Contacts of the helix formed by residues 28 - 44 (chain A) in PDB entry 5LUQ
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 ALA 28 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 1.3 81.7 - - - +
29A LEU* 1.3 74.7 + - + +
30A ALA 3.1 1.1 - - - -
31A GLY* 2.9 14.2 + - - -
32A HIS* 3.7 14.9 - - - -
77A GLU* 3.2 38.3 + - - +
81A CYS* 4.1 3.3 - - - -
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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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28A ALA* 1.3 81.0 - - + +
30A ALA* 1.3 53.2 + - - +
31A GLY 2.6 13.3 + - - -
32A HIS* 2.9 24.6 + - + +
33A GLN* 3.3 33.6 + - + +
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Residues in contact with ALA 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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19A LEU* 3.2 56.2 - - + +
23A ASP* 5.8 0.7 - - - +
26A GLY 6.1 0.2 - - - -
27A ALA* 3.8 21.0 + - - +
28A ALA 3.1 1.0 - - - -
29A LEU* 1.3 75.3 - - - +
31A GLY* 1.3 54.4 + - - +
33A GLN* 4.4 7.6 + - - -
34A LEU* 3.6 1.8 - - - +
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Residues in contact with GLY 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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23A ASP* 6.1 2.7 - - - -
27A ALA* 4.8 1.1 - - - -
28A ALA 2.9 5.7 + - - +
29A LEU 2.6 7.9 + - - -
30A ALA* 1.3 75.9 - - - +
32A HIS* 1.3 53.4 + - - -
33A GLN 3.4 0.2 - - - -
34A LEU* 2.9 12.7 - - - +
35A ILE* 2.8 42.3 + - - +
81A CYS* 3.5 24.6 - - - -
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Residues in contact with HIS 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 ALA 3.7 20.5 + - - -
29A LEU* 2.9 12.6 + - + +
31A GLY* 1.3 72.0 - - - +
33A GLN* 1.3 56.1 + - + +
35A ILE* 2.9 3.4 + - - +
36A ARG* 2.6 53.0 + - - +
77A GLU* 5.9 0.2 - - - +
80A GLU* 3.1 52.8 + - + +
81A CYS* 4.4 3.8 - - - -
84A GLU* 2.7 46.1 + - + +
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Residues in contact with GLN 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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19A LEU* 5.4 4.3 - - + +
29A LEU* 3.3 33.0 + - + +
30A ALA* 4.4 6.2 - - - -
32A HIS* 1.3 74.9 - - + +
34A LEU* 1.3 54.3 + - - +
36A ARG* 3.0 15.3 + - - +
37A GLY* 2.7 33.8 + - - -
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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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15A LEU* 3.4 34.3 - - + +
16A GLN* 3.9 2.0 - - - -
19A LEU* 3.5 51.9 - - + +
20A SER* 4.3 4.7 - - - +
23A ASP* 5.6 3.1 - - + +
30A ALA 3.6 3.4 - - - +
31A GLY* 2.9 17.5 + - - +
33A GLN* 1.3 77.1 - - - +
35A ILE* 1.3 61.9 + - + +
37A GLY* 2.9 4.7 + - - -
38A LEU* 2.8 64.3 + - + +
81A CYS* 6.4 0.4 - - + -
85A ILE* 5.4 6.7 - - + -
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Residues in contact with ILE 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 GLY* 2.8 22.2 + - - +
32A HIS 2.9 0.6 + - - +
34A LEU* 1.3 79.9 - - + +
36A ARG* 1.3 62.3 + - - +
38A LEU* 4.0 5.6 - - + +
39A GLY* 3.0 19.1 + - - -
81A CYS* 3.2 44.0 - - + +
84A GLU* 3.5 19.7 - - + +
85A ILE* 3.4 35.4 - - + +
88A PHE* 3.4 35.8 - - + -
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Residues in contact with ARG 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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32A HIS* 2.6 36.2 + - - +
33A GLN* 3.4 12.4 - - - +
35A ILE* 1.3 73.4 - - - +
