Contacts of the helix formed by residues 11 - 18 (chain A) in PDB entry 4B5G
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.3 6.5 - - - +
10A ASN* 1.3 78.4 - - - +
12A ILE* 1.3 65.5 + - - -
13A ARG 3.2 3.5 + - - -
14A SER* 3.3 2.8 + - - -
15A ALA 3.1 17.7 + - - -
36A GLU 2.9 10.9 + - - -
37A LEU 3.3 12.8 - - - -
38A LYS* 3.7 12.4 - - - +
50V A 3.9 0.2 - - - -
51V G 3.4 15.3 - - - -
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Residues in contact with ILE 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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9A VAL* 3.6 20.3 - - + +
11A GLY* 1.3 72.7 - - - +
13A ARG* 1.3 64.3 + - + +
15A ALA* 3.7 0.3 - - - +
16A TYR* 2.9 53.5 + - + -
20A PHE* 5.5 1.1 - - + -
34A VAL* 4.9 3.1 - - + -
37A LEU* 2.9 45.5 + - + +
39A ALA* 4.5 2.7 - - + -
44A LEU* 4.1 17.9 - - + -
48A MET* 4.2 19.5 - - + +
72A TYR* 3.1 31.9 - - + +
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Residues in contact with ARG 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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11A GLY 3.2 0.6 - - - -
12A ILE* 1.3 79.6 - - + +
14A SER* 1.3 59.6 + - - +
16A TYR* 3.1 3.8 + - - +
17A LYS* 2.9 38.8 + - - +
38A LYS 3.7 4.3 + - - -
39A ALA* 3.4 13.8 - - + +
43A ASP* 3.1 46.1 + - - +
44A LEU* 6.1 0.2 - - + -
48A MET* 3.6 30.9 - - + +
51V G 3.1 58.1 + - - +
52V C 3.4 10.0 + - - -
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Residues in contact with SER 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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9A VAL 5.3 0.2 - - - -
10A ASN 4.3 2.4 + - - -
11A GLY 3.3 8.7 + - - -
13A ARG* 1.3 79.6 - - - +
15A ALA* 1.3 56.5 + - - +
17A LYS* 3.1 19.0 - - - +
18A LYS* 2.2 70.4 + - - +
244A PHE 4.9 0.9 + - - -
50V A 3.6 19.0 + - - -
51V G 3.4 17.6 + - - -
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Residues in contact with ALA 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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9A VAL* 3.7 23.5 + - + +
11A GLY 3.1 13.5 + - - +
12A ILE* 3.7 4.9 - - - +
14A SER* 1.3 78.7 + - - +
16A TYR* 1.3 58.0 + - - +
18A LYS* 3.0 13.7 + - - +
19A GLY 3.1 0.9 + - - -
20A PHE* 2.9 40.5 + - + +
244A PHE* 3.6 25.4 + - + +
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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 ILE* 2.9 47.0 + - + +
13A ARG 3.1 5.8 + - - +
15A ALA* 1.3 78.0 - - - +
17A LYS* 1.3 58.5 + - - +
18A LYS 3.1 0.7 + - - -
19A GLY* 3.5 10.2 + - - -
20A PHE* 4.1 21.4 + + - +
21A TYR* 3.3 44.2 + + + +
22A GLU* 4.5 6.4 - - - +
24A ILE* 3.9 4.0 - - + +
47A ASP* 2.8 30.7 + - + -
48A MET* 3.6 37.5 - - + -
51A PRO* 3.4 16.5 - - - +
72A TYR* 5.0 0.3 + - - -
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Residues in contact with LYS 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 ARG* 2.9 25.5 + - - +
14A SER* 3.1 24.5 - - - +
16A TYR* 1.3 75.7 - - - +
18A LYS* 1.3 61.0 + - + +
19A GLY 3.4 0.7 - - - -
51V G 4.4 11.1 + - - -
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Residues in contact with LYS 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 SER* 2.2 47.2 + - - +
15A ALA 3.0 8.2 + - - +
17A LYS* 1.3 84.0 - - + +
19A GLY* 1.3 55.4 + - - +
20A PHE 3.7 0.2 - - - -
242A GLU* 4.4 3.8 - - - +
243A LYS* 4.0 20.4 + - + +
244A PHE* 3.5 34.0 + - - +
245A SER* 6.0 0.8 - - - +
50V A 2.5 26.7 + - - -
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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