Contacts of the strand formed by residues 27 - 41 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D HIS* 3.9 2.3 + - - -
24D TRP* 2.9 30.1 + - - +
25D SER 3.6 1.4 + - - -
26D TYR* 1.3 78.4 - - - +
28D ILE* 1.3 69.9 + - - +
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Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PRO* 3.2 36.1 - - + -
22D TYR 3.5 10.5 - - - +
23D HIS* 3.5 30.1 - - + +
24D TRP* 3.7 7.2 + - - +
26D TYR 4.2 0.2 + - - -
27D GLY* 1.3 80.8 - - - +
29D ARG* 1.3 65.6 + - - +
30D GLU* 4.2 8.5 + - + +
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Residues in contact with ARG 29 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.7 2.1 - - - +
21D PRO* 3.5 2.8 - - - +
22D TYR* 2.7 59.1 + - + +
24D TRP* 3.7 36.2 - - - +
28D ILE* 1.3 73.7 - - - +
30D GLU* 1.3 61.3 + - - +
31D SER 3.3 25.6 - - - +
32D PHE* 3.7 27.3 - - - +
301D PHE* 3.9 17.3 - - - -
93E GLY 3.4 23.2 + - - -
94E HIS* 3.3 32.8 + - - -
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Residues in contact with GLU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PRO* 3.6 4.3 - - - +
18D LEU* 3.0 29.4 + - - +
20D GLN 5.1 0.4 - - - -
21D PRO* 4.1 27.4 - - + +
28D ILE* 4.2 8.2 + - + +
29D ARG* 1.3 79.0 - - - +
31D SER* 1.3 62.4 + - - +
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Residues in contact with SER 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.6 22.2 - - - +
16D LEU 3.0 24.7 - - - -
17D PRO* 3.8 4.3 - - - -
18D LEU* 3.4 8.1 - - - +
29D ARG* 3.3 21.2 - - - +
30D GLU* 1.3 82.3 - - - +
32D PHE* 1.3 62.6 + - - +
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Residues in contact with PHE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.6 1.7 - - - -
16D LEU* 2.8 40.5 + - + +
18D LEU* 3.5 36.9 - - + +
22D TYR* 4.8 6.1 - + - -
29D ARG* 3.7 16.2 - - - +
31D SER* 1.3 83.1 - - - +
33D ALA* 1.3 62.1 + - - +
34D VAL* 5.3 2.0 - - + -
300D SER 5.1 0.2 - - - -
301D PHE* 3.5 66.2 - + + +
302D THR* 3.7 16.2 - - - +
303D THR* 6.0 0.4 - - + -
327D MSE 4.5 4.9 - - + -
330D LEU* 4.0 28.5 - - + -
331D VAL* 4.1 8.7 - - + -
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Residues in contact with ALA 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU 3.3 8.5 - - - +
15D VAL* 4.5 6.7 - - + -
16D LEU* 6.1 0.2 - - - -
32D PHE* 1.3 75.9 - - - +
34D VAL* 1.3 67.0 + - - +
51D CYS 4.6 0.2 - - - +
52D THR* 4.7 1.9 - - - +
53D VAL* 3.7 31.3 + - + +
57D GLN* 3.4 24.2 - - - +
301D PHE 4.6 4.6 + - - +
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Residues in contact with VAL 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 2.9 42.1 + - + +
16D LEU* 4.7 3.4 - - + -
32D PHE* 5.3 1.8 - - + -
33D ALA* 1.3 80.5 - - - +
35D ASN* 1.3 64.5 + - - +
36D LEU* 3.7 25.6 + - + -
50D GLU* 3.7 16.6 - - + +
51D CYS 3.4 9.2 - - - +
52D THR* 5.4 0.2 - - - -
53D VAL* 3.8 0.9 - - - -
57D GLN* 3.1 3.6 + - - -
301D PHE 4.4 1.8 - - - +
302D THR* 3.9 39.3 - - + -
303D THR* 4.1 13.2 - - + -