37A GLY* 1.3 52.0 + - - +
39A GLY* 3.0 1.6 + - - -
40A GLN* 2.7 58.4 + - - +
84A GLU* 4.6 12.5 + - - +
88A PHE* 4.5 19.9 - - + -
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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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12A LEU* 4.4 6.6 - - - +
15A LEU* 4.8 14.1 - - - -
33A GLN 2.7 17.2 + - - -
34A LEU* 2.9 3.5 + - - -
36A ARG* 1.3 70.2 - - - +
38A LEU* 1.3 53.6 + - - -
39A GLY 2.6 15.7 + - - -
40A GLN* 3.0 11.9 + - - -
41A GLU* 3.6 13.8 + - - +
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Residues in contact with LEU 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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12A LEU* 3.2 44.6 - - + +
15A LEU* 3.6 15.3 - - + -
16A GLN* 3.4 37.9 - - + +
34A LEU* 2.8 43.6 + - + +
35A ILE* 4.0 5.4 - - + +
37A GLY* 1.3 67.8 - - - -
39A GLY* 1.3 56.7 + - - +
42A CYS* 3.3 22.8 - - - +
58A VAL* 5.0 4.4 - - + +
59A PHE* 5.2 0.3 - - - -
62A ASP* 4.7 18.7 - - - +
85A ILE* 6.3 2.0 - - + -
92A PHE* 4.1 8.6 - - - -
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Residues in contact with GLY 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 ILE 3.0 13.7 + - - -
36A ARG 3.0 6.0 + - - -
37A GLY 2.6 7.2 + - - -
38A LEU* 1.3 73.4 - - - +
40A GLN* 1.3 55.0 + - - -
42A CYS* 2.9 8.8 + - - +
43A VAL* 2.7 39.1 + - - +
88A PHE* 4.4 6.5 - - - -
92A PHE* 3.6 18.4 - - - -
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Residues in contact with GLN 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 ARG* 2.7 39.0 + - - +
37A GLY* 3.0 5.0 + - - +
39A GLY* 1.3 68.8 - - - -
41A GLU* 1.3 64.8 + - + +
43A VAL* 2.9 24.6 + - + +
44A LEU* 3.2 18.6 - - + +
88A PHE* 5.6 5.9 - - + -
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Residues in contact with GLU 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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10A CYS 5.2 1.2 + - - -
11A SER* 2.7 31.6 + - - -
12A LEU* 3.4 21.9 - - + +
15A LEU* 4.9 7.3 - - - +
37A GLY* 3.6 7.5 + - - +
39A GLY 3.4 0.4 - - - -
40A GLN* 1.3 78.6 - - - +
42A CYS* 1.3 65.5 + - - +
43A VAL 3.1 0.2 + - - -
44A LEU* 3.4 21.7 + - + +
45A SER* 3.9 4.3 + - - -
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Residues in contact with CYS 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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12A LEU* 3.9 15.2 - - + +
38A LEU 3.3 15.0 - - - +
39A GLY* 2.9 9.7 + - - +
41A GLU* 1.3 79.8 - - - +
43A VAL* 1.3 58.9 + - - +
45A SER* 2.2 29.3 + - - -
55A THR* 3.6 20.7 - - - +
58A VAL* 3.9 19.1 - - - -
59A PHE* 3.3 43.7 - - + -
92A PHE* 5.0 0.7 - - + -
96A MSE 5.6 0.3 - - - +
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Residues in contact with VAL 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 GLY* 2.7 32.6 + - - +
40A GLN* 2.9 13.8 + - + +
42A CYS* 1.3 74.1 - - - +
44A LEU* 1.3 65.5 + - + +
45A SER* 2.6 21.8 + - - +
88A PHE* 5.5 2.9 - - + -
91A ILE* 4.7 8.3 - - + -
92A PHE* 3.6 24.7 - - + -
95A LYS* 3.9 32.2 - - + +
96A MSE 5.5 1.0 - - - +
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Residues in contact with LEU 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 GLN* 3.2 23.5 + - + +
41A GLU* 3.4 12.4 + - + +
43A VAL* 1.3 79.7 - - + +
45A SER* 1.3 51.8 + - - +
46A SER* 2.8 27.4 + - - -
51A LEU* 5.1 0.7 - - - +
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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