Contacts of the strand formed by residues 27 - 41 (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 GLY 27 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23G HIS* 3.3 7.4 - - - +
24G TRP* 2.8 41.6 + - - +
25G SER 3.7 0.4 - - - -
26G TYR* 1.3 80.3 - - - +
28G ILE* 1.3 61.2 + - - +
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Residues in contact with ILE 28 (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* 4.0 25.6 - - + -
22G TYR 3.3 2.7 - - - +
23G HIS* 3.6 37.9 - - + +
24G TRP* 4.0 5.9 + - - +
27G GLY* 1.3 77.0 - - - -
29G ARG* 1.3 60.7 + - - +
30G GLU* 3.9 25.0 + - + +
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Residues in contact with ARG 29 (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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93A GLY 3.4 9.9 + - - -
94A HIS* 3.5 30.2 + - - -
18G LEU* 3.5 7.4 - - - +
21G PRO* 3.6 1.4 - - - +
22G TYR* 2.7 59.3 + - + +
24G TRP* 3.2 46.9 - - + +
28G ILE* 1.3 72.3 - - - +
30G GLU* 1.3 61.0 + - - +
31G SER 3.3 23.3 - - - +
32G PHE* 4.8 11.6 - - + -
301G PHE* 3.4 36.3 - - - -
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Residues in contact with GLU 30 (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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17G PRO* 3.6 5.0 - - - +
18G LEU* 3.1 23.3 + - - +
20G GLN 5.8 0.2 - - - -
21G PRO* 4.7 19.7 - - + -
28G ILE* 3.9 24.3 + - + +
29G ARG* 1.3 76.3 - - - +
31G SER* 1.3 64.3 + - - +
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Residues in contact with SER 31 (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* 3.7 19.7 - - - +
16G LEU 3.1 22.2 - - - -
17G PRO* 3.5 9.6 - - - -
18G LEU* 3.7 6.8 - - - +
29G ARG* 3.3 23.8 + - - +
30G GLU* 1.3 83.9 - - - +
32G PHE* 1.3 66.4 + - - +
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Residues in contact with PHE 32 (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* 3.5 3.6 - - - +
16G LEU* 2.8 41.7 + - + +
18G LEU* 3.5 36.1 - - + +
22G TYR* 4.8 5.6 - + - -
29G ARG* 4.8 11.4 - - - +
31G SER* 1.3 84.0 - - - +
33G ALA* 1.3 64.0 + - - +
34G VAL* 5.5 1.8 - - + -
300G SER 5.2 0.2 - - - -
301G PHE* 3.4 69.1 - + + +
302G THR* 3.9 14.8 - - - +
303G THR* 6.4 0.4 - - + -
327G MSE 4.5 5.2 - - + -
330G LEU* 4.0 26.5 - - + -
331G VAL* 4.3 7.9 - - + -
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Residues in contact with ALA 33 (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 3.3 7.9 - - - +
15G VAL* 4.6 6.5 - - + -
16G LEU* 6.0 0.4 - - - -
32G PHE* 1.3 77.5 - - - +
34G VAL* 1.3 67.5 + - - +
52G THR* 4.6 1.4 - - - -
53G VAL* 3.5 30.2 + - + +
57G GLN* 3.5 26.5 - - + +
301G PHE 4.6 3.8 + - - +
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Residues in contact with VAL 34 (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 4.0 0.3 - - - +
14G LEU* 2.9 52.3 + - + -
16G LEU* 4.6 4.5 - - + -
32G PHE* 5.5 1.8 - - + -
33G ALA* 1.3 79.6 - - - +
35G ASN* 1.3 64.7 + - - +
36G LEU* 4.2 4.5 - - + -
50G GLU* 3.6 27.6 - - + +
51G CYS 3.4 10.8 - - - +
52G THR* 5.2 0.4 - - - -
53G VAL* 3.8 0.9 - - - -
57G GLN* 3.1 4.5 + - - -
301G PHE 4.2 2.9 - - - +
302G THR* 3.9 34.3 - - + -
303G THR* 4.1 14.6 - - + -
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Residues in contact with ASN 35 (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* 4.3 4.7 - - + -
12G ARG 3.9 2.5 - - - -
13G PRO* 3.3 16.2 - - - +
34G VAL* 1.3 71.4 - - - +
36G LEU* 1.3 65.4 + - - +
