Contacts of the helix formed by residues 8 - 16 (chain A) in PDB entry 4BZ5
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 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A TYR* 1.3 85.8 - - - +
9A ASP* 1.3 62.6 + - - -
10A GLN 3.4 2.7 - - - -
11A TYR* 3.8 9.1 - - - +
12A ARG* 2.9 30.3 + - - +
25A TYR* 4.8 0.2 + - - -
43A ARG* 3.9 11.0 - - - -
46A PRO* 5.0 2.5 - - - -
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Residues in contact with ASP 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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8A GLY* 1.3 73.5 - - - +
10A GLN* 1.3 63.4 + - - +
12A ARG* 3.4 8.1 + - - +
13A GLN* 3.2 22.5 + - - +
144B LYS* 5.9 1.0 + - - -
147B GLU* 5.4 4.2 - - - +
195B GLU* 5.6 2.3 - - - +
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Residues in contact with GLN 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 GLY 3.4 0.2 - - - -
9A ASP* 1.3 75.2 - - - +
11A TYR* 1.3 66.3 + - - +
13A GLN* 3.3 18.9 + - - +
14A LEU* 3.0 51.3 + - + +
48A GLN* 6.0 0.4 - - - +
217B PRO 4.4 14.1 - - - +
218B GLY* 3.4 32.1 + - - -
219B THR* 4.0 17.1 - - + +
224B MET* 5.9 2.4 - - - +
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Residues in contact with TYR 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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6A VAL* 3.6 20.4 - - + -
7A TYR* 4.1 3.6 - - - -
8A GLY* 3.6 13.4 - - - +
9A ASP 3.3 0.4 - - - -
10A GLN* 1.3 79.7 - - - +
12A ARG* 1.3 55.8 + - - +
14A LEU* 3.3 6.2 + - - +
15A CYS* 2.9 51.4 + - - -
25A TYR* 3.4 30.5 - + - -
46A PRO* 3.3 34.5 - - + -
113A ALA* 3.1 36.4 + - + -
114A ALA* 4.2 0.9 - - - -
116A GLN* 5.7 0.4 - - - -
117A GLY* 3.8 5.4 - - - -
135A ASN* 2.6 36.7 + - - -
137A GLY* 3.7 9.0 - - - -
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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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8A GLY 2.9 18.2 + - - +
9A ASP* 3.7 8.3 - - - +
11A TYR* 1.3 76.2 - - - +
13A GLN* 1.3 64.5 + - - +
15A CYS* 3.3 1.0 + - - +
16A CYS* 3.0 36.2 + - - -
25A TYR* 3.8 26.5 - - + -
26A ALA* 3.5 27.6 + - - +
29A MET* 4.4 11.3 - - - +
30A ASP* 2.9 43.2 + - - -
377A TYR* 4.1 6.7 + - - -
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Residues in contact with GLN 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 ASP 3.2 11.5 + - - +
10A GLN* 3.6 23.2 - - - +
12A ARG* 1.3 79.5 - - - +
14A LEU* 1.3 65.9 + - + +
16A CYS* 3.3 13.9 + - - +
17A SER* 3.4 13.7 + - - -
223B ASN* 2.5 35.8 + - - +
224B MET* 3.1 27.1 + - - +
225B VAL* 4.0 5.9 - - + +
234B LEU* 5.5 0.2 - - - +
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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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10A GLN* 3.0 47.3 + - + +
11A TYR* 3.8 4.5 - - - +
13A GLN* 1.3 78.7 - - + +
15A CYS* 1.3 61.5 + - - +
17A SER* 2.7 25.3 + - - +
109A ASP* 3.9 35.9 - - + +
110A TYR* 3.4 12.6 - - - +
113A ALA* 3.9 20.0 - - + -
116A GLN* 4.7 7.9 - - - +
224B MET* 3.8 30.5 - - + +
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Residues in contact with CYS 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 TYR* 2.9 59.3 + - - +
12A ARG 3.9 0.2 - - - +
14A LEU* 1.3 76.4 - - - +
16A CYS* 1.3 57.7 + - - +
17A SER 3.4 1.8 + - - -
18A SER* 4.8 1.7 + - - -
21A PHE* 5.2 4.3 - - - +
22A GLY 3.9 4.9 - - - +
25A TYR* 3.8 30.1 + - + +
110A TYR* 3.9 21.1 - - - -
113A ALA* 4.6 7.9 - - - -
114A ALA* 5.2 1.8 - - - -
137A GLY* 4.1 16.8 - - - -
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Residues in contact with CYS 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 ARG* 3.0 26.0 + - - +
13A GLN* 3.3 6.3 + - - +
14A LEU 3.1 0.4 - - - -
15A CYS* 1.3 79.7 - - - +
17A SER* 1.3 57.6 + - - +
18A SER 3.5 0.9 - - - -
22A GLY 3.1 20.2 - - - +
23A ASP* 4.0 12.5 - - + +
25A TYR* 4.0 5.8 - - - -
26A ALA* 3.5 41.5 - - - -
226B ASP* 3.5 17.2 + - - +
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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