Contacts of the helix formed by residues 26 - 41 (chain A) in PDB entry 5L0P
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 SER 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TYR 3.4 3.6 + - - -
25A TRP* 1.3 78.8 - - - +
27A ARG* 1.3 65.0 + - - +
28A ASP* 3.6 8.2 + - - +
29A ASP* 3.0 33.0 + - - -
30A VAL* 3.0 20.8 + - - +
54A ASN* 3.9 7.6 - - - -
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Residues in contact with ARG 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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26A SER* 1.3 75.3 - - - +
28A ASP* 1.3 63.1 + - - +
30A VAL* 3.2 6.8 + - - +
31A ALA* 3.1 19.7 + - + +
51A PHE 4.8 1.6 - - - +
52A GLU* 3.5 28.6 + - - +
53A MET 3.3 31.4 - - - +
54A ASN* 3.9 4.2 - - - +
128A SER* 2.8 48.2 + - - +
129A LEU 3.5 16.6 + - - -
130A ARG* 3.4 26.8 - - - +
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Residues in contact with ASP 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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26A SER* 3.6 7.7 + - - +
27A ARG* 1.3 79.9 - - - +
29A ASP* 1.3 53.2 + - - +
31A ALA* 3.0 11.1 + - - +
32A GLN* 2.8 37.1 + - - +
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Residues in contact with ASP 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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17A HIS* 3.3 34.9 + - - +
18A LEU* 3.6 16.9 - - + +
24A TYR 4.3 2.8 - - - +
25A TRP* 3.6 16.3 - - + -
26A SER* 3.0 37.9 + - - +
27A ARG 3.3 0.2 - - - -
28A ASP* 1.3 75.0 - - - +
30A VAL* 1.3 57.9 + - - +
32A GLN* 3.2 5.6 + - - +
33A TRP* 2.8 32.1 + - - +
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Residues in contact with VAL 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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25A TRP* 4.2 13.2 - - + -
26A SER 3.0 19.0 + - - +
27A ARG 3.3 8.3 - - - +
29A ASP* 1.3 76.6 - - - +
31A ALA* 1.3 62.1 + - - +
33A TRP* 3.2 9.5 + - + +
34A LEU* 3.1 27.8 + - + +
51A PHE* 3.7 36.6 - - + +
53A MET* 3.5 14.8 - - + +
54A ASN 3.8 2.7 - - - +
55A GLY* 3.8 22.9 - - - +
58A LEU* 4.4 15.5 - - + -
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Residues in contact with ALA 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 ARG 3.1 11.8 + - - +
28A ASP* 3.0 15.5 + - - +
30A VAL* 1.3 71.6 - - - +
32A GLN* 1.3 65.4 + - - +
34A LEU* 3.2 22.6 + - - +
35A LYS* 3.2 16.9 + - - +
48A SER* 4.7 21.5 - - - +
51A PHE 6.0 0.4 - - - +
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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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15A PRO* 3.9 12.5 - - - +
17A HIS* 2.6 42.1 + - - -
18A LEU* 4.1 9.6 - - + -
28A ASP 2.8 19.7 + - - +
29A ASP* 3.8 7.6 - - - +
31A ALA* 1.3 72.1 - - - +
33A TRP* 1.3 58.0 + - - +
35A LYS* 3.3 20.3 + - - +
36A TRP* 2.8 29.6 + - + +
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Residues in contact with TRP 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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14A LEU* 4.2 17.9 - - + +
18A LEU* 3.8 12.2 - - + +
25A TRP* 3.5 33.4 - + + -
29A ASP 2.8 13.2 + - - +
30A VAL* 3.2 11.6 + - + +
32A GLN* 1.3 77.3 - - - +
34A LEU* 1.3 93.0 + - + +
36A TRP* 3.3 4.9 + + - +
37A ALA* 2.9 22.9 + - + +
58A LEU* 4.0 21.1 - - + -
66A PHE* 4.2 12.1 - + - -
77A LEU* 3.5 37.7 - - + -
