Contacts of the strand formed by residues 28 - 41 (chain C) 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 ILE 28 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C PRO* 4.1 13.9 - - + -
22C TYR 3.3 5.4 - - - +
23C HIS* 3.1 43.5 - - + +
24C TRP* 3.6 9.5 + - - -
26C TYR 4.3 1.2 - - - +
27C GLY* 1.3 74.6 - - - -
29C ARG* 1.3 60.3 + - - +
30C GLU* 3.5 22.6 + - + +
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Residues in contact with ARG 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.5 7.2 - - + +
21C PRO* 3.4 4.5 - - - +
22C TYR* 2.6 64.5 + - + +
24C TRP* 3.4 35.3 - - - +
28C ILE* 1.3 75.0 - - - +
30C GLU* 1.3 63.3 + - - +
31C SER 3.3 25.6 - - - +
32C PHE* 3.9 18.8 - - - -
301C PHE* 3.5 29.6 - - - -
93H GLY 3.3 19.4 + - - -
94H HIS* 3.4 29.4 + - - -
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C PRO* 3.6 4.5 - - - +
18C LEU* 2.9 27.5 + - - +
20C GLN 5.5 0.9 - - - -
21C PRO* 3.1 36.1 - - - +
28C ILE* 3.5 19.5 - - + +
29C ARG* 1.3 74.9 - - - +
31C SER* 1.3 64.1 + - - +
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.7 21.0 - - - +
16C LEU 2.9 26.0 - - - -
17C PRO* 3.6 3.8 - - - -
18C LEU* 3.7 6.0 - - - +
29C ARG* 3.3 22.2 - - - +
30C GLU* 1.3 84.4 - - - +
32C PHE* 1.3 63.8 + - - +
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Residues in contact with PHE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.6 2.1 - - - -
16C LEU* 2.8 43.7 + - + +
18C LEU* 3.4 37.6 - - + +
22C TYR* 4.9 4.5 - + - -
29C ARG* 3.9 13.5 - - - -
31C SER* 1.3 81.9 - - - +
33C ALA* 1.3 59.1 + - - +
34C VAL* 5.4 2.2 - - + -
300C SER 5.2 0.2 - - - -
301C PHE* 3.4 67.8 - + + +
302C THR* 3.9 14.8 - - - +
303C THR* 6.1 0.4 - - + -
327C MSE 4.8 3.6 - - + -
330C LEU* 4.1 26.2 - - + -
331C VAL* 4.2 9.2 - - + -
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU 3.3 7.2 - - - +
15C VAL* 4.6 6.7 - - + -
32C PHE* 1.3 74.8 - - - +
34C VAL* 1.3 68.7 + - - +
52C THR* 4.7 1.7 - - - -
53C VAL* 3.7 31.1 + - + +
57C GLN* 3.5 24.2 - - + +
301C PHE 4.4 5.0 + - - +
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 2.8 57.5 + - + +
16C LEU* 4.6 3.8 - - + -
32C PHE* 5.4 2.0 - - + -
33C ALA* 1.3 80.6 - - - +
35C ASN* 1.3 63.6 + - - +
36C LEU* 4.2 3.8 - - + -
50C GLU* 3.8 24.0 - - + +
51C CYS 3.5 11.2 - - - +
52C THR* 5.3 0.4 - - - -
53C VAL* 3.7 1.6 - - - -
57C GLN* 3.1 3.1 + - - -
301C PHE 4.2 3.6 - - - +
302C THR* 4.0 34.5 - - + -
303C THR* 4.1 13.0 - - + -
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Residues in contact with ASN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C VAL* 4.4 4.9 - - + -
12C ARG 3.9 2.9 - - - -
13C PRO* 3.3 11.4 - - - +
34C VAL* 1.3 71.5 - - - +
36C LEU* 1.3 64.1 + - - +
37C ILE 3.7 0.5 + - - -
