Contacts of the helix formed by residues 20 - 37 (chain A) in PDB entry 4RQO
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 THR 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.2 14.8 - - + -
14A GLY 3.5 22.2 - - - +
15A PRO* 3.5 1.7 - - + +
16A SER* 2.9 31.1 + - - -
19A HIS* 1.3 77.8 - - - +
21A VAL* 1.3 64.0 + - - +
22A GLY 3.5 0.7 - - - -
23A PRO* 3.6 1.1 - - - +
24A MSE 3.2 24.5 + - - +
61A HIS 2.6 25.6 + - - +
62A GLY* 4.5 2.0 - - - +
66A ALA* 3.5 23.2 - - + +
84A MSE 4.8 6.3 - - + -
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Residues in contact with VAL 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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10A SER* 5.8 3.6 - - - +
11A ILE 6.1 0.2 - - - +
12A GLY* 4.6 5.2 - - - -
13A ILE* 3.1 43.3 - - + +
16A SER 3.0 3.6 + - - -
17A SER* 3.8 10.1 - - - +
20A THR* 1.3 80.4 - - - +
22A GLY* 1.3 63.0 + - - +
24A MSE 3.5 5.2 + - - +
25A LEU* 3.0 41.4 + - + +
76A PRO* 4.2 14.7 - - + +
150A GLY 5.1 1.6 - - - +
151A GLY* 4.0 12.1 - - - -
291A ASN* 3.8 12.8 - - - +
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Residues in contact with GLY 22 (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 SER 3.1 12.3 + - - -
21A VAL* 1.3 75.6 - - - +
23A PRO* 1.3 62.5 - - - +
25A LEU* 3.0 4.0 + - - -
26A ALA 2.9 24.1 + - - -
128A MSE 4.7 0.4 - - - -
147A SER* 3.6 15.5 - - - -
151A GLY 3.8 17.3 - - - -
153A ILE* 3.5 15.4 - - - +
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Residues in contact with PRO 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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18A SER 3.3 19.5 - - - +
19A HIS 3.3 26.9 - - - +
20A THR* 3.6 4.0 - - - +
22A GLY* 1.3 89.6 - - - +
24A MSE 1.3 60.7 + - - +
26A ALA* 3.2 3.1 + - - +
27A ALA* 3.0 22.5 + - - +
54A LEU* 4.0 15.3 - - + -
63A THR* 3.9 8.5 - - + +
66A ALA* 5.3 0.2 - - + -
67A ILE* 3.8 27.2 - - + +
128A MSE 3.8 25.1 - - + -
130A PHE* 4.3 0.9 - - - -
147A SER* 3.9 1.1 - - - +
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Residues in contact with MSE 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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13A ILE* 4.5 10.8 - - - -
20A THR 3.2 18.3 + - - +
21A VAL* 3.6 5.4 - - - +
22A GLY 3.2 0.2 - - - -
23A PRO* 1.3 75.6 - - - +
25A LEU* 1.3 58.4 + - - +
27A ALA* 3.2 5.1 + - - +
28A ASN* 3.1 27.8 + - - -
66A ALA* 3.4 32.3 - - + +
69A ASN* 4.1 14.1 - - + -
70A GLY* 4.0 5.6 - - - +
74A LYS* 3.3 35.2 - - + +
75A ALA 3.6 0.4 - - - +
76A PRO* 3.7 26.7 - - + -
79A VAL* 3.2 31.4 - - + -
84A MSE 4.3 5.8 - - - +
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Residues in contact with LEU 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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21A VAL* 3.0 27.8 + - + +
22A GLY 3.0 7.9 + - - +
24A MSE 1.3 72.2 - - - +
26A ALA* 1.3 60.6 + - - +
28A ASN* 3.6 14.0 - - + +
29A ALA* 2.9 27.7 + - - +
75A ALA* 5.2 1.6 - - + -
76A PRO* 3.5 27.4 - - + -
151A GLY 3.7 21.1 - - - +
153A ILE* 3.5 15.8 - - + +
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Residues in contact with ALA 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 GLY 2.9 12.7 + - - +
23A PRO 3.4 8.5 - - - +
25A LEU* 1.3 75.9 - - - +
27A ALA* 1.3 59.8 + - - +
29A ALA* 3.2 5.1 + - - +
30A PHE* 2.8 28.2 + - - +
128A MSE 3.8 24.9 - - + -
130A PHE* 4.0 4.7 - - + -
145A TYR* 3.8 27.7 - - + -
153A ILE* 3.6 10.7 - - + +
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Residues in contact with ALA 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 PRO 3.0 10.3 + - - +
24A MSE 3.2 5.6 + - - +
26A ALA* 1.3 74.7 - - - +
28A ASN* 1.3 56.7 - - - +
30A PHE* 2.7 24.1 + - - +
31A LEU* 3.0 14.5 + - - +
67A ILE* 3.8 9.4 - - + +
70A GLY* 3.6 25.8 - - - -
71A LEU* 3.7 8.9 - - + +
130A PHE* 3.6 29.1 - - + -