80A LEU* 3.6 27.2 - - + +
81A LEU* 3.9 17.5 - - + -
84A ILE* 3.3 21.2 - - + +
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Residues in contact with LEU 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 VAL* 3.1 21.8 + - + +
31A ALA* 3.2 13.2 + - - +
33A TRP* 1.3 103.2 - - + +
35A LYS* 1.3 58.4 + - - +
37A ALA* 3.2 6.6 + - - +
38A GLU* 2.9 25.0 + - - +
46A ILE* 3.5 35.1 - - + +
47A ASP 4.6 4.7 - - - +
48A SER* 5.2 5.6 - - - +
50A THR* 4.5 2.5 - - - +
51A PHE* 3.7 45.1 - - + +
77A LEU* 3.8 19.3 - - + -
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Residues in contact with LYS 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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31A ALA 3.2 11.3 + - - +
32A GLN* 3.5 21.1 - - - +
34A LEU* 1.3 75.4 - - - +
36A TRP* 1.3 66.0 + - - +
38A GLU* 3.4 11.9 + - - +
39A ASN* 3.2 23.4 + - - +
46A ILE 6.0 1.6 - - - -
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Residues in contact with TRP 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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12A ILE* 2.9 36.8 - - + -
13A ARG 3.5 31.6 + - - -
14A LEU* 3.6 20.4 - - + +
15A PRO* 4.5 13.4 - - + +
18A LEU* 5.1 2.7 - - + -
32A GLN* 2.8 19.8 + - + +
33A TRP* 3.5 9.9 - + - +
34A LEU 3.3 0.2 - - - -
35A LYS* 1.3 78.4 - - - +
37A ALA* 1.3 67.9 + - + +
39A ASN* 3.7 5.3 + - - +
40A GLU* 2.8 64.9 + - + +
41A PHE* 3.9 18.4 - + - -
80A LEU* 4.2 10.8 - - + -
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Residues in contact with ALA 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 TRP* 2.9 17.3 + - + +
34A LEU 3.5 4.5 - - - +
36A TRP* 1.3 81.7 - - + +
38A GLU* 1.3 67.2 + - - +
41A PHE* 2.9 36.8 + - + +
43A LEU* 3.7 2.6 - - + +
77A LEU* 3.7 19.7 - - + -
80A LEU* 3.6 27.8 - - + -
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Residues in contact with GLU 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 LEU 2.9 15.5 + - - +
35A LYS* 3.6 12.8 - - - +
37A ALA* 1.3 76.6 - - - +
39A ASN* 1.3 59.5 + - + +
42A SER* 3.1 10.4 + - - -
43A LEU* 2.9 50.4 + - - +
44A ARG 3.9 2.2 - - - +
45A PRO* 3.4 27.4 - - - +
46A ILE* 2.9 34.7 + - + +
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Residues in contact with ASN 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 LYS 3.2 12.3 + - - +
36A TRP* 3.9 5.0 + - - +
37A ALA 3.2 0.2 - - - -
38A GLU* 1.3 80.8 - - + +
40A GLU* 1.3 69.7 + - - +
41A PHE 3.1 0.9 + - - -
42A SER* 3.5 9.4 + - - +
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Residues in contact with GLU 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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12A ILE* 5.6 5.4 - - + +
13A ARG 5.7 0.7 + - - -
36A TRP* 2.8 59.1 + - + +
37A ALA 3.2 0.2 + - - -
39A ASN* 1.3 79.9 + - - +
41A PHE* 1.3 85.6 + - + +
42A SER* 3.5 1.1 + - - -
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Residues in contact with PHE 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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12A ILE* 4.5 18.8 - - + -
36A TRP* 3.9 7.0 - + - -
37A ALA* 2.9 30.2 + - + +
40A GLU* 1.3 102.7 - - + +
42A SER* 1.3 73.8 + - - +
43A LEU* 3.2 21.5 + - + +
76A GLU* 4.5 24.2 - - - +
80A LEU* 3.9 33.9 - - + -
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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