Contacts of the helix formed by residues 19 - 40 (chain A) in PDB entry 2LOR
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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A HIS 3.2 5.4 + - - -
18A PRO* 1.3 75.8 - - - +
20A LEU* 1.3 61.8 + - - +
22A GLU* 3.9 8.6 - - - +
23A TYR* 3.3 28.6 + - - +
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Residues in contact with LEU 20 (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 4.6 2.0 + - - -
19A GLY* 1.3 72.1 - - - +
21A GLY* 1.3 62.4 + - - +
22A GLU 3.1 0.9 - - - -
23A TYR* 3.1 6.7 + - + +
24A ALA* 2.8 30.9 + - - +
93A LEU* 3.8 29.0 - - + +
94A GLU* 5.1 17.5 - - + +
96A GLY* 6.0 1.8 - - - +
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Residues in contact with GLY 21 (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 ALA* 4.7 13.4 - - - +
17A HIS 5.1 1.4 + - - -
19A GLY 4.4 1.0 - - - +
20A LEU* 1.3 78.3 - - - +
22A GLU* 1.3 57.3 + - - +
24A ALA* 3.3 6.5 + - - +
25A ALA* 2.9 31.5 + - - +
90A TRP* 3.9 33.4 - - - -
94A GLU* 5.3 3.2 + - - -
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 5.7 0.6 + - - -
18A PRO* 3.5 30.3 - - + +
19A GLY* 3.9 16.1 - - - +
20A LEU 3.1 0.4 - - - -
21A GLY* 1.3 76.8 - - - +
23A TYR* 1.3 51.3 + - - +
25A ALA* 3.4 5.6 + - - +
26A CYS* 2.7 47.0 + - - +
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Residues in contact with TYR 23 (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 GLY 3.3 19.5 + - - +
20A LEU* 3.1 7.8 + - + +
22A GLU* 1.3 76.2 - - - +
24A ALA* 1.3 57.2 + - - +
26A CYS* 3.2 8.1 + - + +
27A GLN* 2.7 58.6 + - - +
93A LEU* 5.3 7.6 - - + -
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Residues in contact with ALA 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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20A LEU 2.8 16.4 + - - +
21A GLY* 3.6 8.5 - - - +
23A TYR* 1.3 76.9 - - - +
25A ALA* 1.3 57.3 + - - +
27A GLN* 2.9 18.6 + - - +
28A SER* 2.9 16.0 + - - -
90A TRP* 5.1 15.9 - - + +
93A LEU* 3.8 46.3 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 2.9 17.5 + - - +
22A GLU* 3.8 5.2 - - - +
24A ALA* 1.3 76.6 - - - +
26A CYS* 1.3 53.5 + - - +
28A SER* 3.1 11.0 + - - +
29A HIS* 2.7 37.9 + - - +
86A CYS* 6.1 0.7 - - - -
90A TRP* 4.1 20.3 - - + -
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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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22A GLU* 2.7 31.1 + - - +
23A TYR* 3.5 10.8 - - + +
25A ALA* 1.3 73.7 - - - +
27A GLN* 1.3 57.9 + - - +
29A HIS* 3.7 17.8 + - - +
30A ALA* 3.0 29.5 + - - +
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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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23A TYR* 2.7 37.2 + - - +
24A ALA* 3.1 13.7 - - - +
26A CYS* 1.3 75.0 - - - +
28A SER* 1.3 61.0 + - - +
29A HIS 3.0 1.3 - - - -
30A ALA* 3.2 5.7 + - - +
31A PHE* 3.0 29.6 + - + +
93A LEU* 5.1 13.2 - - + +
100A LYS 5.5 9.1 + - - +
101A ASP* 5.8 3.2 - - - +
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Residues in contact with SER 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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24A ALA 2.9 9.1 + - - -
25A ALA* 3.1 20.1 + - - +
27A GLN* 1.3 76.3 - - - +
29A HIS* 1.3 57.4 + - - +
31A PHE* 3.9 10.4 - - - +
32A MET* 2.9 32.3 + - - +
86A CYS* 4.1 24.3 - - - -
89A LEU* 6.2 6.1 - - - -
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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 ALA 2.7 21.4 + - - +
26A CYS* 3.7 19.8 + - - +
28A SER* 1.3 76.8 + - - +
30A ALA* 1.3 60.0 + - + +
32A MET* 3.2 6.6 + - + +
33A LYS* 2.7 59.6 + - + +
