Contacts of the helix formed by residues 8 - 20 (chain A) in PDB entry 4BPU
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 GLU 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PHE* 5.6 0.3 - - - -
5A ASP* 3.4 32.4 + - - +
7A THR* 1.3 76.5 - - - +
9A LEU* 1.3 57.7 + - - +
10A PRO* 3.5 1.1 - - - -
11A GLU* 3.1 13.5 + - + +
12A LEU* 2.9 48.7 + - + +
351A SER* 4.5 10.4 - - - -
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Residues in contact with LEU 9 (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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4A PHE* 3.9 19.7 - - + -
5A ASP 4.1 1.4 + - - -
6A PRO* 3.2 24.4 - - + +
8A GLU* 1.3 77.6 - - - +
10A PRO* 1.3 62.8 - - + +
12A LEU* 3.0 5.6 + - - +
13A LEU* 2.8 45.3 + - + +
76A TYR* 3.7 31.4 - - + -
323A VAL* 4.2 22.4 - - + -
324A HIS 5.1 0.4 - - - +
325A PRO* 3.5 32.3 - - + +
350A ILE* 4.3 7.6 - - + -
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Residues in contact with PRO 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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6A PRO 4.3 2.7 - - - +
7A THR* 3.3 18.8 - - - +
8A GLU 3.6 0.2 - - - -
9A LEU* 1.3 96.0 - - + +
11A GLU* 1.3 66.9 + - + +
13A LEU* 4.0 10.6 - - + +
14A LYS* 3.3 30.7 + - - +
50A LYS* 5.2 13.7 - - + +
74A ASN* 5.3 1.7 + - - +
76A TYR* 3.6 24.2 - - + +
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Residues in contact with GLU 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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7A THR 5.3 1.6 - - - +
8A GLU* 3.1 13.1 + - - +
9A LEU 3.1 0.4 - - - -
10A PRO* 1.3 87.8 - - + +
12A LEU* 1.3 64.9 + - + +
13A LEU 3.3 0.2 - - - -
14A LYS* 3.4 47.1 + - - +
15A LEU* 3.4 8.7 + - - +
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Residues in contact with LEU 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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4A PHE* 4.2 7.0 - - + -
8A GLU* 2.9 43.4 + - + +
9A LEU* 3.6 5.8 - - - +
11A GLU* 1.3 74.8 - - + +
13A LEU* 1.3 59.8 + - - +
15A LEU* 3.3 4.7 + - + +
16A TYR* 2.8 31.5 + - - +
350A ILE* 3.4 32.4 - - + +
351A SER* 3.9 25.4 - - - +
354A CYS* 3.6 34.6 - - + -
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Residues in contact with LEU 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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9A LEU* 2.8 26.2 + - + +
10A PRO* 4.0 7.6 - - + +
12A LEU* 1.3 74.4 - - - +
14A LYS* 1.3 60.0 + - - +
16A TYR* 4.3 1.3 - - + -
17A TYR* 2.8 60.2 + - + +
74A ASN* 3.9 17.0 - - + +
75A PRO 3.3 24.5 - - - +
76A TYR* 4.0 30.7 - - + +
323A VAL* 4.1 21.5 - - + -
350A ILE* 4.0 16.6 - - + -
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Residues in contact with LYS 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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10A PRO* 3.3 19.7 - - - +
11A GLU* 3.4 34.9 + - - +
12A LEU 3.3 0.2 - - - -
13A LEU* 1.3 79.1 - - - +
15A LEU* 1.3 61.4 + - - +
17A TYR* 4.0 1.7 - - - +
18A ARG* 3.2 23.2 + - - +
71A GLN* 5.6 0.9 - - - +
74A ASN* 3.4 32.2 + - - +
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Residues in contact with LEU 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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11A GLU 3.4 6.7 + - - +
12A LEU* 3.3 9.7 + - + +
13A LEU 3.3 0.4 - - - -
14A LYS* 1.3 78.0 - - - +
16A TYR* 1.3 61.1 + - - +
18A ARG* 3.0 4.5 + - + +
19A ARG* 2.8 52.0 + - + +
20A LEU* 4.0 0.7 + - - +
354A CYS* 3.7 27.6 - - + -
357A LEU* 3.8 30.1 - - + -
358A ASP* 3.8 20.4 - - - +
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Residues in contact with TYR 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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12A LEU 2.8 21.7 + - - +
13A LEU* 3.8 2.5 - - + +
15A LEU* 1.3 72.5 - - - +
17A TYR* 1.3 75.1 + + - +
20A LEU* 3.0 33.3 + - + -
21A PHE* 2.8 52.3 + + + -
22A PRO* 4.7 0.5 - - - +
321A PHE* 2.7 45.3 + - - +
323A VAL* 3.8 17.3 - - + -
330A ILE* 3.9 16.1 - - + +
350A ILE* 3.7 17.5 - - + -
353A ILE* 3.5 34.3 - - + -
354A CYS* 4.4 1.5 - - - -
388A LEU* 4.4 6.8 - - + +
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Residues in contact with TYR 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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13A LEU* 2.8 44.3 + - + +
14A LYS 4.1 1.1 - - - +
16A TYR* 1.3 94.3 - + - +
18A ARG* 1.3 56.3 + - - +
21A PHE* 4.2 5.8 - + - -
23A TYR* 2.5 37.4 + - - +
70A MET* 3.6 21.1 - - + -
71A GLN* 3.3 13.4 + - + +
74A ASN* 3.7 26.7 - - - +
75A PRO* 2.7 42.7 + - + +
76A TYR 4.6 4.0 + - - -
78A ILE* 3.5 34.9 - - + +
321A PHE 5.4 0.7 - - - -
322A SER* 5.5 1.5 - - - -
323A VAL* 5.1 7.0 + - + +
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Residues in contact with ARG 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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14A LYS 3.2 18.0 + - - +
15A LEU* 3.0 7.2 + - + +
17A TYR* 1.3 80.5 - - - +
19A ARG* 1.3 75.1 + - + +
20A LEU 3.8 0.7 - - - -
23A TYR* 5.1 3.8 - - - -
67A GLU* 5.3 3.4 + - - -
71A GLN* 2.9 42.7 + - + +
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Residues in contact with ARG 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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15A LEU* 2.8 32.0 + - + +
18A ARG* 1.3 92.8 - - + +
20A LEU* 1.3 67.6 + - - +
357A LEU* 4.0 34.1 + - + +
358A ASP* 4.8 5.1 + - - -
360A ILE* 5.8 3.0 - - - +
379A ARG 5.5 1.2 - - - +
382A ASP* 3.4 44.0 + - - +
383A TYR* 4.7 2.1 + - - +
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Residues in contact with LEU 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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16A TYR* 3.0 27.2 + - + +
18A ARG 3.8 0.4 - - - -
19A ARG* 1.3 87.8 - - - +
21A PHE* 1.3 69.9 + - - +
22A PRO* 3.1 9.5 - - - +
353A ILE* 3.5 44.4 - - + +
354A CYS* 4.3 12.1 - - - -
357A LEU* 4.0 18.8 - - + -
383A TYR* 3.7 32.3 - - + +
386A THR* 3.7 25.8 - - + +
388A LEU* 4.0 12.9 - - + +
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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