Contacts of the strand formed by residues 28 - 41 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PRO* 3.2 33.4 - - + -
22A TYR 3.3 11.0 - - - +
23A HIS* 3.7 30.1 - - + +
24A TRP* 4.0 2.5 + - - -
26A TYR 3.8 1.6 + - - +
27A GLY* 1.3 86.2 - - - +
29A ARG* 1.3 70.7 + - - +
30A GLU* 4.2 10.0 + - + +
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.8 2.1 - - - +
22A TYR* 2.7 52.0 + - + +
24A TRP* 3.2 43.7 - - + +
28A ILE* 1.3 75.7 - - - +
30A GLU* 1.3 61.1 + - - +
31A SER 3.3 19.3 + - - +
32A PHE* 3.1 42.0 - - - +
33A ALA* 4.9 4.2 - - - +
301A PHE* 5.3 8.8 - - - +
93G GLY 5.3 3.8 + - - -
94G HIS* 3.9 31.2 + - - -
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 3.5 5.2 - - - +
18A LEU* 3.0 28.5 + - - +
20A GLN 5.7 0.4 - - - -
21A PRO* 4.0 23.0 - - + +
28A ILE* 4.2 13.2 + - + +
29A ARG* 1.3 80.8 - - - +
31A SER* 1.3 65.0 + - - +
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.8 19.1 - - - +
16A LEU 3.0 24.5 - - - -
17A PRO* 3.6 4.3 - - - -
18A LEU* 3.6 9.0 - - - +
29A ARG* 3.3 21.3 + - - +
30A GLU* 1.3 83.2 + - - +
32A PHE* 1.3 64.9 + - - +
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Residues in contact with PHE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.7 1.8 - - - +
16A LEU* 2.9 38.4 + - + +
18A LEU* 3.4 34.7 - - + +
22A TYR* 4.8 7.4 - + - -
29A ARG* 3.1 30.7 - - - +
31A SER* 1.3 75.6 - - - +
33A ALA* 1.3 63.8 + - - +
34A VAL* 5.4 2.0 - - + -
300A SER 5.3 0.2 - - - -
301A PHE* 3.4 68.6 - + + +
302A THR* 4.1 5.4 - - - +
303A THR* 6.5 0.4 - - + -
327A MSE 4.8 2.2 - - - -
330A LEU* 3.9 28.3 - - + -
331A VAL* 4.0 16.2 - - + -
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU 3.3 8.7 - - - +
15A VAL* 4.7 7.2 - - + -
16A LEU* 6.0 0.4 - - - -
29A ARG* 4.9 5.0 - - - +
32A PHE* 1.3 76.3 - - - +
34A VAL* 1.3 67.9 + - - +
52A THR* 4.6 1.9 - - - +
53A VAL* 3.4 32.8 + - + +
57A GLN* 3.5 24.7 - - + +
301A PHE 4.7 2.8 + - - +
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 2.9 49.5 + - + +
16A LEU* 4.9 3.6 - - + -
32A PHE* 5.4 1.8 - - + -
33A ALA* 1.3 81.0 - - - +
35A ASN* 1.3 64.6 + - - +
36A LEU* 4.3 4.5 - - + -
50A GLU* 3.5 23.1 - - + +
51A CYS 3.4 10.8 - - - +
52A THR* 5.1 0.7 - - - -
53A VAL* 3.8 0.9 - - - -
57A GLN* 3.1 2.9 + - - -
301A PHE 4.1 3.8 - - - +
302A THR* 3.8 39.9 - - + -
303A THR* 3.9 14.6 - - + -
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Residues in contact with ASN 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.4 6.1 - - + -
12A ARG 3.9 3.1 - - - -
13A PRO* 3.3 11.7 - - - +
34A VAL* 1.3 71.3 - - - +
36A LEU* 1.3 65.0 + - - +
37A ILE 3.8 0.2 + - - -
