Contacts of the helix formed by residues 22 - 35 (chain y) 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 THR 22 (chain y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20y SER 4.4 3.1 - - - +
21y ASP* 1.3 78.1 - - - +
23y ILE* 1.3 64.6 + - - +
24y GLU* 3.3 12.3 + - - +
25y ASN* 3.1 38.5 + - - +
26y VAL* 3.3 14.9 + - - +
52y ASP 3.9 8.5 - - - -
53y GLY* 4.0 8.5 - - - +
54y ARG 3.1 16.8 - - - +
55y THR* 3.9 12.3 - - + -
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Residues in contact with ILE 23 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22y THR* 1.3 74.9 - - - +
24y GLU* 1.3 60.8 + - - +
26y VAL* 3.8 4.8 - - + +
27y LYS* 3.1 46.0 + - + +
43y LEU* 4.4 10.3 - - + -
50y LEU* 3.6 48.2 - - + +
51y GLU 2.9 28.7 - - - +
52y ASP* 3.8 4.9 + - - +
54y ARG 3.1 8.9 + - - +
55y THR 4.5 2.2 - - - -
56y LEU* 4.2 18.4 - - + -
59y TYR* 4.0 16.2 - - + -
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Residues in contact with GLU 24 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22y THR* 3.0 8.7 + - - +
23y ILE* 1.3 80.1 - - - +
25y ASN* 1.3 65.5 + - - +
27y LYS* 3.4 6.2 + - - +
28y ALA* 3.0 23.4 + - - +
38y PRO* 5.2 2.9 - - - +
52y ASP* 3.3 45.1 + - + +
53y GLY* 5.8 0.9 - - - -
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Residues in contact with ASN 25 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20y SER 4.9 0.7 - - - +
21y ASP* 3.4 25.6 - - + +
22y THR* 3.1 36.5 + - - +
24y GLU* 1.3 78.7 - - - +
26y VAL* 1.3 57.2 + - - +
28y ALA* 3.2 9.1 + - - +
29y LYS* 3.0 35.6 + - - +
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Residues in contact with VAL 26 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3y ILE* 4.8 0.9 - - + -
5y VAL* 5.2 0.2 - - + -
15y LEU* 3.3 20.2 - - + -
17y VAL* 4.4 7.0 - - + -
21y ASP* 4.3 9.4 - - + -
22y THR 3.3 15.0 - - - +
23y ILE* 3.8 8.7 - - + +
25y ASN* 1.3 74.9 - - - +
27y LYS* 1.3 60.7 + - - +
29y LYS* 3.0 12.0 + - + +
30y ILE* 2.9 30.0 + - + +
43y LEU* 4.2 19.7 - - + -
56y LEU* 3.9 31.0 - - + -
67y LEU* 4.5 13.5 - - + -
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Residues in contact with LYS 27 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23y ILE* 3.1 30.4 + - - +
24y GLU* 3.7 5.6 - - - +
26y VAL* 1.3 76.9 - - - +
28y ALA* 1.3 57.6 + - - +
30y ILE* 3.3 2.5 + - - -
31y GLN* 3.0 23.9 + - - +
38y PRO* 3.5 32.8 + - + +
41y GLN* 3.0 60.5 + - + +
42y ARG* 4.9 1.2 - - - +
43y LEU* 4.0 19.3 - - + +
50y LEU 4.7 7.1 + - - -
52y ASP* 3.3 34.9 + - - +
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Residues in contact with ALA 28 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24y GLU 3.0 13.9 + - - +
25y ASN* 3.3 12.3 - - - +
27y LYS* 1.3 78.3 - - - +
29y LYS* 1.3 55.8 + - - +
31y GLN* 3.2 9.8 + - - +
32y ASP* 3.0 34.1 + - - +
38y PRO* 4.2 13.4 - - + +
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Residues in contact with LYS 29 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15y LEU* 3.1 30.0 - - + +
16y GLU 3.0 22.6 + - - +
17y VAL* 3.6 27.3 - - + +
21y ASP* 4.1 22.8 + - - -
25y ASN* 3.0 24.6 + - - +
26y VAL* 3.0 6.5 + - - +
28y ALA* 1.3 75.5 - - + +
30y ILE* 1.3 60.1 + - - +
32y ASP* 3.3 25.0 - - - +
33y LYS* 3.4 10.2 + - - +
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Residues in contact with ILE 30 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5y VAL* 3.6 37.5 - - + -
13y ILE* 5.1 5.8 - - + -
15y LEU* 4.6 8.1 - - + -
26y VAL* 2.9 16.1 + - + +
27y LYS 3.6 0.9 - - - +
28y ALA 3.2 0.2 - - - -
29y LYS* 1.3 74.3 - - - +
31y GLN* 1.3 61.5 + - - +
32y ASP 3.2 0.2 - - - -
33y LYS* 3.4 4.6 + - - -
34y GLU* 2.8 42.5 + - + +
36y ILE* 5.2 1.8 - - + +
41y GLN* 3.5 32.1 - - - +
43y LEU* 3.8 26.5 - - + -
69y LEU* 4.2 18.2 - - + -
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Residues in contact with GLN 31 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27y LYS 3.0 11.8 + - - +
28y ALA* 3.2 14.1 + - - +
30y ILE* 1.3 77.1 - - - +
32y ASP* 1.3 65.0 + - - +
35y GLY* 2.7 32.6 + - - +
36y ILE 3.2 24.5 - - - +
37y PRO* 3.6 15.6 - - - +
38y PRO* 3.4 31.1 - - + +
41y GLN* 4.1 0.4 - - - +
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Residues in contact with ASP 32 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28y ALA* 3.0 19.8 + - - +
29y LYS* 3.3 17.2 - - - +
31y GLN* 1.3 85.7 - - - +
33y LYS* 1.3 60.0 - - + +
35y GLY 4.7 0.5 + - - -
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Residues in contact with LYS 33 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13y ILE* 3.6 39.6 - - + +
14y THR* 3.0 41.4 + - - +
15y LEU* 5.4 6.5 - - + -
29y LYS 3.4 10.5 + - - +
30y ILE* 4.5 2.9 - - - +
31y GLN 3.4 0.2 - - - -
32y ASP* 1.3 78.8 - - + +
34y GLU* 1.3 67.2 + - + +
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Residues in contact with GLU 34 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332x TYR* 5.9 1.0 - - - -
7y THR* 3.6 28.0 + - + +
9y THR* 5.3 4.3 + - - +
11y LYS* 5.1 4.3 + - - +
13y ILE* 3.7 38.7 - - + +
30y ILE* 2.8 29.6 + - + +
33y LYS* 1.3 81.7 - - - +
35y GLY* 1.3 60.4 + - - +
36y ILE* 3.5 21.3 + - + +
69y LEU* 5.3 0.2 - - + -
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Residues in contact with GLY 35 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332x TYR* 4.1 14.7 + - - -
31y GLN* 2.7 29.8 + - - -
32y ASP 4.7 0.6 + - - -
33y LYS 3.9 0.2 - - - -
34y GLU* 1.3 74.2 - - - +
36y ILE* 1.3 61.0 + - - +
37y PRO* 3.7 7.4 - - - +
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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