37G ILE 3.7 0.2 + - - -
50G GLU* 3.3 2.3 - - - -
51G CYS* 2.9 38.7 + - + +
52G THR 4.7 2.0 + - - -
53G VAL* 3.3 13.8 - - - +
57G GLN* 3.2 30.1 + - - +
60G THR* 3.3 27.5 + - - -
61G ALA* 3.6 15.9 - - - +
64G LEU* 3.9 20.5 - - + +
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Residues in contact with LEU 36 (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 4.3 0.4 - - - -
11G VAL* 3.1 10.6 - - - +
12G ARG* 2.9 48.7 + - + +
14G LEU* 3.6 34.5 - - + -
34G VAL* 4.2 2.9 - - + -
35G ASN* 1.3 73.2 - - - +
37G ILE* 1.3 61.3 + - - +
38G GLU* 5.0 6.5 - - + +
48G ILE* 5.1 2.7 - - + -
49G GLY 3.5 4.5 - - - +
50G GLU* 3.7 20.6 - - + +
64G LEU* 4.6 0.2 - - - -
305G ILE* 3.6 27.4 - - + -
335G ILE* 4.2 6.5 - - + -
360G LEU* 4.6 13.7 - - + -
365G VAL* 3.8 19.7 - - + -
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Residues in contact with ILE 37 (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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9G VAL* 4.6 0.7 - - + -
10G ARG 3.5 13.5 - - - +
11G VAL* 4.2 9.4 - - + -
36G LEU* 1.3 73.9 - - - +
38G GLU* 1.3 72.2 + - - +
39G ILE* 4.2 18.2 - - + -
47G GLY 3.8 0.9 - - - +
48G ILE* 3.5 2.9 - - - -
49G GLY* 2.9 47.7 + - - +
50G GLU* 3.8 2.9 - - - +
64G LEU* 4.1 20.6 - - + -
68G ALA* 3.6 28.9 - - + -
108G GLY* 3.5 27.8 - - - +
109G ILE* 4.5 8.3 - - + -
112G ALA* 3.8 1.9 - - + +
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Residues in contact with GLU 38 (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 3.9 0.2 - - - +
9G VAL* 3.3 7.3 - - - +
10G ARG* 2.9 78.6 + - + +
12G ARG* 3.2 37.4 + - + +
36G LEU* 5.0 6.5 - - + +
37G ILE* 1.3 79.5 - - - +
39G ILE* 1.3 62.8 + - - +
40G GLU 4.0 0.8 + - - -
46G VAL* 4.0 8.5 - - + -
47G GLY 3.3 4.3 - - - -
48G ILE* 4.2 28.2 - - + +
360G LEU* 4.8 2.6 - - - +
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Residues in contact with ILE 39 (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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6G ILE* 3.6 34.8 - - + -
8G ASN 3.8 2.5 - - - +
9G VAL* 4.6 4.3 - - + -
37G ILE* 4.2 12.3 - - + -
38G GLU* 1.3 75.9 - - - +
40G GLU* 1.3 59.2 + - - +
45G THR 3.7 1.2 - - - +
46G VAL* 3.3 2.0 - - - -
47G GLY* 2.8 40.6 + - - +
71G LEU* 3.6 19.7 - - + -
109G ILE* 4.0 5.6 - - + +
112G ALA* 3.7 20.6 - - + +
113G MSE 3.5 30.7 - - + +
116G LEU* 3.7 23.1 - - + +
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Residues in contact with GLU 40 (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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6G ILE* 3.6 5.5 - - - +
7G SER* 2.7 40.6 + - - +
8G ASN* 3.0 27.2 + - + +
10G ARG* 2.6 38.1 + - - +
38G GLU 4.0 0.8 - - - -
39G ILE* 1.3 73.2 - - - +
41G ALA* 1.3 65.7 + - - +
44G GLY* 4.1 16.1 - - - +
45G THR 3.3 7.6 - - - +
46G VAL* 3.8 17.6 - - + +
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Residues in contact with ALA 41 (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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4G VAL* 3.6 16.2 - - + -
5G LYS 3.1 14.1 - - - +
6G ILE* 4.2 1.3 - - - +
7G SER* 3.4 2.3 + - - -
39G ILE 4.1 0.6 + - - -
40G GLU* 1.3 85.9 - - - +
42G ASP* 1.3 58.5 + - - +
43G ASP* 3.0 22.0 - - - +
44G GLY* 2.9 16.5 + - - -
45G THR* 2.7 13.7 + - - +
76G PRO* 5.6 1.1 - - + -
116G LEU* 4.3 19.0 - - + +
120G LEU* 4.7 1.6 - - + -
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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