50A GLU* 3.4 2.0 - - - -
51A CYS* 3.0 34.4 + - + +
52A THR 4.8 1.6 + - - -
53A VAL* 3.3 19.8 - - + +
57A GLN* 3.0 34.3 + - - +
60A THR* 3.4 6.5 + - - -
61A ALA* 3.3 31.6 - - - +
64A LEU* 3.9 20.7 - - + +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG 4.4 0.2 - - - -
11A VAL* 3.2 9.5 - - - +
12A ARG* 2.9 49.8 + - + +
14A LEU* 3.6 34.3 - - + -
34A VAL* 4.3 2.2 - - + -
35A ASN* 1.3 74.6 - - - +
37A ILE* 1.3 60.4 - - - +
38A GLU* 4.8 5.2 - - - +
48A ILE* 5.2 3.4 - - + -
49A GLY 3.5 3.4 - - - +
50A GLU* 3.7 20.9 - - + +
305A ILE* 3.4 31.0 - - + -
335A ILE* 4.1 7.0 - - + -
360A LEU* 4.8 8.1 - - + -
365A VAL* 3.8 22.7 - - + -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.6 0.4 - - + -
10A ARG 3.4 11.9 - - - +
11A VAL* 4.0 11.0 - - + -
36A LEU* 1.3 74.3 - - - +
38A GLU* 1.3 71.9 + - - +
39A ILE* 4.2 18.8 - - + -
47A GLY 3.8 0.5 - - - +
48A ILE* 3.5 2.4 - - - -
49A GLY 2.9 43.0 + - - +
50A GLU* 3.8 2.7 - - - +
64A LEU* 4.0 19.1 - - + -
68A ALA* 3.6 31.0 - - + -
108A GLY* 3.4 33.9 - - - +
109A ILE* 4.2 5.6 - - + +
112A ALA* 3.9 1.5 - - + +
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.1 7.8 - - - +
10A ARG* 2.7 78.7 + - + +
12A ARG* 2.8 46.1 + - - -
36A LEU* 4.8 6.7 - - + +
37A ILE* 1.3 78.3 - - - +
39A ILE* 1.3 62.0 + - - +
40A GLU 4.0 0.8 + - - -
46A VAL* 4.0 8.0 - - + +
47A GLY 3.4 3.4 - - - -
48A ILE* 3.9 30.3 - - + +
360A LEU* 5.3 2.3 - - - +
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.5 43.5 - - + -
8A ASN 3.6 2.0 - - - -
9A VAL* 4.0 9.4 - - + -
37A ILE* 4.2 11.7 - - + -
38A GLU* 1.3 77.5 - - - +
40A GLU* 1.3 59.0 + - - +
46A VAL* 3.4 2.2 - - - -
47A GLY* 2.8 39.3 + - - +
71A LEU* 3.7 15.7 - - + -
109A ILE* 3.9 6.1 - - + +
112A ALA* 3.5 26.0 - - + -
113A MSE 3.6 26.5 - - + +
116A LEU* 3.8 14.8 - - + +
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.6 5.0 - - - +
7A SER* 2.8 32.0 + - - +
8A ASN* 2.8 37.4 + - + +
10A ARG* 2.8 41.0 + - - +
38A GLU 4.0 1.2 - - - -
39A ILE* 1.3 72.9 - - - +
41A ALA* 1.3 65.6 + - - +
44A GLY* 4.1 12.6 - - - +
45A THR 3.5 3.8 - - - +
46A VAL* 3.6 20.5 - - + +
116A LEU* 5.0 0.7 - - - -
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 3.5 19.1 - - + -
5A LYS 3.4 8.1 - - - +
6A ILE* 4.2 2.2 - - + +
7A SER* 3.5 2.8 + - - -
39A ILE 4.0 1.2 + - - -
40A GLU* 1.3 84.3 - - - +
42A ASP* 1.3 58.3 + - - +
43A ASP* 2.9 27.4 + - - +
44A GLY* 2.9 13.0 + - - -
45A THR 2.8 12.8 + - - +
76A PRO* 5.6 0.4 - - + -
116A LEU* 4.1 20.2 - - + +
120A LEU* 4.7 1.8 - - + -
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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