Contacts of the helix formed by residues 24 - 37 (chain A) in PDB entry 4DUB
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 LYS 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 2.8 12.0 + - - +
23A ASP* 1.3 84.5 - - + +
25A PRO* 1.3 66.1 - - - +
27A GLN* 3.3 30.8 + - + +
28A ALA* 3.1 19.9 + - - +
432A ASP* 2.7 29.9 + - - +
433A ILE 3.2 25.7 + - - +
434A LYS* 4.7 4.0 - - - +
435A GLU* 3.2 12.6 - - + +
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Residues in contact with PRO 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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20A LEU* 3.9 24.7 - - + +
22A THR* 3.8 16.6 - - + +
23A ASP* 3.3 11.4 - - - +
24A LYS* 1.3 88.5 - - - +
26A VAL* 1.3 60.7 + - + +
28A ALA* 3.2 1.4 + - - +
29A LEU* 2.8 40.0 + - + +
189A GLN* 5.6 5.4 - - - +
435A GLU* 3.3 12.6 - - + +
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Residues in contact with VAL 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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25A PRO* 1.3 76.5 - - + +
27A GLN* 1.3 56.9 + - + +
29A LEU* 3.1 12.0 + - + +
30A MET* 2.8 33.1 + - - +
325A TRP* 5.8 0.4 - - + -
329A PRO* 3.9 37.9 - - + -
330A ALA* 5.2 7.6 - - + -
356A LEU* 4.1 20.6 - - + +
358A PRO* 4.1 13.9 - - + -
435A GLU* 2.8 28.6 + - - +
439A LEU* 4.9 4.0 - - + -
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Residues in contact with GLN 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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24A LYS* 3.3 25.2 + - + +
26A VAL* 1.3 76.2 - - + +
28A ALA* 1.3 61.7 + - - +
30A MET* 3.4 10.3 + - - +
31A LYS* 3.3 34.3 + - - +
325A TRP* 4.3 22.9 - - + -
433A ILE* 3.0 52.8 + - - +
435A GLU* 2.8 24.2 + - - +
439A LEU* 6.0 0.9 - - + -
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Residues in contact with ALA 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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19A LEU 4.5 8.1 - - - +
20A LEU* 3.5 25.8 - - + -
22A THR* 4.1 10.5 - - + +
24A LYS 3.1 13.5 + - - +
25A PRO 3.6 1.6 - - - +
26A VAL 3.2 0.2 - - - -
27A GLN* 1.3 75.7 - - - +
29A LEU* 1.3 64.1 + - - +
31A LYS* 3.1 27.9 + - - +
32A ILE* 3.1 17.0 + - + +
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Residues in contact with LEU 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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20A LEU* 4.2 16.6 - - + -
25A PRO* 2.8 30.2 + - + +
26A VAL* 3.6 11.2 - - + +
28A ALA* 1.3 75.4 - - - +
30A MET* 1.3 58.9 + - - +
32A ILE* 3.2 10.1 + - + +
33A ALA* 2.9 28.2 + - - +
40A PHE* 3.8 30.8 - - + -
42A PHE* 4.1 18.4 - - + -
51A TYR* 3.5 41.3 - - + +
356A LEU* 3.9 16.9 - - + +
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Residues in contact with MET 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 VAL* 2.8 22.4 + - + +
27A GLN* 3.6 14.8 - - - +
28A ALA 3.2 0.2 - - - -
29A LEU* 1.3 77.0 - - - +
31A LYS* 1.4 57.6 + - + +
33A ALA* 3.3 3.9 + - - +
34A ASP* 3.0 33.4 + - - +
325A TRP* 3.8 25.4 - - + -
356A LEU* 4.0 17.5 - - + +
358A PRO* 3.7 25.6 - - + -
359A GLN* 3.5 19.7 - - + +
362A ARG* 3.6 41.5 - - - +
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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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27A GLN* 3.3 21.8 + - - +
28A ALA* 3.1 18.3 + - - +
30A MET* 1.4 72.7 - - + +
32A ILE* 1.4 66.7 + - + +
34A ASP* 3.4 15.2 + - - +
35A GLU* 3.3 19.9 + - - +
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Residues in contact with ILE 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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8A PRO* 4.0 8.1 - - + -
19A LEU* 4.3 30.7 - - + +
20A LEU* 5.1 1.8 - - + -
28A ALA 3.1 16.3 + - - +
29A LEU* 3.2 17.0 + - + +
31A LYS* 1.4 72.1 - - + +
33A ALA* 1.3 53.9 + - - +
35A GLU* 3.0 14.2 + - - +
36A LEU* 2.8 54.4 + - + +
40A PHE* 3.7 22.0 - - + -
42A PHE* 4.2 24.5 - - + -
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Residues in contact with ALA 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 LEU 2.9 14.0 + - - +
30A MET 3.5 9.0 - - - +
32A ILE* 1.3 75.0 - - - +
34A ASP* 1.3 57.7 + - - +
37A GLY* 2.7 39.6 + - - +
40A PHE* 3.7 16.9 - - + -
53A SER* 3.7 11.2 - - - +
356A LEU* 4.2 2.5 - - + -
359A GLN* 3.6 28.6 + - + -
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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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30A MET* 3.0 19.8 + - - +
31A LYS* 3.5 17.5 - - - +
33A ALA* 1.3 78.8 - - - +
35A GLU* 1.4 60.2 + - - +
37A GLY* 4.7 1.2 + - - -
359A GLN* 2.9 22.3 + - - +
362A ARG* 6.1 0.2 - - - -
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Residues in contact with GLU 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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8A PRO* 5.9 2.9 - - - +
31A LYS 3.3 7.7 + - - +
32A ILE* 3.0 15.9 + - - +
34A ASP* 1.4 81.0 - - - +
36A LEU* 1.3 79.6 + - + +
37A GLY 3.6 0.2 - - - -
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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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6A PRO* 4.2 25.6 - - + +
7A GLN 3.6 11.7 - - - +
8A PRO* 3.4 42.8 - - + -
32A ILE* 2.8 30.0 + - + +
35A GLU* 1.3 98.0 - - + +
37A GLY* 1.3 58.2 + - - +
39A ILE 4.3 1.5 - - - +
40A PHE* 3.7 24.2 - - + -
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Residues in contact with GLY 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 ALA* 2.7 38.4 + - - +
34A ASP 4.6 1.7 + - - -
35A GLU 3.6 1.2 - - - -
36A LEU* 1.3 73.7 - - - +
38A GLU* 1.3 64.1 + - - -
39A ILE* 3.2 4.5 + - - -
40A PHE* 4.4 4.9 - - - -
53A SER* 4.3 4.1 + - - -
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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