Contacts of the helix formed by residues 23 - 33 (chain A) in PDB entry 5GT8
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 TYR 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.9 19.5 - - + -
19A GLY 3.5 14.6 - - - -
20A LEU* 2.9 11.1 + - + +
22A LEU* 1.3 95.8 - - + +
24A THR* 1.3 64.1 + - - +
25A HIS 3.2 2.7 - - - -
26A PRO* 3.7 6.1 - - + -
27A LEU* 3.0 42.2 + - + +
53A LEU* 6.2 0.9 - - + -
63A LEU* 4.0 21.1 - - + -
64A PRO* 2.9 41.6 + - + -
66A SER* 2.8 30.6 - - - -
68A PHE* 5.0 2.9 - - + -
69A LEU* 3.4 31.2 - - + +
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Residues in contact with THR 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 LEU 3.4 2.8 + - - -
21A TRP* 2.8 28.8 + - - -
23A TYR* 1.3 77.8 - - - +
25A HIS* 1.3 62.8 + - - +
28A ILE* 3.0 54.1 + - + +
206A PHE* 3.8 26.7 - - + -
207A TYR* 4.4 6.5 - - + +
24C THR* 4.0 9.6 - - + -
25C HIS* 3.4 28.5 - - - +
28C ILE* 4.6 0.2 - - + -
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Residues in contact with HIS 25 (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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21A TRP 4.7 0.4 + - - -
22A LEU 5.0 1.0 + - - +
23A TYR* 4.3 0.2 - - - +
24A THR* 1.3 80.0 - - - +
26A PRO* 1.3 76.5 - - + +
28A ILE* 3.9 2.9 - - - +
29A LYS* 3.4 31.7 + - - +
21C TRP* 3.5 40.2 + + + +
24C THR* 3.3 35.5 - - + +
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Residues in contact with PRO 26 (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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22A LEU 4.5 4.5 - - - +
23A TYR* 3.5 24.9 - - + +
25A HIS* 1.3 98.7 - - + +
27A LEU* 1.3 65.3 + - - +
29A LYS* 2.9 22.5 + - + +
30A LEU* 3.1 17.1 + - + +
62A GLU* 3.4 34.1 - - + +
63A LEU* 3.8 18.8 - - + -
64A PRO* 4.5 4.7 - - + -
21C TRP* 4.5 7.4 - - + -
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Residues in contact with LEU 27 (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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15A VAL* 6.0 2.0 - - + -
20A LEU* 3.7 21.3 - - + -
23A TYR* 3.0 38.0 + - + +
26A PRO* 1.3 76.0 - - + +
28A ILE* 1.3 64.5 + - - +
30A LEU* 2.9 11.9 + - + +
31A LEU* 2.9 29.4 + - + +
42A PHE* 4.2 18.6 - - + -
44A LEU* 4.2 16.6 - - + -
53A LEU* 3.9 28.7 - - + -
63A LEU* 5.1 2.0 - - + -
206A PHE* 3.5 33.9 - - + -
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Residues in contact with ILE 28 (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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24A THR* 3.0 39.6 + - + +
25A HIS* 3.9 4.0 - - - +
26A PRO 3.2 0.2 + - - -
27A LEU* 1.3 74.5 - - - +
29A LYS* 1.3 63.9 + - - +
31A LEU* 2.9 9.0 + - + -
32A PHE* 2.9 36.8 + - + +
33A LEU* 4.0 8.2 + - + +
202A ILE* 4.1 22.2 - - + -
206A PHE* 4.3 13.0 - - + -
24C THR* 4.3 3.8 - - + -
28C ILE* 3.3 33.9 - - + -
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Residues in contact with LYS 29 (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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25A HIS* 3.4 25.1 + - - +
26A PRO* 2.9 14.6 + - - +
28A ILE* 1.3 78.6 - - - +
30A LEU* 1.3 62.9 + - + +
33A LEU* 3.1 52.8 + - + +
36A ARG* 3.3 45.9 + - + +
37A SER* 4.1 9.1 + - - +
62A GLU* 3.1 34.4 + - + +
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Residues in contact with LEU 30 (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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26A PRO 3.1 14.1 + - - +
27A LEU* 2.9 16.6 + - + +
29A LYS* 1.3 77.0 - - + +
31A LEU* 1.3 60.7 + - - +
34A PRO* 6.0 1.4 - - - +
37A SER* 4.0 26.4 + - - -
39A CYS* 4.2 8.5 - - + -
42A PHE* 3.7 44.6 - - + +
53A LEU* 5.3 1.3 - - + -
55A VAL* 4.3 12.6 - - + -
59A GLY* 4.1 26.5 - - - +
62A GLU* 4.6 10.3 - - + -
63A LEU* 4.9 9.2 - - + -
232A LEU* 4.0 18.4 - - - +
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Residues in contact with LEU 31 (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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27A LEU* 2.9 29.6 + - + +
28A ILE* 2.9 2.6 + - - -
30A LEU* 1.3 79.7 - - - +
32A PHE* 1.3 85.8 + - + +
33A LEU 4.0 0.2 - - - -
42A PHE* 3.3 32.1 - - + -
44A LEU* 5.0 3.1 - - + -
194A LEU* 3.3 22.5 - - - +
201A LEU* 4.8 2.9 - - + -
205A LEU* 4.3 16.6 - - + -
206A PHE* 4.1 23.3 - - + -
230A PHE* 3.3 35.6 - - + -
232A LEU* 4.7 6.0 - - - +
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Residues in contact with PHE 32 (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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28A ILE* 2.9 25.2 + - + +
31A LEU* 1.3 110.1 - - + +
33A LEU* 1.3 76.1 + - + +
34A PRO* 3.5 13.2 - - - +
194A LEU* 3.9 36.4 - - + +
195A PRO* 5.3 3.4 - - + +
198A ALA* 3.5 39.9 - - + -
201A LEU* 3.6 24.0 - - + -
202A ILE* 3.8 26.9 - - + -
205A LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 33 (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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28A ILE* 4.7 6.7 - - + +
29A LYS* 3.1 39.7 + - + +
30A LEU 5.8 0.2 - - - -
32A PHE* 1.3 94.8 - - + +
34A PRO* 1.3 60.5 - - - +
35A ARG* 2.8 12.2 + - + +
36A ARG* 3.5 40.8 + - + +
37A SER* 3.6 5.9 + - - -
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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