Contacts of the helix formed by residues 32 - 46 (chain A) in PDB entry 5L0U
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 TRP 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A SER* 3.0 13.7 + - - +
31A LYS* 1.3 127.9 - - + +
33A LYS* 1.3 65.4 + - - +
34A VAL 3.2 3.3 + - - -
35A PHE* 3.2 13.5 + + - +
36A ILE* 3.0 25.8 + - + +
323A GLU* 3.8 22.4 - - + -
326A GLN* 3.7 43.1 - - + -
327A PHE* 3.7 41.1 - + + -
330A ALA* 3.6 16.5 - - + +
331A ASN* 3.5 19.7 - - - +
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Residues in contact with LYS 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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30A SER* 2.9 26.5 + - - +
31A LYS 3.4 1.4 - - - -
32A TRP* 1.3 76.5 - - - +
34A VAL* 1.3 58.4 + - + +
36A ILE* 4.4 6.1 - - - -
37A ASP* 2.7 67.3 + - - +
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Residues in contact with VAL 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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31A LYS 5.1 2.2 + - - +
32A TRP 3.2 1.2 + - - -
33A LYS* 1.3 83.1 - - + +
35A PHE* 1.3 71.7 + - + +
37A ASP* 3.8 5.0 - - - +
38A GLN* 2.9 29.0 + - + +
41A ARG* 5.0 1.6 + - - -
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Residues in contact with PHE 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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32A TRP* 3.2 14.3 + + - +
34A VAL* 1.3 87.4 - - + +
36A ILE* 1.3 64.0 + - - +
38A GLN* 3.1 6.5 + - + +
39A ILE* 2.9 28.8 + - - +
308A TRP* 3.7 25.1 - + + -
320A ASN* 5.3 6.7 - - - -
323A GLU* 3.8 41.3 - - + -
324A LEU* 3.8 24.5 - - + -
327A PHE* 3.6 50.3 - + + -
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Residues in contact with ILE 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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30A SER* 4.1 19.1 - - - +
32A TRP* 3.0 24.4 + - + +
33A LYS* 3.7 5.4 - - - +
35A PHE* 1.3 75.7 - - - +
37A ASP* 1.3 68.7 + - - +
39A ILE* 3.3 10.8 + - + +
40A ASN* 3.0 23.3 + - + +
327A PHE* 3.9 15.3 - - + -
331A ASN* 3.7 19.5 - - + +
334A VAL* 5.9 7.2 - - + -
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Residues in contact with ASP 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 LYS* 2.7 61.7 + - - +
34A VAL* 3.8 4.2 - - - +
36A ILE* 1.3 76.1 - - - +
38A GLN* 1.3 65.4 + - - +
40A ASN* 3.3 7.4 + - - +
41A ARG* 2.9 45.4 + - + +
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Residues in contact with GLN 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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34A VAL* 2.9 16.1 + - + +
35A PHE* 3.1 13.4 + - + +
37A ASP* 1.3 78.1 - - - +
39A ILE* 1.3 56.7 + - - +
41A ARG* 2.6 34.7 + - - +
42A SER* 2.9 57.1 + - - +
308A TRP* 3.2 37.9 - - + +
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Residues in contact with ILE 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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35A PHE 2.9 15.2 + - - +
36A ILE* 3.6 8.7 - - - +
38A GLN* 1.3 76.9 - - - +
40A ASN* 1.3 57.7 + - - +
42A SER* 3.3 1.0 + - - -
43A LEU* 2.8 36.5 + - + +
308A TRP* 3.6 44.1 - - + +
327A PHE* 3.5 37.5 - - + -
334A VAL* 3.6 28.3 - - + -
338A ILE* 4.1 6.7 - - + -
341A ARG* 4.5 10.8 - - - +
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Residues in contact with ASN 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 ILE* 3.0 16.0 + - + +
37A ASP* 3.3 11.6 + - - +
39A ILE* 1.3 78.5 - - - +
41A ARG* 1.3 64.5 + - - +
43A LEU* 3.3 6.1 + - - +
44A GLU* 2.8 54.3 + - - +
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Residues in contact with ARG 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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34A VAL 5.0 1.2 + - - -
37A ASP* 2.9 39.4 + - + +
38A GLN* 2.6 46.5 + - - +
40A ASN* 1.3 81.7 - - - +
42A SER* 1.3 58.0 + - - +
44A GLU* 3.1 6.2 + - - +
45A ASN* 2.8 44.8 + - - +
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Residues in contact with SER 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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38A GLN* 2.9 35.2 + - - +
39A ILE 3.8 3.1 - - - -
41A ARG* 1.3 75.5 - - - +
43A LEU* 1.3 61.6 + - - +
45A ASN* 3.4 8.9 + - - +
46A TYR* 3.1 23.2 + - - +
307A PRO* 3.8 18.2 + - - +
308A TRP* 3.7 15.9 - - - -
309A VAL* 3.7 10.2 - - - +
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Residues in contact with LEU 43 (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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39A ILE* 2.8 24.9 + - + +
40A ASN* 3.7 6.3 - - - +
42A SER* 1.3 75.3 - - - +
44A GLU* 1.3 66.0 + - + +
46A TYR* 3.2 25.7 + - + +
308A TRP 6.0 0.4 - - - +
309A VAL* 4.2 13.8 - - + +
337A GLU* 5.6 2.5 - - - +
341A ARG* 3.4 54.7 - - - +
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Residues in contact with GLU 44 (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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40A ASN* 2.8 42.1 + - - +
41A ARG* 3.6 6.1 - - - +
43A LEU* 1.3 77.5 - - + +
45A ASN* 1.3 65.4 + - - +
46A TYR 3.4 4.7 + - - +
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Residues in contact with ASN 45 (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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41A ARG* 2.8 30.3 + - - +
42A SER* 3.7 7.7 - - - +
43A LEU 3.2 0.2 - - - -
44A GLU* 1.3 78.7 - - - +
46A TYR* 1.3 62.1 + - - +
47A GLU* 3.5 11.5 + - - +
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Residues in contact with TYR 46 (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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42A SER 3.1 12.4 + - - +
43A LEU* 3.2 25.2 + - + +
44A GLU 4.2 3.8 - - - +
45A ASN* 1.3 78.0 - - - +
47A GLU* 1.3 71.0 + - - +
48A PRO* 3.4 44.9 - - + +
49A CYS 4.4 2.8 + - - -
304A GLN* 4.4 5.5 + - - -
306A LYS* 3.8 27.4 - - + -
309A VAL* 4.0 22.9 - - + -
310A HIS* 3.3 34.6 + + - -
341A ARG* 5.9 3.1 - - - -
345A PHE* 4.1 15.2 - - - -
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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