Contacts of the helix formed by residues 23 - 34 (chain A) in PDB entry 4D0G
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 GLY 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLY 3.3 0.6 - - - -
22A VAL* 1.3 81.0 - - - +
24A LYS* 1.3 55.9 + - - +
26A CYS* 3.1 2.1 + - - +
27A LEU* 2.8 42.1 + - - +
124A ASN* 3.6 4.2 + - - -
900A GTP 3.0 40.7 + - - -
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Residues in contact with LYS 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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16A ILE* 3.5 35.2 - - + +
17A ILE* 3.3 36.1 - - - +
18A GLY* 2.9 25.1 + - - +
19A ASP 2.9 7.9 + - - -
22A VAL* 3.5 13.5 - - + -
23A GLY* 1.3 76.7 - - - +
25A SER* 1.3 63.5 + - - +
27A LEU* 3.4 5.8 + - - +
28A LEU 3.2 17.0 + - - -
66A ASP* 3.8 9.9 - - - +
67A THR 3.8 19.1 - - - -
69A GLY* 4.1 5.1 - - - +
90A VAL* 4.2 2.0 - - + -
900A GTP 2.7 50.4 + - - +
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Residues in contact with SER 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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24A LYS* 1.3 75.8 - - - +
26A CYS* 1.3 57.0 + - - +
28A LEU* 3.3 3.0 + - - +
29A HIS* 2.9 41.9 + - - -
40A CYS* 4.1 8.7 - - - -
41A PRO* 6.4 0.4 - - - -
42A HIS 6.1 0.9 - - - -
43A THR* 2.7 6.7 + - - -
47A GLU* 5.3 2.2 - - - -
66A ASP* 2.7 22.4 + - - -
900A GTP 3.0 12.0 + - - -
1175A MG 1.9 33.6 - - - -
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Residues in contact with CYS 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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23A GLY 3.6 4.0 - - - +
25A SER* 1.3 74.1 - - - +
27A LEU* 1.3 60.0 + - - +
29A HIS* 3.6 3.4 - - - +
30A GLN* 2.8 31.9 + - - +
36A PHE* 3.4 19.2 - - + -
38A ALA* 3.4 16.4 - - - -
40A CYS* 2.1 47.3 - - - -
155A ALA* 3.5 11.6 - - + +
900A GTP 2.9 30.2 + - + +
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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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16A ILE* 4.9 4.0 - - + -
23A GLY 2.8 22.9 + - - +
24A LYS* 3.6 5.6 - - - +
26A CYS* 1.3 70.9 - - - +
28A LEU* 1.3 67.6 + - - +
30A GLN* 3.3 3.4 + - - +
31A PHE* 3.0 25.0 + - - +
88A LEU* 4.6 13.5 - - + -
90A VAL* 3.7 39.3 - - + -
122A ILE* 4.2 12.1 - - + -
124A ASN* 3.8 23.6 - - + +
153A ALA* 4.6 9.2 - - + -
155A ALA* 3.6 13.9 - - + +
161A VAL* 3.9 21.3 - - + +
165A PHE* 4.7 5.6 - - + -
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Residues in contact with LEU 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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16A ILE* 3.8 11.7 - - + +
24A LYS 3.2 10.1 + - - +
25A SER* 3.4 7.6 - - - +
27A LEU* 1.3 77.9 - - - +
29A HIS* 1.3 68.5 + - + +
31A PHE* 3.3 3.6 + - - +
32A THR* 3.1 50.9 + - + +
47A GLU* 4.7 0.9 - - - +
48A PHE* 4.9 0.7 - - - -
49A GLY* 4.1 15.7 - - - +
64A ILE* 3.9 37.2 - - + +
66A ASP* 3.7 31.0 - - + +
165A PHE* 4.7 3.4 - - - -
638C ILE* 4.2 15.3 - - + -
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Residues in contact with HIS 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 SER* 2.9 36.8 + - - +
26A CYS* 3.9 6.5 - - - +
27A LEU 3.2 0.2 - - - -
28A LEU* 1.3 85.2 - - + +
30A GLN* 1.3 63.2 + - - +
32A THR* 4.1 6.2 + - - -
33A GLU* 3.0 29.4 + - + +
35A LYS 3.6 15.8 - - - +
36A PHE* 6.2 0.2 - - - -
37A MET 5.1 11.5 + - - +
40A CYS* 5.4 4.0 - - - -
47A GLU* 3.8 10.9 + - - -
638C ILE* 3.7 32.5 - - + +
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Residues in contact with GLN 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 CYS 2.8 21.4 + - - +
27A LEU 3.7 4.0 - - - +
29A HIS* 1.3 71.9 - - - +
31A PHE* 1.3 58.2 + - - +
34A LYS* 3.0 50.8 + - - +
35A LYS* 3.6 7.8 + - - +
36A PHE* 3.6 20.6 - - - +
155A ALA* 2.9 32.0 + - - +
156A LYS 3.9 8.5 + - - -
157A THR 4.8 0.4 - - - -
158A GLY* 3.8 25.8 - - - +
161A VAL* 3.8 16.6 - - + -
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Residues in contact with PHE 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 3.0 16.9 + - - +
28A LEU 3.6 4.3 - - - +
30A GLN* 1.3 79.6 - - - +
32A THR* 1.3 64.3 + - + +
33A GLU 3.6 0.5 + - - -
34A LYS* 4.2 2.8 + - - +
51A ARG* 2.5 73.4 + - + +
53A ILE* 4.2 18.4 - - + -
62A LEU* 4.0 6.5 - - + -
64A ILE* 3.7 26.7 - - + -
161A VAL* 3.9 5.1 - - + +
162A GLU* 3.7 27.4 - - + -
165A PHE* 3.4 52.3 - + + -
166A LEU* 5.4 0.7 - - + -
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Residues in contact with THR 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 LEU* 3.1 39.9 + - + +
29A HIS* 4.1 7.1 + - - -
31A PHE* 1.3 94.1 - - + +
33A GLU* 1.3 63.2 + - - +
34A LYS 3.9 0.2 - - - -
49A GLY* 5.1 2.6 - - - -
50A THR 3.9 28.3 - - - +
51A ARG* 4.3 8.7 - - + +
64A ILE* 4.1 6.3 - - + -
638C ILE* 5.9 2.8 - - - +
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Residues in contact with GLU 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 HIS* 3.0 17.0 + - + +
32A THR* 1.3 83.5 - - - +
34A LYS* 1.3 55.4 + - - +
35A LYS* 2.7 29.0 + - + +
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Residues in contact with LYS 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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30A GLN* 3.0 36.5 + - - +
31A PHE 4.2 6.7 + - - +
32A THR 3.9 0.2 - - - -
33A GLU* 1.3 74.7 - - - +
35A LYS* 1.3 56.3 + - - +
51A ARG* 3.7 14.3 - - - +
162A GLU* 3.3 27.0 + - + +
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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