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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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26A CYS 3.0 19.8 + - - +
27A GLN* 3.2 6.3 + - - +
29A HIS* 1.3 81.2 - - + +
31A PHE* 1.3 64.4 - - - +
33A LYS* 3.0 9.8 + - - +
34A GLY* 3.0 19.9 + - - -
104A THR* 4.6 8.6 + - + +
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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 GLN 3.0 16.5 + - - +
28A SER* 3.9 10.8 - - - +
30A ALA* 1.3 76.6 - - - +
32A MET* 1.3 65.0 + - + +
34A GLY* 3.3 2.4 + - - -
35A VAL* 2.9 57.4 + - + +
82A GLU* 5.8 6.1 - - - -
100A LYS* 6.3 2.0 - - - -
102A ARG* 4.2 38.1 - - + -
104A THR* 5.0 7.5 + - - -
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Residues in contact with MET 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER 2.9 22.4 + - - +
29A HIS* 3.6 7.2 - - + +
31A PHE* 1.3 82.4 - - + +
33A LYS* 1.3 60.3 + - - +
35A VAL* 3.8 5.5 - - + +
36A PHE* 2.9 39.3 + - + +
78A VAL* 6.2 3.8 - - + -
82A GLU* 4.6 25.8 - - + +
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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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29A HIS* 2.7 43.7 + - + +
30A ALA* 3.0 9.6 + - - +
32A MET* 1.3 71.3 - - - +
34A GLY* 1.3 60.3 + - - +
36A PHE* 3.1 9.3 + - + +
37A THR* 2.8 40.1 + - + +
106A GLN* 3.2 40.7 - - - +
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Residues in contact with GLY 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 ALA 3.0 12.3 + - - -
31A PHE 3.3 2.7 + - - -
33A LYS* 1.3 73.2 - - - +
35A VAL* 1.3 58.5 + - - +
37A THR* 2.4 24.4 + - - -
38A PHE* 2.9 18.2 + - - +
104A THR* 4.0 26.8 - - - +
106A GLN* 5.6 2.2 - - - +
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Residues in contact with VAL 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 PHE* 2.9 51.3 + - + +
32A MET* 3.8 7.6 - - + +
34A GLY* 1.3 76.3 - - - +
36A PHE* 1.3 58.9 + - - +
38A PHE* 3.5 6.8 - - + +
39A VAL* 2.8 37.5 + - + +
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Residues in contact with PHE 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 MET* 2.9 30.1 + - + +
33A LYS* 3.1 11.2 + - + +
35A VAL* 1.3 79.5 - - - +
37A THR* 1.3 60.8 + - + +
39A VAL* 3.0 12.6 - - + +
40A THR* 2.9 44.9 + - + -
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Residues in contact with THR 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* 2.8 29.2 + - + +
34A GLY* 2.4 28.3 + - - -
36A PHE* 1.3 78.0 - - + +
38A PHE* 1.3 55.9 + - - +
40A THR* 3.4 11.9 - - + +
41A GLY* 3.0 24.1 + - - -
106A GLN* 5.1 15.2 - - + +
107A ARG 5.9 2.9 - - - +
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Residues in contact with PHE 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 GLY 2.9 17.2 + - - +
35A VAL* 3.5 8.7 - - + +
37A THR* 1.3 75.7 + - - +
39A VAL* 1.3 62.6 + - + +
41A GLY* 2.6 26.0 + - - -
42A THR* 4.1 1.7 + - - +
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Residues in contact with VAL 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 VAL* 2.8 31.0 + - + +
36A PHE* 3.0 23.6 - - + +
38A PHE* 1.3 78.6 - - + +
40A THR* 1.3 68.9 + - - +
42A THR* 3.1 27.7 - - + +
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Residues in contact with THR 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 PHE* 2.9 37.6 + - + +
37A THR* 3.4 15.5 - - + +
39A VAL* 1.3 76.6 - - - +
41A GLY* 1.3 56.3 + - - +
42A THR 3.0 10.4 + - - -
43A GLY* 3.5 14.4 + - - +
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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
------------------------------------------------------------
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