Contacts of the strand formed by residues 27 - 41 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B HIS* 3.6 6.3 - - - +
24B TRP* 3.1 30.9 + - - +
25B SER 3.6 1.8 + - - -
26B TYR* 1.3 76.9 - - - +
28B ILE* 1.3 68.9 + - - +
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PRO* 3.2 36.6 - - + -
22B TYR 3.5 3.1 - - - +
23B HIS* 4.0 27.1 - - + +
24B TRP* 3.6 9.3 + - - +
26B TYR 3.9 1.3 + - - +
27B GLY* 1.3 81.9 - - - +
29B ARG* 1.3 63.2 + - - +
30B GLU* 3.8 19.3 + - + +
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.5 6.6 - - + +
22B TYR* 2.8 63.1 + - + +
24B TRP* 3.5 31.5 - - + +
28B ILE* 1.3 72.9 - - - +
30B GLU* 1.3 58.8 + - - +
31B SER 3.0 28.3 - - - +
32B PHE* 4.3 20.9 - - - -
301B PHE* 3.2 36.0 - - - -
93F GLY 2.9 23.0 + - - -
94F HIS* 3.1 33.1 + - - -
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO* 3.7 3.6 - - - +
18B LEU* 3.0 25.8 + - - +
20B GLN 5.5 0.7 - - - -
21B PRO* 4.5 18.7 - - + +
28B ILE* 3.8 23.1 + - + +
29B ARG* 1.3 72.7 - - - +
31B SER* 1.3 63.0 + - - +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.8 18.7 - - - +
16B LEU 3.0 20.6 - - - -
17B PRO* 3.4 10.5 - - - -
18B LEU* 3.6 9.3 - - - +
29B ARG* 3.0 23.8 + - - +
30B GLU* 1.3 81.1 + - - +
32B PHE* 1.3 64.5 + - - +
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Residues in contact with PHE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.6 3.4 - - - +
16B LEU* 2.9 36.5 + - + +
18B LEU* 3.3 38.6 - - + -
22B TYR* 6.3 1.8 - + - -
29B ARG* 4.3 13.0 - - - -
31B SER* 1.3 77.3 - - - +
33B ALA* 1.3 64.2 + - - +
34B VAL* 5.3 1.3 - - + -
301B PHE* 3.5 51.6 - + + +
302B THR* 3.2 29.4 - - - -
303B THR* 5.2 3.1 - - + -
327B MSE 4.9 3.1 - - + -
330B LEU* 4.8 12.8 - - + -
331B VAL* 3.7 18.2 - - + -
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU 3.0 20.0 - - - +
15B VAL* 4.2 5.4 - - + -
16B LEU* 5.9 0.2 - - - -
32B PHE* 1.3 78.9 - - - +
34B VAL* 1.3 69.5 + - - +
51B CYS 4.6 0.2 - - - +
52B THR* 4.7 1.9 - - - -
53B VAL* 3.9 25.7 + - + +
57B GLN* 3.1 25.4 - - - +
301B PHE 4.2 6.9 - - - +
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG 3.8 0.9 - - - +
14B LEU* 2.8 53.1 + - + -
16B LEU* 4.5 4.5 - - + -
32B PHE* 5.3 2.5 - - + -
33B ALA* 1.3 81.9 - - - +
35B ASN* 1.3 64.3 + - - +
36B LEU* 4.4 3.6 - - + -
50B GLU* 4.0 15.0 - - + +
51B CYS 3.4 9.4 - - - +
53B VAL* 3.9 1.1 - - - -
57B GLN* 3.2 2.5 + - - -
301B PHE 4.3 0.4 - - - +
302B THR* 3.8 39.7 - - + -
303B THR* 3.9 24.7 - - + -
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Residues in contact with ASN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.4 3.8 - - + -
12B ARG 3.8 2.9 - - - -
13B PRO* 3.4 10.0 - - - +
