Contacts of the helix formed by residues 29 - 42 (chain A) in PDB entry 1GXH
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 GLU 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ASP* 1.3 75.9 - - - +
30A LYS* 1.3 58.8 + - + +
31A LYS 3.3 1.6 - - - -
32A GLN* 2.9 27.3 + - - +
33A ASP* 2.9 27.1 + - - +
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Residues in contact with LYS 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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28A ASP* 2.8 28.6 + - - +
29A GLU* 1.3 77.2 - - + +
31A LYS* 1.3 59.3 + - - +
33A ASP* 2.7 34.9 + - - -
34A ASP* 2.9 27.9 + - - +
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Residues in contact with LYS 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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18A ILE* 4.7 5.9 - - - +
21A ASP* 2.8 36.3 + - - +
26A GLU* 3.2 22.4 - - + +
27A GLY* 3.5 21.8 - - - -
28A ASP* 3.9 6.7 - - + +
30A LYS* 1.3 75.7 - - - +
32A GLN* 1.3 57.7 + - + +
34A ASP* 3.0 25.5 + - - +
35A ASN* 3.1 21.9 + - - +
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Residues in contact with GLN 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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21A ASP* 4.9 2.5 - - - +
22A ILE* 3.2 45.3 + - + +
25A CYS* 3.2 33.0 - - - +
27A GLY* 4.2 12.8 - - - -
28A ASP 4.1 3.8 + - - -
29A GLU* 2.9 34.1 + - - +
31A LYS* 1.3 77.4 - - - +
33A ASP* 1.3 56.2 + - - +
34A ASP 3.2 0.2 - - - -
35A ASN* 3.4 4.7 + - - +
36A LEU* 2.9 39.3 + - + +
53A TYR* 6.0 0.4 - - - +
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Residues in contact with ASP 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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29A GLU 2.9 11.4 + - - +
30A LYS* 2.7 39.7 + - - +
32A GLN* 1.3 72.3 - - - +
34A ASP* 1.3 58.5 - - - +
36A LEU* 2.9 27.1 + - - +
37A GLU* 3.1 14.9 + - - +
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Residues in contact with ASP 34 (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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3A LEU* 4.8 15.8 - - - +
18A ILE* 5.4 0.7 - - - +
30A LYS* 2.9 19.9 + - - +
31A LYS* 3.0 40.1 + - - +
32A GLN 3.2 0.4 - - - -
33A ASP* 1.3 74.6 - - - +
35A ASN* 1.3 68.7 + - - +
37A GLU* 3.8 6.0 + - - +
38A HIS* 3.4 18.1 + - - +
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Residues in contact with ASN 35 (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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18A ILE* 3.2 53.9 - - + +
19A ILE* 4.3 0.2 - - - +
22A ILE* 3.1 50.1 - - + +
31A LYS* 3.1 10.7 + - - +
32A GLN 3.4 1.8 - - - +
34A ASP* 1.3 85.9 + - - +
36A LEU* 1.3 65.4 + - - +
38A HIS* 2.8 3.8 + - - +
39A PHE* 2.7 43.9 + - - +
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Residues in contact with LEU 36 (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 ILE* 5.1 2.7 - - + -
32A GLN* 2.9 32.0 + - + +
33A ASP* 2.9 14.6 + - - +
35A ASN* 1.3 83.6 - - - +
37A GLU* 1.3 64.4 + - - +
39A PHE* 3.5 4.6 + - + +
40A ILE* 3.0 30.1 + - - +
49A SER* 3.3 34.8 - - - +
52A ILE* 4.1 18.4 - - + -
53A TYR* 3.6 29.2 - - + +
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Residues in contact with GLU 37 (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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33A ASP 3.1 9.8 + - - +
34A ASP* 4.0 8.3 - - - +
36A LEU* 1.3 74.8 - - - +
38A HIS* 1.3 76.5 + - - +
40A ILE* 2.8 17.3 + - + +
41A SER* 2.6 49.3 + - - -
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Residues in contact with HIS 38 (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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3A LEU* 3.4 34.6 - - + +
4A LYS 3.5 13.0 - - - -
10A TYR* 2.8 39.4 + + - -
18A ILE* 3.5 17.9 - - + -
34A ASP 3.4 11.1 + - - +
35A ASN 2.8 12.8 + - - +
37A GLU* 1.3 87.8 + - - +
39A PHE* 1.3 52.9 + - - +
41A SER* 2.8 22.3 + - - -
42A VAL* 3.0 38.7 + - + +
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Residues in contact with PHE 39 (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 PHE* 3.7 14.6 - + + -
18A ILE* 5.7 0.2 - - - -
19A ILE* 3.2 30.3 - - + -
35A ASN* 2.7 30.4 + - - +
36A LEU* 3.6 8.7 - - + +
38A HIS* 1.3 67.1 - - - +
40A ILE* 1.3 58.4 + - - +
42A VAL* 4.7 0.2 - - - -
43A THR* 2.5 26.2 + - + +
45A HIS* 5.0 1.2 - - + +
48A GLY* 3.3 38.8 - - - -
49A SER* 3.9 4.7 - - - -
51A LEU* 4.1 4.7 - - + -
52A ILE* 3.2 31.6 - - + -
66A VAL* 3.4 28.0 - - + -
70A ILE* 3.8 18.8 - - + -
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Residues in contact with ILE 40 (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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36A LEU 3.0 26.2 - - - +
37A GLU* 2.8 14.0 + - + +
39A PHE* 1.3 76.5 - - + +
41A SER* 1.3 65.2 + - - +
42A VAL 3.7 0.2 - - - -
43A THR* 3.2 1.7 + - - -
44A GLU* 2.9 32.8 + - - -
45A HIS 4.1 7.9 + - - +
46A PRO* 5.2 4.5 - - + +
48A GLY* 3.9 20.4 - - - +
49A SER* 3.8 19.3 - - - +
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Residues in contact with SER 41 (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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37A GLU* 2.6 37.7 + - - -
38A HIS* 2.8 18.0 + - - -
40A ILE* 1.3 83.0 - - - +
42A VAL* 1.3 61.4 + - - -
44A GLU* 3.7 11.1 + - - +
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Residues in contact with VAL 42 (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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4A LYS 3.1 28.5 - - - +
5A ASN 4.1 3.1 - - - -
6A SER* 3.5 18.8 - - - +
7A ILE* 3.2 28.3 + - + +
10A TYR* 3.4 18.6 - - + -
15A PHE* 3.5 31.2 - - + -
38A HIS* 3.0 29.0 + - + +
41A SER* 1.3 72.6 - - - +
43A THR* 1.3 62.0 + - - +
44A GLU* 3.6 2.9 + - - +
74A ARG* 3.5 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