Contacts of the helix formed by residues 13 - 23 (chain V) in PDB entry 3BBX
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 13 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A G 4.3 3.6 + - - -
77A U 5.8 1.1 - - - -
98A G 4.3 10.5 - - - -
9V ARG* 4.6 1.5 + - - +
12V GLN* 1.3 100.1 + - - +
14V LYS* 1.3 66.5 + - - -
15V GLY 3.1 4.0 + - - -
16V ALA* 3.6 2.4 + - - +
17V SER* 3.0 23.7 + - - -
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Residues in contact with LYS 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A U 4.8 16.6 + - - +
92A C 5.1 3.2 + - - -
93A C 2.2 52.9 + - - -
94A A 4.6 7.0 - - - +
95A U 5.7 4.9 - - + +
98A G 4.6 9.8 + - + +
13V GLY* 1.3 71.0 - - - -
15V GLY* 1.3 68.7 + - - +
17V SER* 3.2 16.1 + - - -
18V ARG* 3.1 28.8 + - + +
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Residues in contact with GLY 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A A 3.0 25.7 + - - -
95A U 3.3 24.5 - - - -
12V GLN 5.8 0.2 - - - -
13V GLY* 3.1 2.4 - - - -
14V LYS* 1.3 82.5 - - - +
16V ALA* 1.3 61.0 + - - +
18V ARG* 3.8 3.6 + - - +
19V ARG* 3.5 14.0 + - - +
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Residues in contact with ALA 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V ARG* 5.5 1.3 - - - +
11V GLU* 3.6 36.8 - - + +
12V GLN 4.9 2.1 + - - +
13V GLY 3.6 5.5 + - - +
14V LYS 3.5 0.4 - - - -
15V GLY* 1.3 71.0 - - - +
17V SER* 1.3 68.0 + - - +
19V ARG* 2.7 41.6 + - - +
20V LEU* 2.9 29.8 + - + +
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Residues in contact with SER 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A G 5.3 2.1 + - - -
77A U 5.0 6.0 + - - -
9V ARG* 2.9 28.4 + - - +
13V GLY 3.0 16.2 + - - -
14V LYS* 3.3 15.2 - - - -
16V ALA* 1.3 76.2 - - - +
18V ARG* 1.3 66.7 + - - +
20V LEU* 2.9 23.3 + - - +
21V ARG* 3.1 34.2 + - - +
27V PRO* 4.7 3.5 - - - +
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Residues in contact with ARG 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A C 2.4 26.3 + - - -
93A C 1.1 101.1 + - - +
94A A 4.4 6.5 - - - +
14V LYS* 3.1 38.0 + - + +
15V GLY 4.3 3.4 - - - +
17V SER* 1.3 78.0 - - - +
19V ARG* 1.3 60.5 + - + +
21V ARG* 3.5 17.9 + - - +
22V ALA* 3.3 19.1 + - - +
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Residues in contact with ARG 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A A 3.7 26.4 + - - +
95A U 3.3 27.3 + - - -
11V GLU* 3.0 29.9 + - - -
15V GLY* 3.5 8.0 - - - +
16V ALA* 2.7 45.7 + - - +
18V ARG* 1.3 70.6 - - + +
20V LEU* 1.3 68.1 + - + +
22V ALA* 2.9 23.5 + - - +
23V ALA* 3.3 7.1 + - - +
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Residues in contact with LEU 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V ARG* 3.8 33.9 - - - +
10V LYS* 5.6 7.9 - - + +
11V GLU* 6.0 1.6 - - - +
16V ALA* 2.9 32.7 + - + +
17V SER* 2.9 5.6 + - - +
19V ARG* 1.3 79.2 - - + +
21V ARG* 1.3 57.4 + - - +
23V ALA* 3.2 11.4 + - - +
25V LYS* 2.6 53.1 + - + +
26V PHE* 4.7 3.6 - - - +
27V PRO 5.4 1.6 - - - -
41V GLU* 3.6 27.4 - - + +
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Residues in contact with ARG 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A G 5.6 1.0 + - - -
77A U 5.1 7.7 + - - -
17V SER* 3.1 40.0 + - - +
18V ARG* 3.5 19.0 - - - +
19V ARG 3.1 0.4 - - - -
20V LEU* 1.3 73.6 - - - +
22V ALA* 1.3 65.1 + - - +
23V ALA 3.1 0.7 - - - -
24V ASN* 3.1 14.4 + - - +
25V LYS 2.9 12.3 - - - +
26V PHE* 4.2 3.4 - - + -
27V PRO* 3.1 35.7 - - + +
85V LYS* 4.6 18.0 + - - +
86V LEU 4.9 2.2 - - - +
87V GLN* 3.0 48.0 - - - +
88V HIS* 4.3 4.9 - - - +
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Residues in contact with ALA 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18V ARG 3.3 9.6 + - - +
19V ARG* 2.9 15.3 + - - +
21V ARG* 1.3 79.7 - - - +
23V ALA* 1.3 55.8 + - + +
24V ASN* 3.2 7.9 + - - +
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Residues in contact with ALA 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19V ARG 3.3 6.8 + - - +
20V LEU* 3.2 9.9 + - - +
21V ARG 3.1 0.8 - - - -
22V ALA* 1.3 77.0 - - - +
24V ASN* 1.3 63.2 + - - +
25V LYS* 2.7 34.4 + - + +
43V ASP* 4.9 0.7 - - - +
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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