Contacts of the strand formed by residues 6 - 24 (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 ILE 6 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F LYS* 1.3 72.8 - - - +
7F SER* 1.3 58.4 + - - +
8F ASN 3.8 11.7 - - - +
9F VAL* 4.2 9.6 - - + -
39F ILE* 3.6 22.7 - - + -
40F GLU 3.3 15.7 - - - +
41F ALA* 4.1 1.1 - - - +
71F LEU* 3.8 21.8 - - + +
72F VAL* 3.7 7.8 - - - +
73F GLY* 2.8 28.6 + - - -
74F HIS* 2.9 24.0 + - + +
76F PRO* 4.2 11.4 - - + -
113F MSE 3.6 39.3 - - + -
116F LEU* 4.5 7.2 - - + -
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Residues in contact with SER 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LYS 3.5 1.6 + - - -
6F ILE* 1.3 74.5 - - - +
8F ASN* 1.3 75.2 + - - +
40F GLU* 2.8 23.6 + - - -
41F ALA 3.3 18.2 + - - -
42F ASP* 3.7 20.4 - - - -
72F VAL* 3.7 16.6 - - - +
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Residues in contact with ASN 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 3.7 2.3 - - - +
7F SER* 1.3 97.4 + - - +
9F VAL* 1.3 71.1 + - - +
10F ARG* 4.3 11.0 - - - +
40F GLU* 2.9 50.9 + - - +
72F VAL* 4.5 4.5 - - - -
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Residues in contact with VAL 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 4.2 15.3 - - + -
8F ASN* 1.3 83.0 + - - +
10F ARG* 1.3 64.7 + - - +
37F ILE* 4.6 0.9 - - + -
38F GLU 3.3 11.0 - - - +
39F ILE* 4.4 11.7 - - + -
65F TYR* 3.7 14.5 + - + -
68F ALA* 3.7 30.1 - - + +
69F LYS* 3.9 37.9 - - + +
71F LEU* 4.5 2.9 - - + -
72F VAL* 4.0 10.7 - - + +
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Residues in contact with ARG 10 (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* 4.3 11.7 - - - +
9F VAL* 1.3 79.1 - - - +
11F VAL* 1.3 66.3 - - - +
12F ARG* 4.8 9.0 - - + +
36F LEU 3.8 0.3 - - - +
37F ILE* 3.5 3.9 - - - +
38F GLU* 2.8 82.2 + - + +
40F GLU* 3.4 38.7 + - - +
46F VAL* 4.2 16.2 - - - +
65F TYR* 4.6 4.7 - - - -
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Residues in contact with VAL 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ARG* 1.3 76.9 - - - +
12F ARG* 1.3 69.3 + - - +
13F PRO* 3.6 9.8 - - + +
35F ASN* 4.3 11.7 - - + -
36F LEU 3.1 9.4 - - - +
37F ILE* 4.1 7.9 - - + -
61F ALA* 4.1 20.9 - - + +
64F LEU* 3.8 25.6 - - + -
65F TYR* 3.7 46.5 - - + +
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Residues in contact with ARG 12 (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* 4.8 8.7 - - + +
11F VAL* 1.3 80.2 - - - +
13F PRO* 1.3 67.7 - - - +
14F LEU* 3.5 12.4 + - + +
35F ASN* 4.5 0.4 - - - -
36F LEU* 3.0 42.3 + - + +
38F GLU* 3.0 44.0 + - + +
360F LEU* 5.9 1.2 - - - +
362F GLU* 2.8 39.8 + - - -
365F VAL* 3.4 19.2 - - - +
366F ALA 4.5 0.2 - - - +
369F GLU* 3.0 45.4 + - - +
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Residues in contact with PRO 13 (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* 3.6 11.0 - - + +
12F ARG* 1.3 84.7 - - - +
14F LEU* 1.3 64.9 + - - +
34F VAL 3.7 0.2 - - - +
35F ASN* 3.4 24.7 - - - +
57F GLN* 3.7 6.7 - - + +
61F ALA* 3.9 19.5 - - + -
369F GLU* 3.6 10.4 - - + +
372F TYR* 3.5 48.2 - - + +
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Residues in contact with LEU 14 (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* 3.5 17.0 - - + +
13F PRO* 1.3 76.2 - - - +
15F VAL* 1.3 64.2 - - - +
16F LEU* 4.1 19.7 - - + -
33F ALA* 3.2 3.5 - - - +
34F VAL* 2.8 42.5 + - + +
36F LEU* 3.7 26.9 - - + -
57F GLN* 2.9 16.5 + - - +
335F ILE* 4.1 15.9 - - + -
365F VAL* 3.6 22.7 - - + +
368F GLY 3.6 4.0 - - - -
369F GLU* 3.4 32.5 - - + +
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Residues in contact with VAL 15 (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* 1.3 80.4 - - - +
16F LEU* 1.3 63.7 + - - +
17F PRO 4.3 0.2 - - - -
31F SER* 3.7 21.5 - - - +
32F PHE 3.6 5.6 - - - +
33F ALA* 4.6 4.0 - - + -
57F GLN* 3.7 15.0 - - - +
368F GLY* 3.2 5.8 + - - -
371F ARG* 3.2 49.4 + - + +
372F TYR* 3.5 24.9 - - + -
375F SER* 4.6 6.3 - - - +