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Residues in contact with ASN 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 MSE 3.1 14.9 + - - +
25A LEU* 3.6 17.5 - - + +
27A ALA* 1.3 79.1 - - - +
29A ALA* 1.3 62.4 + - - +
31A LEU* 3.4 7.9 + - - +
32A GLN* 3.2 23.7 + - - +
70A GLY 3.0 18.2 + - - -
73A ASN* 4.0 13.6 - - - +
74A LYS 2.8 30.6 + - - +
75A ALA* 3.4 22.1 - - - +
76A PRO* 4.0 4.9 - - - +
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Residues in contact with ALA 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 LEU 2.9 19.0 + - - +
26A ALA* 3.5 6.1 - - - +
27A ALA 3.1 0.2 - - - -
28A ASN* 1.3 75.9 - - - +
30A PHE* 1.3 58.3 + - - +
32A GLN* 3.4 14.9 + - - +
33A LEU* 2.9 26.7 + - - +
145A TYR* 3.7 20.8 + - + +
153A ILE* 4.6 6.7 - - + -
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Residues in contact with PHE 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 ALA 2.8 12.9 + - - +
27A ALA* 2.7 15.7 + - - +
29A ALA* 1.3 69.0 - - - +
31A LEU* 1.3 65.1 + - + +
33A LEU* 3.1 13.6 + - + +
34A LEU* 3.0 47.6 + - + +
46A VAL* 4.5 7.9 - - + -
71A LEU* 4.7 8.1 - - + -
130A PHE* 3.2 63.0 - + + -
131A SER 4.2 4.5 - - - -
132A ALA* 3.8 23.3 - - + -
141A ILE* 4.0 9.6 - - + -
143A GLN* 3.9 23.3 - - + -
145A TYR* 3.6 9.0 - + - +
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Residues in contact with LEU 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 ALA 3.0 9.5 + - - +
28A ASN* 3.6 6.1 - - - +
30A PHE* 1.3 79.3 - - + +
32A GLN* 1.3 56.7 + - - +
34A LEU* 2.9 30.0 + - + +
35A GLU* 2.9 17.8 + - - +
40A PHE* 5.4 2.4 - - + -
70A GLY 3.4 17.7 - - - +
71A LEU* 3.3 29.6 - - + +
73A ASN* 3.5 26.9 - - - +
99A LEU* 3.8 36.6 - - + -
100A ALA* 3.8 16.2 - - + -
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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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28A ASN 3.2 13.5 + - - +
29A ALA* 3.6 15.0 - - - +
30A PHE 3.3 0.4 - - - -
31A LEU* 1.3 77.5 - - - +
33A LEU* 1.3 56.5 + - - +
35A GLU* 3.6 9.8 + - + +
36A GLN* 3.0 28.8 + - - +
73A ASN* 5.9 1.8 - - - +
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Residues in contact with LEU 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 ALA 2.9 14.0 + - - +
30A PHE* 3.1 17.9 + - + +
32A GLN* 1.3 74.8 - - - +
34A LEU* 1.3 60.0 + - + +
36A GLN* 3.8 18.8 - - - +
37A LYS* 3.2 39.5 + - + +
141A ILE* 3.5 29.0 - - + +
143A GLN* 3.9 41.5 - - + +
145A TYR* 4.5 3.6 - - - +
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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 PHE* 3.0 38.2 + - + +
31A LEU* 2.9 14.4 + - + +
33A LEU* 1.3 77.9 - - - +
35A GLU* 1.3 66.4 + - - +
37A LYS* 6.4 0.2 - - + -
38A ASN* 3.1 2.4 + - - -
39A LEU* 2.9 37.3 + - + +
40A PHE* 3.4 18.1 + - + +
43A THR* 3.8 28.5 - - + +
46A VAL* 4.9 1.6 - - + -
99A LEU* 4.5 11.9 - - + -
132A ALA* 4.0 13.5 - - + -
141A ILE* 3.6 31.2 - - + -
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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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31A LEU* 2.9 12.4 + - - +
32A GLN* 3.8 12.1 - - + +
34A LEU* 1.3 77.2 - - - +
36A GLN* 1.3 57.2 + - - +
38A ASN* 2.6 29.9 + - - +
40A PHE* 3.2 32.2 - - - +
102A LYS* 3.3 32.5 + - - +
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Residues in contact with GLN 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 GLN 3.0 19.4 + - - +
33A LEU* 4.1 17.6 - - - +
34A LEU 3.3 0.4 - - - -
35A GLU* 1.3 77.7 - - - +
37A LYS* 1.3 82.5 + - - +
38A ASN* 3.1 10.3 + - - +
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Residues in contact with LYS 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 LEU* 3.2 23.4 + - + +
36A GLN* 1.3 94.8 - - - +
38A ASN* 1.3 70.9 + - - +
39A LEU* 3.2 25.1 + - + +
141A ILE* 3.7 29.7 - - + +
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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