Contacts of the helix formed by residues 18 - 24 (chain A) in PDB entry 2XAC
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 ILE 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLN* 5.8 1.1 - - - +
17A TRP* 1.3 97.1 - - - +
19A ASP* 1.3 59.7 + - - +
20A VAL* 3.1 4.5 - - - +
21A TYR* 3.7 3.0 - - - +
22A THR* 3.1 34.2 + - - +
141C GLU 5.7 0.2 - - - -
204C LEU* 5.7 4.5 - - - -
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Residues in contact with ASP 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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10A HIS* 5.5 2.4 - - - +
11A GLN* 3.0 37.4 + - - +
15A VAL* 4.4 11.3 - - + +
16A SER* 3.0 20.2 + - - +
17A TRP 3.3 0.8 - - - -
18A ILE* 1.3 73.3 - - - +
20A VAL* 1.3 59.7 + - - +
22A THR* 3.5 7.7 + - - -
23A ARG* 3.2 29.6 + - - +
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Residues in contact with VAL 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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15A VAL* 4.1 12.6 - - + +
16A SER 2.8 9.5 + - - +
17A TRP* 3.1 36.3 - - + -
18A ILE 3.7 0.4 - - - +
19A ASP* 1.3 77.3 - - - +
21A TYR* 1.3 73.3 + - - +
23A ARG* 3.5 4.3 + - - +
24A ALA* 3.0 23.2 + - - +
49B PRO* 4.2 11.9 - - + -
52B VAL* 4.0 26.2 - - + -
78B MET* 4.1 19.2 - - + +
79B GLN 3.2 18.4 - - - +
80B ILE* 4.9 2.2 - - + -
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Residues in contact with TYR 21 (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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17A TRP* 4.1 25.1 - + + -
18A ILE* 3.5 6.8 + - - +
20A VAL* 1.3 79.7 - - - +
22A THR* 1.3 60.8 + - + +
24A ALA 2.9 13.4 + - - -
25A THR* 2.4 42.5 + - + +
60A CYS* 5.4 4.5 + - - -
61A CYS 5.0 0.9 - - - -
62A PRO* 3.5 34.3 - - + +
48B VAL* 3.8 24.0 - - + -
49B PRO* 3.5 36.8 - - + -
172C PHE* 4.9 5.4 - + + -
203C GLY* 4.5 6.4 - - - -
204C LEU* 4.4 32.5 - - + -
221C LEU* 4.6 7.2 - - + +
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Residues in contact with THR 22 (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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18A ILE 3.1 18.6 + - - +
19A ASP* 3.5 12.3 + - - -
21A TYR* 1.3 76.9 - - - +
23A ARG* 1.3 68.8 + - - +
25A THR* 3.3 12.6 + - - -
27A GLN* 3.4 14.7 + - - -
172C PHE* 3.2 52.2 - - + -
204C LEU* 4.6 13.0 - - + -
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Residues in contact with ARG 23 (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 VAL* 4.9 13.1 - - - +
19A ASP 3.2 18.8 + - - +
20A VAL 3.7 4.3 - - - +
21A TYR 3.2 0.4 - - - -
22A THR* 1.3 81.0 + - - +
24A ALA* 1.3 56.8 + - - +
27A GLN* 3.9 4.5 + - - +
29A ARG* 2.8 23.9 + - - -
30B GLU* 2.6 29.5 + - - +
53B THR* 2.9 46.0 + - + +
54B VAL* 3.9 1.6 - - - +
55B GLN* 4.8 0.2 - - - +
76B VAL* 5.8 2.4 - - - +
78B MET* 4.5 16.4 - - - +
97B GLU* 3.3 24.0 + - - -
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Residues in contact with ALA 24 (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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20A VAL 3.0 16.0 + - - +
21A TYR* 2.9 9.7 + - - +
23A ARG* 1.3 74.6 - - - +
25A THR* 1.3 58.7 + - - +
29A ARG* 4.3 2.0 - - - +
59A GLY* 4.4 1.6 - - - -
60A CYS* 3.5 6.1 - - - +
49B PRO* 4.4 6.0 - - + +
51B CYS* 3.1 49.6 - - - +
52B VAL* 3.5 17.0 - - - -
53B THR* 3.4 10.3 - - - +
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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