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Residues in contact with LEU 16 (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* 4.1 12.8 - - + -
15F VAL* 1.3 81.7 - - - +
17F PRO* 1.3 67.5 - - + +
18F LEU* 4.5 0.9 - - - +
31F SER* 3.6 3.4 - - - -
32F PHE* 2.8 46.1 + - + +
34F VAL* 4.4 11.9 - - + -
303F THR* 3.5 31.9 - - + -
331F VAL* 4.3 23.1 - - + +
333F GLU 5.5 3.4 - - - +
335F ILE* 4.4 25.4 - - + +
364F LEU 4.6 3.1 - - - +
368F GLY* 3.8 18.8 - - - -
371F ARG* 4.3 4.3 - - - +
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Residues in contact with PRO 17 (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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16F LEU* 1.3 89.8 - - + +
18F LEU* 1.3 62.3 + - - +
30F GLU 3.8 2.2 - - - +
31F SER* 3.6 12.1 - - - -
331F VAL* 3.6 8.2 - - + +
332F GLN* 3.1 32.6 + - + +
371F ARG* 3.3 45.8 - - - +
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Residues in contact with LEU 18 (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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16F LEU 4.5 0.9 - - - +
17F PRO* 1.3 81.4 - - - +
19F LYS* 1.3 67.8 + - - +
20F GLN* 3.3 15.3 + - - +
22F TYR* 4.0 13.7 - - + -
29F ARG 3.4 26.0 - - - +
30F GLU 3.1 10.3 + - - +
31F SER* 3.5 18.4 - - - +
32F PHE* 3.5 58.6 - - + +
330F LEU* 3.5 17.9 - - + +
331F VAL* 4.4 2.5 - - + -
332F GLN* 3.9 10.7 + - - +
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Residues in contact with LYS 19 (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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18F LEU* 1.3 73.8 - - - +
20F GLN* 1.3 67.9 - - + +
328F TRP* 5.9 4.7 - - - -
329F GLN* 3.0 34.8 + - - +
330F LEU* 2.9 13.9 + - - +
331F VAL 3.4 22.2 - - - +
332F GLN* 3.5 32.0 + - - +
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Residues in contact with GLN 20 (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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18F LEU* 3.3 20.5 - - - +
19F LYS* 1.3 84.1 - - + +
21F PRO* 1.3 87.0 - - + +
22F TYR* 3.4 2.3 + - - +
30F GLU* 4.7 2.2 - - - -
144F GLN* 4.7 27.6 + - + +
330F LEU* 4.8 6.1 + - + +
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Residues in contact with PRO 21 (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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20F GLN* 1.3 100.5 - - + +
22F TYR* 1.3 60.5 + - - +
23F HIS* 3.8 21.2 + - + -
28F ILE* 3.3 25.1 - - + -
29F ARG 3.8 1.1 - - - +
30F GLU* 3.6 23.1 - - - +
144F GLN* 5.1 4.2 + - - -
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Residues in contact with TYR 22 (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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18F LEU* 4.0 13.9 - - + -
20F GLN 3.4 1.1 + - - +
21F PRO* 1.3 74.1 - - - +
23F HIS* 1.3 76.1 + - - +
24F TRP* 3.7 4.2 + - + -
28F ILE* 3.2 4.8 - - - -
29F ARG* 2.7 85.5 + - + +
32F PHE* 4.9 5.8 - + - -
142F PHE* 3.7 28.0 - + - -
144F GLN* 3.5 27.6 - - - +
169F LYS* 5.3 6.8 + - - +
301F PHE* 3.4 24.9 - + - -
330F LEU* 4.5 11.7 - - + -
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Residues in contact with HIS 23 (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* 3.8 19.1 + - + -
22F TYR* 1.3 87.3 - - - +
24F TRP* 1.3 61.9 + - - +
27F GLY 3.7 4.5 - - - +
28F ILE* 3.4 32.9 - - + +
144F GLN* 5.5 1.6 - - - +
146F GLU* 3.2 49.5 + - + +
169F LYS* 4.0 16.5 + - - -
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Residues in contact with TRP 24 (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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89B GLN* 3.2 35.2 - - + -
93B GLY* 3.9 23.3 - - - +
94B HIS* 4.0 14.6 - + - -
22F TYR* 4.0 5.2 - - + -
23F HIS* 1.3 75.9 - - - +
25F SER* 1.3 69.0 - - - +
26F TYR* 2.9 47.4 + + + -
27F GLY* 3.1 35.3 + - - +
28F ILE 3.6 14.4 + - - +
29F ARG* 3.2 55.4 - - + +
169F LYS* 5.3 3.8 - - - +
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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