Contacts of the strand formed by residues 6 - 24 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G LYS* 1.3 73.6 - - - +
7G SER* 1.3 59.9 + - - +
8G ASN 4.0 9.6 - - - +
9G VAL* 4.3 4.7 - - + -
39G ILE* 3.6 25.1 - - + -
40G GLU 3.6 7.0 - - - +
41G ALA* 4.2 1.1 - - - +
71G LEU* 3.6 27.4 - - + +
72G VAL* 3.5 10.3 - - - +
73G GLY* 2.7 28.9 + - - -
74G HIS* 2.9 23.5 + - + +
75G SER 4.4 1.3 - - - +
76G PRO* 4.1 16.6 - - + -
82G LEU* 5.3 0.2 - - + -
113G MSE 3.6 39.3 - - + -
116G LEU* 4.5 2.7 - - + -
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Residues in contact with SER 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS 3.4 1.8 + - - -
6G ILE* 1.3 73.8 - - - +
8G ASN* 1.3 84.0 + - - +
40G GLU* 2.7 21.8 + - - +
41G ALA 3.4 12.6 + - - -
42G ASP* 3.8 21.3 - - - -
72G VAL* 3.6 17.4 - - - +
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Residues in contact with ASN 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 3.8 2.0 - - - +
7G SER* 1.3 108.1 + - - +
9G VAL* 1.3 72.4 + - - +
10G ARG* 4.1 9.9 - - - +
38G GLU 3.9 0.6 - - - +
39G ILE* 3.8 0.2 - - - -
40G GLU* 3.0 49.1 + - - +
72G VAL* 4.4 4.5 - - - -
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Residues in contact with VAL 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 4.3 11.7 - - + -
8G ASN* 1.3 83.6 - - - +
10G ARG* 1.3 64.3 + - - +
37G ILE* 4.6 1.3 - - + -
38G GLU 3.3 8.7 - - - +
39G ILE* 4.6 8.7 - - + -
65G TYR* 3.6 17.6 + - + +
68G ALA* 3.5 31.4 - - + +
69G LYS* 3.8 38.8 - - + +
71G LEU* 4.6 2.9 - - + -
72G VAL* 3.9 14.8 - - + +
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Residues in contact with ARG 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ASN* 4.1 11.7 - - - +
9G VAL* 1.3 78.1 - - - +
11G VAL* 1.3 65.0 + - - +
12G ARG* 5.0 9.2 - - + +
36G LEU 3.7 0.3 - - - +
37G ILE* 3.5 4.0 - - - +
38G GLU* 2.9 79.4 + - + +
40G GLU* 2.6 38.2 + - - +
46G VAL* 4.1 16.6 - - - +
65G TYR* 4.5 5.6 - - - -
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Residues in contact with VAL 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ARG* 1.3 79.6 - - - +
12G ARG* 1.3 66.9 + - - +
13G PRO* 3.6 14.9 - - + +
35G ASN* 4.3 11.9 - - + -
36G LEU 3.1 9.4 - - - +
37G ILE* 4.2 7.9 - - + -
61G ALA* 4.1 17.0 - - + +
64G LEU* 3.7 29.2 - - + -
65G TYR* 3.7 41.8 - - + +
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Residues in contact with ARG 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ARG* 5.0 8.5 - - + +
11G VAL* 1.3 81.2 - - - +
13G PRO* 1.3 67.1 - - - +
14G LEU* 3.4 13.0 - - + +
35G ASN* 4.5 0.2 - - - -
36G LEU* 2.9 43.1 + - + +
38G GLU* 3.2 39.9 + - - +
360G LEU* 5.2 3.2 - - - +
362G GLU* 3.7 23.0 + - - -
365G VAL* 3.6 23.2 - - - +
366G ALA* 4.9 2.4 - - - +
369G GLU* 2.8 44.7 + - - +
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Residues in contact with PRO 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G VAL* 3.6 12.1 - - + +
12G ARG* 1.3 83.2 - - - +
14G LEU* 1.3 66.2 + - - +
34G VAL 3.7 0.2 - - - +
35G ASN* 3.3 24.5 - - - +
57G GLN* 3.7 7.9 - - + +
61G ALA* 3.9 19.7 - - + -
369G GLU* 3.6 10.5 - - + +
372G TYR* 3.6 47.4 - - + +
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Residues in contact with LEU 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ARG* 3.4 17.5 - - + +
13G PRO* 1.3 83.4 - - - +
15G VAL* 1.3 65.1 + - - +
16G LEU* 4.1 14.6 - - + -
33G ALA* 3.3 2.8 - - - -
34G VAL* 2.9 34.6 + - + +
36G LEU* 3.6 28.3 - - + -
57G GLN* 3.0 16.4 + - - +
335G ILE* 4.0 20.6 - - + -
365G VAL* 3.6 19.5 - - + +
368G GLY* 3.6 10.1 - - - -
369G GLU* 3.3 26.9 - - + +
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Residues in contact with VAL 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 1.3 80.0 - - - +
16G LEU* 1.3 57.4 + - - +