34B VAL* 1.3 72.1 - - - +
36B LEU* 1.3 64.0 + - - +
37B ILE 3.7 0.2 + - - -
50B GLU* 3.4 2.2 - - - -
51B CYS* 3.0 37.0 + - + +
52B THR 4.8 1.6 + - - -
53B VAL* 3.5 9.4 - - - +
57B GLN* 3.0 34.6 + - - +
60B THR* 3.3 12.7 + - - -
61B ALA* 3.2 37.9 - - - +
64B LEU* 3.8 20.9 - - + +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG 4.3 0.2 - - - -
11B VAL* 3.2 8.7 - - - +
12B ARG* 2.9 46.9 + - + +
14B LEU* 3.5 36.1 - - + -
34B VAL* 4.4 2.7 - - + -
35B ASN* 1.3 74.4 - - - +
37B ILE* 1.3 61.8 + - - +
38B GLU* 4.2 11.7 - - + +
48B ILE* 5.2 1.8 - - + -
49B GLY 3.5 4.0 - - - +
50B GLU* 3.7 19.3 - - + +
305B ILE* 3.4 28.5 - - + -
335B ILE* 4.2 2.9 - - + -
360B LEU* 4.5 17.5 - - + -
365B VAL* 3.9 18.4 - - + -
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.5 3.1 - - + -
10B ARG 3.5 10.3 - - - +
11B VAL* 4.2 11.4 - - + -
36B LEU* 1.3 74.8 - - - +
38B GLU* 1.3 71.7 + - - +
39B ILE* 4.1 19.3 - - + -
47B GLY 3.8 0.9 - - - +
48B ILE* 3.6 2.4 - - - -
49B GLY 3.0 40.6 + - - +
50B GLU* 3.9 3.4 - - - +
64B LEU* 3.9 20.4 - - + -
68B ALA* 3.6 29.8 - - + -
108B GLY* 3.4 33.7 - - - +
109B ILE* 4.2 4.9 - - + +
112B ALA* 3.8 1.9 - - + +
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.2 6.4 - - - +
10B ARG* 2.9 75.1 + - + +
12B ARG* 2.8 41.3 + - + -
36B LEU* 4.6 9.6 - - + +
37B ILE* 1.3 79.8 - - - +
39B ILE* 1.3 62.6 + - - +
40B GLU 4.0 0.8 + - - -
46B VAL* 4.0 11.3 - - + +
47B GLY 3.4 4.7 - - - +
48B ILE* 4.6 21.7 - - + +
360B LEU* 4.8 3.8 - - - +
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 3.5 44.4 - - + -
8B ASN 3.7 2.7 - - - -
9B VAL* 4.2 9.6 - - + -
37B ILE* 4.1 14.8 - - + -
38B GLU* 1.3 76.3 - - - +
40B GLU* 1.3 59.0 + - - +
46B VAL* 3.5 2.7 - - - -
47B GLY* 2.8 35.9 + - - +
71B LEU* 3.8 15.5 - - + -
109B ILE* 3.9 4.9 - - + +
112B ALA* 3.6 25.6 - - + -
113B MSE 3.7 27.1 - - + +
116B LEU* 3.8 15.3 - - + +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 3.5 4.5 - - - -
7B SER* 2.7 39.5 + - - +
8B ASN* 2.8 25.6 + - - +
10B ARG* 2.9 33.2 + - - +
38B GLU 4.0 1.4 + - - -
39B ILE* 1.3 74.7 - - - +
41B ALA* 1.3 65.1 + - - +
44B GLY* 4.0 16.5 - - - +
45B THR 3.4 4.5 - - - +
46B VAL* 3.6 25.1 - - + +
116B LEU* 4.9 0.4 - - - -
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 3.6 20.0 - - + -
5B LYS 3.4 8.3 - - - +
6B ILE* 4.1 2.5 - - - +
7B SER* 3.5 3.2 + - - -
39B ILE 4.1 0.8 + - - -
40B GLU* 1.3 84.2 - - - +
42B ASP* 1.3 57.5 + - - +
43B ASP* 3.0 21.1 - - - +
44B GLY 2.9 18.4 + - - -
45B THR* 2.8 12.7 + - - +
76B PRO* 5.0 1.6 - - + -
116B LEU* 4.1 19.3 - - + +
120B LEU* 4.9 0.7 - - + -
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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