Contacts of the helix formed by residues 17 - 25 (chain A) in PDB entry 4RTP
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 LEU 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LYS* 3.7 28.5 - - + +
15A TYR 3.2 0.4 - - - -
16A PRO* 1.3 80.7 - - + +
18A LEU* 1.3 65.0 + - - +
19A ASP 3.1 2.9 - - - +
20A ASP* 3.2 14.1 + - + +
21A ILE* 3.1 47.6 + - + +
179A TYR* 5.2 1.3 - - - +
184A TYR* 5.2 1.6 - - - +
226A SER* 4.9 4.3 - - - -
245A VAL* 5.2 8.3 - - + -
263A GLU* 3.8 40.6 - - + +
265A LEU* 4.6 7.4 - - + -
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Residues in contact with LEU 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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3A LYS* 3.8 17.9 - - + +
4A ASN 5.1 0.2 - - - +
14A LYS* 3.3 17.7 + - + +
15A TYR* 3.6 35.7 - - + +
16A PRO 3.4 1.4 - - - -
17A LEU* 1.3 78.2 - - - +
19A ASP* 1.3 62.7 + - - +
21A ILE* 3.4 8.3 + - + +
22A LYS* 3.2 33.5 + - + +
40A SER* 3.9 16.8 - - - +
41A VAL* 3.9 29.8 - - + -
44A ASN* 3.7 32.1 - - + +
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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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3A LYS* 3.5 26.9 + - - +
16A PRO 3.8 14.0 - - - +
17A LEU 3.1 0.4 - - - -
18A LEU* 1.3 79.7 - - - +
20A ASP* 1.3 58.7 + - - +
22A LYS* 3.8 7.9 + - - +
23A ARG* 3.4 22.2 + - - +
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Residues in contact with ASP 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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17A LEU* 3.2 18.8 + - + +
19A ASP* 1.3 77.3 - - - +
21A ILE* 1.3 65.1 + - - +
23A ARG* 3.4 2.5 + - - -
24A HIS* 2.7 37.8 + - + +
245A VAL* 3.8 28.5 - - + -
265A LEU* 3.5 11.5 - - + +
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Residues in contact with ILE 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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14A LYS* 6.1 0.9 - - + -
17A LEU* 3.1 35.1 + - + +
18A LEU* 3.6 11.4 - - + +
19A ASP 3.4 0.2 - - - -
20A ASP* 1.3 76.9 - - - +
22A LYS* 1.3 55.9 + - + +
24A HIS 3.0 3.1 + - - -
25A LEU* 2.8 48.5 + - + +
41A VAL* 4.5 17.3 - - + -
179A TYR* 3.7 46.0 - - + +
224A LEU* 3.8 7.1 - - + +
226A SER* 4.2 2.7 - - - -
265A LEU* 3.8 25.6 - - + -
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Residues in contact with LYS 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 LEU* 3.2 22.5 + - + +
19A ASP* 4.2 7.9 - - - +
21A ILE* 1.3 77.6 - - + +
23A ARG* 1.3 62.1 + - - +
24A HIS 3.5 0.3 + - - -
25A LEU* 3.6 22.1 + - - +
41A VAL* 6.3 0.2 - - + -
44A ASN* 3.1 32.5 + - + +
45A THR* 3.9 24.7 - - + +
46A ASP 5.0 1.0 - - - +
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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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19A ASP 3.4 15.7 + - - +
20A ASP* 3.4 6.5 + - - +
21A ILE 3.2 0.8 - - - -
22A LYS* 1.3 77.9 - - - +
24A HIS* 1.3 74.0 + - + +
25A LEU 5.1 0.6 - - - +
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Residues in contact with HIS 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 ASP* 2.7 32.6 + - + +
21A ILE 3.0 4.9 + - - +
23A ARG* 1.3 88.7 - - + +
25A LEU* 1.3 59.5 + - - +
26A PRO* 3.3 11.6 - - - +
224A LEU* 3.8 13.3 - - + +
243A HIS* 3.3 58.4 - + + +
245A VAL* 5.6 4.5 - - + -
265A LEU* 4.0 15.6 - - + +
267A LEU* 3.5 24.3 - - + +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 2.8 28.4 + - + +
22A LYS* 3.6 14.8 + - - +
23A ARG 3.5 1.5 - - - +
24A HIS* 1.3 77.5 - - - +
26A PRO* 1.3 78.1 - - + +
31A LEU* 4.2 9.6 - - + -
41A VAL* 4.7 6.1 - - + -
45A THR* 4.6 13.5 - - + -
47A PHE* 4.1 23.8 - - + -
177A VAL* 3.7 23.1 - - + -
178A VAL 4.6 0.7 - - - +
179A TYR* 4.1 14.4 - - + -
224A LEU* 3.8 24.2 - - + -
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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