31G SER* 3.7 21.5 - - - +
32G PHE 3.5 5.8 - - - +
33G ALA* 4.7 3.8 - - + -
57G GLN* 3.8 13.2 - - - +
368G GLY* 3.1 9.1 + - - -
371G ARG* 2.7 55.0 + - + +
372G TYR* 3.5 28.3 - - + +
375G SER* 4.3 6.7 - - - +
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Residues in contact with LEU 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 4.4 10.8 - - + -
15G VAL* 1.3 81.9 - - - +
17G PRO* 1.3 67.3 - - + +
18G LEU* 4.7 1.4 - - - +
31G SER* 3.5 2.5 - - - -
32G PHE* 2.8 46.7 + - + +
34G VAL* 4.6 9.2 - - + -
303G THR* 3.4 33.0 - - + -
331G VAL* 4.2 21.8 - - + -
333G GLU 5.1 4.9 - - - +
335G ILE* 4.2 28.9 - - + +
364G LEU* 4.5 2.5 - - + +
368G GLY* 3.9 12.3 - - - -
371G ARG* 3.8 14.1 - - - +
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Residues in contact with PRO 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G VAL* 3.8 0.7 - - + +
16G LEU* 1.3 87.0 - - + +
18G LEU* 1.3 64.0 + - - +
30G GLU 3.6 4.7 - - - +
31G SER* 3.5 12.1 - - - -
331G VAL* 3.8 6.4 - - - +
332G GLN* 3.0 29.7 + - + +
333G GLU 4.5 0.3 + - - -
371G ARG* 3.2 44.4 - - - +
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Residues in contact with LEU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LEU 4.7 0.4 - - - +
17G PRO* 1.3 79.0 - - - +
19G LYS* 1.3 67.4 + - - +
20G GLN* 3.6 14.8 - - - +
22G TYR* 3.7 21.5 - - + -
29G ARG* 3.5 23.6 - - + +
30G GLU 3.1 13.5 + - - +
31G SER* 3.7 15.0 - - - +
32G PHE* 3.5 52.5 - - + +
330G LEU* 3.2 22.2 - - + +
331G VAL* 4.2 3.6 - - + +
332G GLN* 3.8 8.2 - - - +
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Residues in contact with LYS 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G LEU* 1.3 72.9 - - - +
20G GLN* 1.3 66.6 + - + +
328G TRP* 5.9 3.9 - - - -
329G GLN* 3.1 34.1 + - - +
330G LEU* 3.0 13.1 + - - +
331G VAL 3.4 14.6 - - - +
332G GLN* 3.3 39.5 - - - +
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Residues in contact with GLN 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G LEU* 3.6 18.6 - - - +
19G LYS* 1.3 84.4 - - + +
21G PRO* 1.3 85.9 - - + +
22G TYR* 3.4 2.1 + - - -
30G GLU* 5.8 0.7 - - - -
144G GLN* 3.4 38.6 + - - +
330G LEU 4.9 0.2 + - - -
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Residues in contact with PRO 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G GLN* 1.3 97.7 - - + +
22G TYR* 1.3 60.8 + - - +
23G HIS* 3.8 17.1 + - + -
28G ILE* 4.0 32.1 - - + -
29G ARG 3.6 8.3 - - - +
30G GLU* 4.7 15.0 - - + -
144G GLN* 4.1 5.5 + - - -
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Residues in contact with TYR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G LEU* 3.7 15.7 - - + -
20G GLN 3.4 1.3 + - - +
21G PRO* 1.3 71.4 - - - +
23G HIS* 1.3 78.5 + - - +
24G TRP* 3.5 5.3 + - + -
28G ILE* 3.3 3.0 - - - -
29G ARG* 2.7 68.4 + - + +
32G PHE* 4.8 5.2 - + - -
142G PHE* 3.7 35.4 - + - -
144G GLN* 4.1 18.6 - - + +
169G LYS* 6.0 2.3 - - - +
301G PHE* 3.3 35.9 - + - -
330G LEU* 4.3 13.5 - - + -
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Residues in contact with HIS 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G PRO* 3.8 17.9 + - + -
22G TYR* 1.3 82.5 - - - +
24G TRP* 1.3 61.6 + - - +
27G GLY 3.3 7.0 - - - +
28G ILE* 3.6 25.6 - - + +
144G GLN* 5.6 0.6 - - - +
146G GLU* 3.5 51.6 + - + +
169G LYS* 5.8 4.7 - - - +
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Residues in contact with TRP 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLN* 3.2 45.3 - - + -
93A GLY* 3.7 21.8 - - - +
94A HIS* 3.7 18.2 - + - -
22G TYR* 3.9 12.6 - - + -
23G HIS* 1.3 75.4 - - - +
25G SER* 1.3 72.2 + - - +
26G TYR* 2.9 34.8 + + + -
27G GLY* 2.8 53.6 + - - +
28G ILE 3.9 9.4 + - - +
29G ARG* 3.2 44.3 - - + +
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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