Contacts of the strand formed by residues 6 - 23 (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 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LYS* 1.3 74.0 - - - +
7A SER* 1.3 60.0 + - - +
8A ASN 3.8 9.6 - - - +
9A VAL* 4.2 4.5 - - + -
39A ILE* 3.5 26.5 - - + -
40A GLU 3.6 9.0 - - - +
41A ALA* 4.2 1.1 - - - +
71A LEU* 3.7 20.0 - - + +
72A VAL* 3.5 16.9 - - - +
73A GLY* 2.7 29.3 + - - -
74A HIS* 2.8 24.6 + - + +
76A PRO* 4.2 15.9 - - + -
113A MSE 3.6 39.0 - - + -
116A LEU* 4.5 4.7 - - + -
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Residues in contact with SER 7 (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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5A LYS 3.5 1.4 + - - -
6A ILE* 1.3 74.6 - - - +
8A ASN* 1.3 89.0 + - - +
40A GLU* 2.8 18.0 + - - -
41A ALA 3.5 11.3 + - - -
42A ASP* 3.6 21.7 + - - -
72A VAL* 3.5 16.6 - - - +
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Residues in contact with ASN 8 (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* 3.7 2.4 - - - +
7A SER* 1.3 110.0 + - - +
9A VAL* 1.3 68.9 + - - +
10A ARG* 3.9 18.8 - - - +
39A ILE 3.6 0.2 - - - -
40A GLU* 2.8 51.8 + - + +
72A VAL* 5.1 2.9 - - - -
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.2 7.9 - - + -
8A ASN* 1.3 82.9 - - - +
10A ARG* 1.3 64.5 + - - +
37A ILE* 4.6 1.1 - - + -
38A GLU 3.1 9.0 - - - +
39A ILE* 4.0 23.3 - - + -
65A TYR* 3.9 22.6 + - + +
68A ALA* 3.7 44.2 - - + +
69A LYS* 4.1 11.9 - - + +
71A LEU* 4.7 2.5 - - + -
72A VAL* 5.1 6.5 - - + +
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Residues in contact with ARG 10 (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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8A ASN* 3.9 22.4 - - - +
9A VAL* 1.3 75.7 - - - +
11A VAL* 1.3 66.4 + - - +
12A ARG* 4.1 11.1 + - + +
36A LEU 3.8 0.3 - - - +
37A ILE* 3.4 3.9 - - - +
38A GLU* 2.7 70.8 + - + +
40A GLU* 2.8 35.5 + - - +
46A VAL* 3.7 21.8 - - - +
65A TYR* 4.8 3.8 - - - -
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Residues in contact with VAL 11 (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* 1.3 79.2 - - - +
12A ARG* 1.3 65.4 + - - +
13A PRO* 3.5 10.5 - - + +
35A ASN* 4.4 5.8 - - + -
36A LEU 3.2 8.5 - - - +
37A ILE* 4.0 9.9 - - + -
61A ALA* 3.9 29.8 - - + +
64A LEU* 3.8 22.0 - - + -
65A TYR* 3.6 46.4 - - + +
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Residues in contact with ARG 12 (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* 4.7 12.8 - - + +
11A VAL* 1.3 81.5 - - - +
13A PRO* 1.3 66.5 - - - +
14A LEU* 3.5 11.1 + - + +
35A ASN* 4.5 0.7 - - - -
36A LEU* 2.9 39.9 + - + +
38A GLU* 2.8 37.0 + - - -
360A LEU* 5.9 2.0 - - - +
362A GLU* 2.9 38.8 + - - -
365A VAL* 3.5 19.2 - - - +
366A ALA 4.3 0.2 - - - +
369A GLU* 2.7 50.6 + - + +
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Residues in contact with PRO 13 (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* 3.5 10.5 - - + +
12A ARG* 1.3 84.3 - - - +
14A LEU* 1.3 66.3 + - - +
34A VAL 3.8 0.2 - - - +
35A ASN* 3.3 24.5 - - - +
57A GLN* 3.7 3.8 - - + +
61A ALA* 3.9 19.7 - - + -
369A GLU* 3.5 17.6 - - + +
372A TYR* 3.6 43.4 - - + +
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Residues in contact with LEU 14 (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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12A ARG* 3.5 12.8 - - + +
13A PRO* 1.3 74.4 - - - +
15A VAL* 1.3 64.3 + - - +
16A LEU* 4.2 20.6 - - + -
33A ALA* 3.3 2.8 - - - -
34A VAL* 2.9 34.1 + - + +
36A LEU* 3.6 31.9 - - + -
57A GLN* 3.0 16.7 + - - +
335A ILE* 4.1 14.8 - - + -
365A VAL* 3.3 37.2 - - + +
368A GLY 3.7 4.3 - - - -
369A GLU* 3.3 24.0 - - + +
