Contacts of the helix formed by residues 20 - 34 (chain I) in PDB entry 6RAR
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 SER 20 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D C 3.9 7.8 + - - -
39D G 2.7 24.5 + - - -
18I HIS* 3.3 1.6 - - - +
19I PRO* 1.3 79.0 - - - +
21I ARG* 1.3 63.6 + - - +
22I LEU* 3.2 2.8 + - - +
23I ASP* 3.1 39.4 + - - +
24I LYS* 3.1 22.9 + - - +
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Residues in contact with ARG 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B A 6.3 2.5 - - - -
7B C 4.7 17.5 + - - -
8B A 4.0 17.8 - - - -
37D T 6.0 0.9 - - - -
38D C 3.3 30.8 + - - +
39D G 3.2 11.6 + - - +
19I PRO 3.2 2.7 + - - +
20I SER* 1.3 70.9 - - - +
22I LEU* 1.3 63.7 + - + +
24I LYS* 3.2 28.7 + - - +
25I GLU* 3.0 39.1 + - - +
122I GLY* 2.9 29.7 + - - -
123I VAL* 4.6 0.4 - - - +
127I THR* 3.1 33.9 + - - +
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Residues in contact with LEU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D G 3.0 36.2 + - - +
40D G 4.0 25.1 - - - +
20I SER* 3.7 2.2 - - - +
21I ARG* 1.3 77.1 - - + +
23I ASP* 1.3 64.8 + - - +
25I GLU* 3.1 22.8 + - + +
26I LYS* 3.1 22.3 + - - +
130I LYS* 6.0 0.4 - - - +
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Residues in contact with ASP 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I HIS* 4.0 27.3 - - + +
20I SER* 3.1 30.2 + - - +
22I LEU* 1.3 77.9 - - - +
24I LYS* 1.3 57.5 + - - +
26I LYS* 3.4 15.0 + - - +
27I ILE* 3.0 34.7 + - + +
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Residues in contact with LYS 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LEU* 2.7 42.7 + - + +
16I GLU* 4.8 1.2 + - - +
18I HIS* 3.0 24.5 + - + +
19I PRO* 3.7 17.6 - - - +
20I SER 3.1 7.6 + - - +
21I ARG* 3.2 35.9 + - - +
23I ASP* 1.3 76.4 - - - +
25I GLU* 1.3 60.7 + - + +
27I ILE* 4.4 1.6 - - - -
28I ILE* 3.0 36.5 + - + +
121I CYS 2.6 30.1 + - - +
122I GLY* 3.7 13.6 - - - +
123I VAL* 4.2 5.6 - - + -
127I THR* 5.4 0.4 - - + -
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Residues in contact with GLU 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ARG* 3.0 30.9 + - - +
22I LEU* 3.1 27.3 + - - +
24I LYS* 1.3 77.8 - - - +
26I LYS* 1.3 57.8 + - - +
29I SER* 2.9 31.9 + - - -
127I THR* 4.3 13.4 - - + +
130I LYS* 2.8 40.7 + - + +
131I ILE* 3.2 24.5 - - + +
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Residues in contact with LYS 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I LEU 3.1 11.1 + - - +
23I ASP* 3.8 20.4 - - - +
24I LYS 3.3 0.2 - - - -
25I GLU* 1.3 76.0 - - - +
27I ILE* 1.3 84.0 + - - +
28I ILE 3.1 1.6 - - - -
29I SER* 3.8 5.7 - - - -
30I GLU* 3.0 57.3 + - + +
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Residues in contact with ILE 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ILE* 4.0 29.0 - - + +
14I GLN* 3.6 22.0 - - + +
15I LEU* 4.0 15.5 - - + +
18I HIS* 3.4 30.7 - - + +
23I ASP* 3.0 25.2 + - + +
24I LYS* 4.0 8.7 - - - +
26I LYS* 1.3 92.8 - - - +
28I ILE* 1.3 61.4 + - - +
30I GLU* 3.8 5.8 + - - +
31I ALA* 3.4 20.8 + - - +
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Residues in contact with ILE 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ILE* 5.8 1.8 - - + -
15I LEU* 3.8 21.3 - - + -
24I LYS 3.0 20.7 + - - +
26I LYS 3.1 0.2 - - - -
27I ILE* 1.3 75.7 - - + +
29I SER* 1.3 64.6 + - - +
30I GLU 3.2 0.2 - - - -
31I ALA* 3.3 6.4 + - - +
32I MET* 3.0 47.0 + - + +
39I PHE* 6.2 2.9 - - + -
40I PHE* 4.5 5.2 - - + -
123I VAL* 3.7 20.2 - - + -
127I THR* 3.7 28.0 - - + -
128I ILE* 4.3 14.8 - - + -
131I ILE* 3.4 19.5 - - + -
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Residues in contact with SER 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I GLU 2.9 23.0 + - - -
26I LYS* 3.8 7.6 - - - -
28I ILE* 1.3 76.0 - - - +
30I GLU* 1.3 58.8 + - - +
32I MET* 3.4 4.1 + - - +
33I GLU* 2.8 43.5 + - - +
131I ILE* 2.9 27.4 - - - +
134I LYS* 4.2 8.5 - - - -
135I PHE* 4.2 4.3 - - - -
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Residues in contact with GLU 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LYS* 3.0 50.9 + - + +
27I ILE* 4.2 5.3 - - - +
29I SER* 1.3 76.0 - - - +
31I ALA* 1.3 54.4 + - - +
33I GLU* 3.1 16.1 + - - +
34I ASP* 2.7 47.5 + - - +
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Residues in contact with ALA 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ILE* 4.0 21.1 - - + -
27I ILE 3.4 12.8 + - - +
28I ILE* 3.3 6.4 + - - +
30I GLU* 1.3 76.3 - - - +
32I MET* 1.3 62.9 + - - +
34I ASP* 3.3 2.2 + - - -
35I GLY 3.1 15.8 + - - -
36I ILE* 3.3 34.3 + - + +
39I PHE* 4.7 0.7 - - + -
40I PHE* 3.6 21.9 - - + -
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Residues in contact with MET 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I ILE* 3.0 37.7 + - + +
29I SER 3.6 4.7 - - - +
31I ALA* 1.3 78.1 - - - +
33I GLU* 1.3 57.5 + - - +
35I GLY* 2.9 19.8 + - - -
40I PHE* 3.3 27.8 - - + -
128I ILE* 3.6 31.9 - - + +
131I ILE* 3.8 7.2 - - + -
132I ALA* 3.7 22.7 - - + +
135I PHE* 3.7 43.7 - - + -
138I TYR* 3.6 20.3 - - + -
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Residues in contact with GLU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I SER* 2.8 36.9 + - - +
30I GLU* 3.6 13.4 - - - +
32I MET* 1.3 76.8 - - - +
34I ASP* 1.3 64.6 + - - +
35I GLY* 3.1 1.7 + - - -
135I PHE* 3.4 26.1 - - + -
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Residues in contact with ASP 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I GLU* 5.2 13.4 - - + +
6I LEU* 5.5 5.9 + - - +
30I GLU* 2.7 29.9 + - - +
31I ALA* 3.6 6.0 - - - +
33I GLU* 1.3 75.0 - - - +
35I GLY* 1.3 63.8 + - - +
36I ILE* 3.6 21.2 - - + +
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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