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Residues in contact with ASN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 4.5 5.4 - - + -
12D ARG 4.0 3.1 - - - -
13D PRO* 3.3 11.0 - - - +
34D VAL* 1.3 70.7 - - - +
36D LEU* 1.3 66.1 + - - +
37D ILE 3.7 0.3 + - - -
50D GLU* 3.4 1.3 - - - -
51D CYS* 3.0 33.7 + - + +
52D THR 4.6 1.8 + - - -
53D VAL* 3.2 13.2 - - - +
57D GLN* 3.0 35.1 + - - +
60D THR* 3.1 26.9 + - - -
61D ALA* 3.4 16.7 - - - +
64D LEU* 3.8 21.5 - - + +
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 3.2 9.7 - - - +
12D ARG* 2.9 47.0 + - + +
14D LEU* 3.5 33.7 - - + -
34D VAL* 3.7 15.5 - - + -
35D ASN* 1.3 74.8 - - - +
37D ILE* 1.3 60.0 + - - +
38D GLU* 4.2 11.9 - - - +
48D ILE* 4.6 4.9 - - + -
49D GLY 3.5 7.2 - - - +
50D GLU* 4.0 5.8 - - + +
305D ILE* 3.9 23.6 - - + -
335D ILE* 4.2 2.0 - - + -
360D LEU* 4.3 20.9 - - + -
365D VAL* 4.1 17.9 - - + -
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Residues in contact with ILE 37 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.3 4.0 - - + -
10D ARG 3.4 9.4 - - - +
11D VAL* 4.4 7.9 - - + +
36D LEU* 1.3 74.4 - - - +
38D GLU* 1.3 73.2 + - - +
39D ILE* 4.0 15.5 - - + -
47D GLY 3.8 1.2 - - - +
48D ILE* 3.5 4.2 - - - +
49D GLY* 2.9 46.1 + - - +
50D GLU* 3.9 2.9 - - - +
64D LEU* 4.0 15.5 - - + -
68D ALA* 3.7 28.7 - - + -
108D GLY* 3.5 27.6 - - - +
109D ILE* 3.8 16.2 - - + +
112D ALA* 3.9 1.3 - - + +
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Residues in contact with GLU 38 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D ASN 4.1 0.2 - - - +
9D VAL* 3.2 7.4 - - - +
10D ARG* 2.8 77.5 + - + +
12D ARG* 2.8 47.3 + - - -
36D LEU* 4.6 7.9 - - + +
37D ILE* 1.3 75.8 - - - +
39D ILE* 1.3 62.8 + - - +
40D GLU 4.0 0.6 + - - -
46D VAL* 4.2 4.4 - - + +
47D GLY 3.5 2.9 - - - -
48D ILE* 3.8 32.1 - - + +
360D LEU* 5.5 0.5 - - - +
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Residues in contact with ILE 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.7 33.0 - - + -
8D ASN 3.8 2.7 - - - -
9D VAL* 4.2 8.7 - - + -
37D ILE* 4.0 15.5 - - + -
38D GLU* 1.3 76.5 - - - +
40D GLU* 1.3 61.5 + - - +
46D VAL* 3.5 2.2 - - - -
47D GLY 2.8 39.5 + - - +
71D LEU* 3.7 23.8 - - + -
109D ILE* 3.9 5.2 - - + +
112D ALA* 3.5 26.7 - - + +
113D MSE 3.7 16.2 - - + +
116D LEU* 3.8 23.5 - - + +
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Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.5 6.2 - - - +
7D SER* 2.8 35.0 + - - +
8D ASN* 2.9 40.5 + - - +
10D ARG* 3.1 28.4 + - - +
38D GLU 4.0 0.8 - - - -
39D ILE* 1.3 74.3 - - - +
41D ALA* 1.3 65.7 + - - +
44D GLY* 4.3 11.0 - - - +
45D THR 3.5 4.0 - - - +
46D VAL* 3.7 21.2 - - + +
116D LEU* 5.0 0.2 - - - -
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.7 20.2 - - + -
5D LYS 3.3 8.5 - - - +
6D ILE* 4.2 1.6 - - - +
7D SER* 3.4 6.6 + - - -
39D ILE 4.1 0.8 + - - -
40D GLU* 1.3 80.6 - - - +
42D ASP* 1.3 58.3 + - - +
43D ASP* 2.8 27.2 + - - +
44D GLY* 2.8 13.2 + - - -
45D THR* 2.8 13.4 + - - +
76D PRO* 5.0 0.7 - - + -
116D LEU* 4.2 18.8 - - + +
120D LEU* 4.8 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