Contacts of the helix formed by residues 17 - 28 (chain R) in PDB entry 5GJQ
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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15R PRO 3.1 7.3 + - - +
16R ASP* 1.3 72.7 - - - +
18R ARG* 1.3 54.2 + - - +
19R ILE 2.7 0.2 + - - -
20R ALA* 2.3 43.0 + - + +
21R GLN* 3.4 2.3 + - - -
146R ARG* 3.6 26.2 - - - +
149R LEU* 4.2 25.8 - - + +
150R PHE* 4.5 18.2 - - + +
186R LEU* 4.9 2.5 - - + -
212R GLU 5.2 0.4 + - - -
213R LEU* 3.5 53.6 + - + +
286R TRP* 4.1 32.3 - - + -
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Residues in contact with ARG 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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16R ASP* 3.2 17.2 - - + -
17R LEU* 1.3 76.8 - - - +
19R ILE* 1.3 65.2 + - + +
21R GLN* 3.2 10.0 + - - +
22R LEU* 2.9 34.2 + - + +
213R LEU 5.2 8.5 - - - +
286R TRP* 5.7 0.4 - - - -
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Residues in contact with ILE 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R PRO* 6.2 2.7 - - + -
16R ASP* 4.0 23.3 - - + +
17R LEU 2.7 3.8 + - - -
18R ARG* 1.3 77.2 - - + +
20R ALA* 1.3 56.2 + - - +
22R LEU* 3.4 5.4 + - - +
23R ARG* 2.9 28.4 + - + +
41R LEU* 4.9 17.0 - - + +
44R ALA* 4.7 17.0 - - + +
48R ASN* 4.8 6.5 - - - -
50R MET* 3.4 32.1 - - + -
53R TYR* 2.9 42.8 - - + +
57R LEU* 6.3 0.4 - - + -
150R PHE* 4.1 1.8 - - + -
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Residues in contact with ALA 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R LEU* 2.3 30.1 + - + +
19R ILE* 1.3 68.8 - - - +
21R GLN* 1.3 65.1 + - - +
23R ARG* 2.9 17.6 + - - +
24R PHE* 2.8 24.5 + - - +
149R LEU 5.4 0.9 - - - +
150R PHE* 3.5 43.5 - - + +
152R MET* 6.4 0.4 - - + -
286R TRP* 5.1 3.8 - - + -
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Residues in contact with GLN 21 (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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17R LEU 3.4 1.6 + - - -
18R ARG* 3.2 13.8 + - - +
20R ALA* 1.3 78.6 - - - +
22R LEU* 1.3 61.9 + - - +
24R PHE* 3.3 7.2 + - - +
25R LEU* 2.9 63.4 + - - +
284R LYS 4.2 10.0 + - - -
285R ASP* 3.7 21.2 + - - +
286R TRP* 2.7 49.4 - - + +
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Residues in contact with LEU 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18R ARG* 2.9 22.5 + - + +
19R ILE* 3.8 4.9 - - - +
21R GLN* 1.3 79.5 - - - +
23R ARG* 1.3 66.9 + - - +
25R LEU* 3.1 17.6 + - + +
26R LEU* 2.9 21.1 + - - +
37R VAL* 5.0 13.8 - - - +
40R GLU* 4.9 16.4 - - + -
41R LEU* 4.9 17.5 - - + +
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Residues in contact with ARG 23 (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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19R ILE* 2.9 17.2 + - + +
20R ALA* 3.1 18.2 - - - +
22R LEU* 1.3 75.7 - - - +
24R PHE* 1.3 81.7 + - - +
26R LEU* 2.8 19.4 + - - +
27R SER* 3.0 15.5 + - - -
41R LEU* 5.4 6.7 - - + +
53R TYR* 6.1 4.9 - - + -
57R LEU* 4.9 26.6 - - + +
60R SER* 5.8 4.4 + - - -
150R PHE 5.7 3.7 + - - -
151R TYR* 4.9 16.0 + - - +
152R MET* 4.6 16.4 - - - +
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Residues in contact with PHE 24 (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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20R ALA 2.8 13.6 + - - +
21R GLN* 3.5 9.4 - - + +
23R ARG* 1.3 85.6 - - - +
25R LEU* 1.3 66.5 + - - +
27R SER* 2.2 40.3 + - - -
28R LEU* 3.1 11.4 + - + +
283R LYS 4.0 13.7 - - - -
284R LYS 4.0 7.4 - - - -
285R ASP 2.7 31.6 - - - -
286R TRP* 4.1 15.9 - - + -
289R ALA* 3.7 31.2 - - + -
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Residues in contact with LEU 25 (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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21R GLN* 2.9 42.9 + - - +
22R LEU* 3.1 24.2 + - + +
24R PHE* 1.3 75.6 - - - +
26R LEU* 1.3 56.6 + - - +
28R LEU* 2.1 37.4 - - + +
31R HIS* 4.3 3.6 - - - -
37R VAL* 5.2 13.9 - - + -
284R LYS* 3.0 40.4 - - + +
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Residues in contact with LEU 26 (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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22R LEU 2.9 9.7 + - - +
23R ARG* 2.8 13.0 + - - +
25R LEU* 1.3 78.1 - - - +
27R SER* 1.3 66.0 + - - +
28R LEU* 3.5 2.6 + - - +
30R GLU* 5.4 1.2 - - - +
31R HIS* 4.7 11.5 - - + +
32R ARG* 6.0 1.8 - - + -
33R GLY 3.9 20.9 - - - +
37R VAL* 5.6 6.2 - - + +
38R ARG* 4.9 22.2 - - + +
57R LEU* 6.5 1.8 - - + -
61R LEU* 4.2 25.1 - - + -
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Residues in contact with SER 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R ARG* 3.0 12.4 + - - -
24R PHE* 2.2 49.3 + - - -
26R LEU* 1.3 77.7 - - - +
28R LEU* 1.3 76.9 + - - +
30R GLU* 5.0 1.0 - - - +
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Residues in contact with LEU 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R PHE* 3.5 9.9 - - + +
25R LEU* 2.1 50.7 - - + +
26R LEU 4.1 0.2 - - - +
27R SER* 1.3 98.5 + - - +
29R PRO* 1.3 68.4 - - + +
30R GLU* 2.6 18.1 + - - +
31R HIS* 3.4 19.5 - - + -
283R LYS 5.5 4.5 - - - +
284R LYS* 5.5 2.2 - - - +
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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