10.7 + - + +
29F ARG* 1.3 74.3 - - - +
31F SER* 1.3 63.2 + - - +
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Residues in contact with SER 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 3.7 18.4 - - - +
16F LEU 3.1 26.7 - - - -
17F PRO* 3.6 5.8 - - - -
18F LEU* 3.5 7.0 - - - +
29F ARG* 3.4 14.2 - - - +
30F GLU* 1.3 84.0 + - - +
32F PHE* 1.3 70.6 + - - +
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Residues in contact with PHE 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 3.6 2.8 - - - +
16F LEU* 2.8 44.8 + - + +
18F LEU* 3.5 36.9 - - + +
22F TYR* 4.9 6.5 - + - -
29F ARG* 4.4 15.0 - - - -
31F SER* 1.3 81.8 - - - +
33F ALA* 1.3 59.6 + - - +
34F VAL* 5.3 2.0 - - + -
300F SER 5.2 0.2 - - - -
301F PHE* 3.5 65.7 - + + +
302F THR* 3.9 15.5 - - - +
303F THR* 6.4 0.2 - - + -
327F MSE 4.7 4.3 - - + -
330F LEU* 4.1 27.6 - - + -
331F VAL* 4.3 7.2 - - + -
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Residues in contact with ALA 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LEU 3.2 14.1 - - - +
15F VAL* 4.6 6.3 - - + -
16F LEU* 5.7 0.7 - - - -
32F PHE* 1.3 77.2 - - - +
34F VAL* 1.3 68.9 + - - +
51F CYS 4.7 0.3 - - - +
52F THR* 4.8 1.9 - - - +
53F VAL* 3.8 27.7 + - + +
57F GLN* 3.5 19.7 - - + +
301F PHE 4.4 5.0 + - - +
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Residues in contact with VAL 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ARG 4.0 0.2 - - - +
14F LEU* 2.8 58.7 + - + +
16F LEU* 4.4 4.5 - - + -
32F PHE* 5.3 1.6 - - + -
33F ALA* 1.3 82.6 - - - +
35F ASN* 1.3 60.8 + - - +
36F LEU* 4.1 4.9 - - + -
50F GLU* 3.9 19.3 - - + +
51F CYS 3.5 9.9 - - - +
53F VAL* 3.8 1.3 - - - -
57F GLN* 3.0 3.3 + - - -
301F PHE 4.3 1.6 - - - +
302F THR* 3.9 38.6 - - + -
303F THR* 3.9 15.9 - - + -
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Residues in contact with ASN 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F VAL* 4.3 4.7 - - + -
12F ARG 3.9 3.4 - - - -
13F PRO* 3.4 12.0 - - - +
34F VAL* 1.3 71.9 - - - +
36F LEU* 1.3 64.3 + - - +
37F ILE 3.7 0.2 + - - -
50F GLU* 3.4 1.6 - - - -
51F CYS* 3.0 33.5 + - + +
52F THR 4.7 1.8 + - - -
53F VAL* 3.4 12.6 - - + +
57F GLN* 3.0 29.6 + - - +
60F THR* 3.3 26.9 + - - -
61F ALA* 3.3 24.0 - - - +
64F LEU* 3.8 20.9 - - + +
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Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ARG 4.4 0.2 - - - -
11F VAL* 3.1 10.0 - - - +
12F ARG* 3.0 49.8 + - + +
14F LEU* 3.7 32.3 - - + -
34F VAL* 3.9 3.8 - - + -
35F ASN* 1.3 74.6 - - - +
37F ILE* 1.3 62.5 + - - +
38F GLU* 4.2 7.4 - - + +
48F ILE* 5.0 2.7 - - + -
49F GLY 3.5 3.4 - - - +
50F GLU* 3.8 18.4 - - + +
305F ILE* 3.4 33.7 - - + -
335F ILE* 4.2 5.8 - - + -
360F LEU* 4.5 11.4 - - + -
365F VAL* 4.0 18.4 - - + -
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Residues in contact with ILE 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 4.6 0.9 - - + -
10F ARG 3.5 12.1 - - - +
11F VAL* 4.1 11.2 - - + -
36F LEU* 1.3 75.8 - - - +
38F GLU* 1.3 71.3 + - - +
39F ILE* 4.2 19.1 - - + -
47F GLY 3.8 0.9 - - - +
48F ILE* 3.5 2.8 - - - +
49F GLY* 2.9 48.6 + - - +
50F GLU* 3.9 2.7 - - - +
64F LEU* 4.0 20.4 - - + -
68F ALA* 3.6 28.9 - - + -
108F GLY* 3.5 27.1 - - - +
109F ILE* 4.1 6.3 - - + +
112F ALA* 3.8 1.9 - - + +
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Residues in contact with GLU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ASN 4.1 0.2 - - - +
9F VAL* 3.3 6.2 - - - +
10F ARG* 2.8 81.1 + - + +
12F ARG* 3.0 39.2 + - + -
36F LEU* 4.9 7.0 - - + +
37F ILE* 1.3 79.4 - - - +
39F ILE* 1.3 62.2 + - - +
40F GLU 4.1 0.6 + - - -
46F VAL* 4.0 8.7 - - + -
47F GLY 3.4 4.5 - - - -
48F ILE* 4.3 24.5 - - + +
360F LEU* 5.0 2.1 - - - +
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Residues in contact with ILE 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 3.6 42.6 - - + -
8F ASN 3.8 2.7 - - - -
9F VAL* 4.4 10.1 - - + -
37F ILE* 4.2 12.8 - - + -
38F GLU* 1.3 75.7 - - - +
40F GLU* 1.3 59.4 + - - +
45F THR 3.9 0.5 - - - +
46F VAL* 3.3 3.0 - - - -
47F GLY* 2.7 39.3 + - - +
71F LEU* 3.8 14.8 - - + -
109F ILE* 3.9 4.9 - - + +
112F ALA* 3.5 27.4 - - + +
113F MSE 3.8 25.8 - - + +
116F LEU* 4.0 15.1 - - + +
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Residues in contact with GLU 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 3.3 7.4 - - - +
7F SER* 2.8 40.2 + - - +
8F ASN* 2.9 32.3 + - - +
10F ARG* 3.4 29.1 + - - +
38F GLU 4.1 0.6 - - - -
39F ILE* 1.3 74.5 - - - +
41F ALA* 1.3 65.3 + - - +
44F GLY* 4.1 15.1 - - - +
45F THR 3.4 9.9 - - - +
46F VAL* 3.8 14.7 - - + +
116F LEU* 5.1 0.7 - - - -
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Residues in contact with ALA 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 3.9 15.5 - - + -
5F LYS 3.4 11.7 - - - +
6F ILE* 4.1 2.7 - - - +
7F SER* 3.3 9.2 + - - +
39F ILE 4.1 0.6 + - - -
40F GLU* 1.3 78.8 - - - +
42F ASP* 1.3 58.9 + - - +
43F ASP* 3.0 21.8 - - - +
44F GLY* 2.9 17.2 + - - -
45F THR* 2.8 13.3 + - - +
76F PRO* 5.7 1.1 - - + -
116F LEU* 4.1 19.7 - - + +
120F LEU* 4.8 1.6 - - + -
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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