Contacts of the helix formed by residues 15 - 19 (chain R) in PDB entry 3L73
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 ARG 15 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221Q TYR* 3.9 7.3 + - - -
225Q HIS* 3.8 4.8 + - - -
14R ARG* 1.3 78.0 - - - +
16R GLU* 1.3 66.5 + - - +
17R ASP* 3.4 4.0 - - - +
18R VAL* 3.3 16.2 + - + +
19R MET* 3.5 9.8 + - - +
32R ARG* 3.0 48.9 + - - +
35R PHE* 4.9 9.0 - - - +
36R SER* 3.1 23.0 + - - -
20T PRO 3.4 17.2 + - - -
21T PHE* 3.5 22.2 + - - +
22T GLU 2.9 16.1 + - - +
23T GLN 2.7 29.5 + - - +
24T ARG* 3.8 14.0 - - + +
25T ALA 5.9 0.8 - - - +
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Residues in contact with GLU 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R ARG 3.9 0.6 + - - -
15R ARG* 1.3 73.5 - - - +
17R ASP* 1.3 81.7 + - - +
19R MET* 3.2 28.2 + - - +
20R ASP 4.9 0.3 + - - -
24T ARG* 5.0 4.4 - - - +
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Residues in contact with ASP 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R ARG* 3.4 3.0 + - - +
16R GLU* 1.3 99.8 - - - +
18R VAL* 1.3 62.8 + - + +
19R MET 3.4 2.1 + - - -
20R ASP* 5.0 3.2 + - - +
23R THR* 5.1 12.6 - - - +
24R SER 5.4 0.5 - - - +
25R SER* 5.3 2.4 - - - -
28R SER* 3.5 33.8 + - - +
31R ASP* 5.0 8.5 - - - +
32R ARG* 4.7 12.2 - - - +
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Residues in contact with VAL 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235N ARG* 2.9 14.3 + - - +
14R ARG* 2.7 42.5 + - + +
15R ARG* 3.7 17.0 - - + +
16R GLU 3.3 0.4 - - - -
17R ASP* 1.3 81.0 - - - +
19R MET* 1.3 57.9 + - - +
20R ASP 3.5 1.8 - - - -
23R THR 5.9 0.7 - - - -
25R SER* 3.6 30.5 - - - +
28R SER* 3.8 2.7 - - - +
32R ARG* 3.6 28.0 - - - +
22T GLU* 3.4 35.9 - - + +
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Residues in contact with MET 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235N ARG* 3.6 6.4 + - - +
11R SER* 3.7 37.4 + - - +
14R ARG* 3.4 35.6 - - - +
15R ARG 3.5 8.2 + - - +
16R GLU* 3.2 21.4 + - - +
17R ASP 3.4 0.4 - - - -
18R VAL* 1.3 79.2 - - - +
20R ASP* 1.3 61.3 + - + +
21R ALA* 3.6 3.3 + - - +
24T ARG* 4.7 5.8 - - - +
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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