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Residues in contact with VAL 15 (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* 1.3 80.3 - - - +
16A LEU* 1.3 66.0 + - - +
31A SER* 3.8 21.8 - - - +
32A PHE 3.7 6.1 - - - +
33A ALA* 4.5 4.9 - - + +
57A GLN* 3.8 15.3 - - - +
368A GLY* 3.2 6.7 + - - -
371A ARG* 3.3 48.3 + - + +
372A TYR* 3.5 26.2 - - + +
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Residues in contact with LEU 16 (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* 4.2 15.5 - - + -
15A VAL* 1.3 84.8 - - - +
17A PRO* 1.3 71.8 - - + +
18A LEU* 4.7 1.0 - - - +
31A SER* 3.0 3.5 - - - -
32A PHE* 2.9 46.4 + - + +
33A ALA* 6.0 0.2 - - - -
34A VAL* 4.9 3.6 - - + -
303A THR* 3.5 33.0 - - + -
331A VAL* 5.0 15.2 - - + +
333A GLU 5.1 9.2 - - - +
334A ASP* 5.5 0.9 - - - +
335A ILE* 4.1 25.8 - - + +
364A LEU 4.5 3.6 - - - +
368A GLY* 3.9 17.5 - - - -
371A ARG* 4.5 4.7 - - - +
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Residues in contact with PRO 17 (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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16A LEU* 1.3 87.6 - - + +
18A LEU* 1.3 61.0 - - - +
30A GLU 3.5 12.1 - - - +
31A SER* 3.6 4.0 - - - -
331A VAL* 3.8 6.2 - - - +
332A GLN* 2.9 37.5 + - + +
333A GLU 4.6 0.5 + - - -
371A ARG* 3.3 46.9 - - - +
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Residues in contact with LEU 18 (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* 1.3 76.9 - - - +
19A LYS* 1.3 68.2 + - - +
20A GLN* 3.3 15.5 + - - +
22A TYR* 3.8 23.8 - - + -
29A ARG* 3.8 9.9 - - - +
30A GLU* 3.0 12.8 + - - +
31A SER* 3.6 23.8 - - - +
32A PHE* 3.4 59.5 - - + +
330A LEU* 3.5 19.7 - - + +
331A VAL* 4.3 4.0 - - + -
332A GLN* 3.8 10.0 + - - -
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Residues in contact with LYS 19 (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* 1.3 72.1 - - - +
20A GLN* 1.3 63.4 + - + +
328A TRP* 6.0 3.4 - - - -
329A GLN* 3.1 34.3 + - - +
330A LEU* 3.0 12.3 + - - +
331A VAL 3.5 21.5 - - - +
332A GLN* 3.4 36.3 + - - +
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Residues in contact with GLN 20 (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* 3.4 23.0 - - - +
19A LYS* 1.3 82.4 - - + +
21A PRO* 1.3 83.9 - - + +
22A TYR* 3.5 0.9 + - - +
30A GLU* 5.7 1.3 - - - -
144A GLN* 3.3 43.7 + - - +
330A LEU* 4.7 1.8 + - + +
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Residues in contact with PRO 21 (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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20A GLN* 1.3 102.8 - - + +
22A TYR* 1.3 59.3 + - - +
23A HIS* 3.8 19.6 + - + -
28A ILE* 3.2 23.1 - - + -
29A ARG 3.6 6.7 - - - +
30A GLU* 4.0 22.0 - - + +
144A GLN* 4.6 3.1 + - - -
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Residues in contact with TYR 22 (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 18.4 - - + -
20A GLN 3.5 0.8 + - - +
21A PRO* 1.3 71.4 - - - +
23A HIS* 1.3 78.9 + - - +
24A TRP* 3.9 7.0 + - + -
28A ILE* 3.3 4.8 - - - -
29A ARG* 2.7 63.9 + - + +
32A PHE* 4.8 5.4 - + - -
142A PHE* 4.0 25.4 - + - -
144A GLN* 4.0 27.6 - - - +
169A LYS* 5.5 7.1 - - - +
301A PHE* 3.5 39.7 - + - -
330A LEU* 4.8 10.1 - - + -
93G GLY 6.0 0.7 - - - -
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Residues in contact with HIS 23 (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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21A PRO* 3.8 21.4 + - + -
22A TYR* 1.3 90.1 - - - +
24A TRP* 1.3 65.6 + - - +
27A GLY 4.0 4.3 - - - -
28A ILE* 3.7 29.1 - - + +
144A GLN* 5.9 0.2 + - - -
146A GLU* 3.5 49.2 + - + +
169A LYS* 6.0 1.9 - - - -
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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