50C GLU* 3.4 2.0 - - - -
51C CYS* 2.9 34.9 + - + +
52C THR 4.9 1.4 + - - -
53C VAL* 3.6 10.3 - - - +
57C GLN* 3.0 30.6 + - - +
60C THR* 3.3 26.3 + - - -
61C ALA* 3.4 25.6 - - - +
64C LEU* 3.8 20.6 - - + +
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG 4.3 0.2 - - - -
11C VAL* 3.2 9.0 - - - +
12C ARG* 3.0 49.7 + - + +
14C LEU* 3.4 35.7 - - + -
34C VAL* 4.0 2.6 - - + -
35C ASN* 1.3 74.8 - - - +
37C ILE* 1.3 61.0 + - - +
38C GLU* 4.2 3.6 - - + +
48C ILE* 5.1 4.7 - - + -
49C GLY 3.4 4.7 - - - +
50C GLU* 3.8 17.5 - - + +
64C LEU* 4.1 0.6 - - - +
305C ILE* 3.5 26.5 - - + -
335C ILE* 4.1 3.1 - - + -
360C LEU* 4.5 17.0 - - + -
365C VAL* 3.8 20.9 - - + -
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Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 4.4 0.9 - - + -
10C ARG 3.3 17.0 - - - +
11C VAL* 4.1 11.0 - - + -
36C LEU* 1.3 75.8 - - - +
38C GLU* 1.3 69.3 + - - +
39C ILE* 4.0 19.5 - - + -
47C GLY 3.7 0.9 - - - +
48C ILE* 3.6 2.8 - - - -
49C GLY 2.9 39.1 + - - +
50C GLU* 4.0 2.2 - - - +
64C LEU* 4.0 20.9 - - + -
68C ALA* 3.7 28.7 - - + -
108C GLY* 3.4 35.7 - - - +
109C ILE* 4.1 4.3 - - + +
112C ALA* 3.7 2.1 - - + +
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Residues in contact with GLU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ASN 4.0 0.2 - - - +
9C VAL* 3.2 5.7 - - - -
10C ARG* 2.7 88.3 + - + +
12C ARG* 2.9 43.3 + - - -
36C LEU* 5.2 4.6 - - + +
37C ILE* 1.3 78.1 - - - +
39C ILE* 1.3 63.4 + - - +
40C GLU 4.0 0.4 - - - -
46C VAL* 4.0 1.6 - - + -
47C GLY 3.3 4.5 - - - -
48C ILE* 3.5 29.1 - - + +
360C LEU* 5.2 3.5 - - - +
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.7 37.7 - - + -
8C ASN 3.7 2.0 - - - +
9C VAL* 4.5 5.4 - - + +
37C ILE* 4.0 15.7 - - + -
38C GLU* 1.3 79.0 - - - +
40C GLU* 1.3 58.9 + - - +
46C VAL* 3.4 2.2 - - - -
47C GLY* 2.7 39.1 + - - +
71C LEU* 3.7 24.9 - - + -
109C ILE* 3.8 13.2 - - + +
112C ALA* 3.6 26.7 - - + +
113C MSE 3.8 10.1 - - + +
116C LEU* 3.8 18.5 - - + +
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.5 6.6 - - - +
7C SER* 2.7 32.0 + - - +
8C ASN* 2.8 35.7 + - + +
10C ARG* 3.1 33.6 + - - +
38C GLU 4.0 1.0 - - - -
39C ILE* 1.3 73.4 - - - +
41C ALA* 1.3 67.5 + - - +
44C GLY* 4.2 11.6 + - - +
45C THR 3.4 10.1 - - - +
46C VAL* 3.6 16.4 - - + +
116C LEU* 5.0 0.4 - - - -
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C VAL* 3.6 19.7 - - + -
5C LYS 3.4 7.2 - - - +
6C ILE* 4.2 2.2 - - - +
7C SER* 3.5 5.4 + - - -
39C ILE 4.1 0.8 + - - -
40C GLU* 1.3 81.7 - - - +
42C ASP* 1.3 59.0 + - - +
43C ASP* 2.9 26.4 + - - +
44C GLY* 3.0 12.3 + - - -
45C THR* 2.8 11.6 + - - +
76C PRO* 5.0 1.8 - - + -
116C LEU* 4.2 20.1 - - + +
120C 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