Contacts of the helix formed by residues 20 - 36 (chain X) in PDB entry 2O5B
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 ASP 20 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16X LYS 4.1 2.6 + - - -
17X VAL 3.2 4.8 + - - -
19X ALA* 1.3 83.3 - - + +
21X ILE* 1.3 55.6 + - - +
22X ALA* 4.0 5.2 + - - +
23X GLY* 3.2 26.1 + - - -
24X HIS* 2.5 46.4 + - + +
118X LYS* 4.6 9.6 + - - -
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Residues in contact with ILE 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X TRP* 4.7 10.8 - - + +
17X VAL* 3.1 19.3 + - + +
18X GLU* 3.9 36.5 + - + +
19X ALA 4.0 1.0 - - - -
20X ASP* 1.3 70.7 + - - +
22X ALA* 1.3 70.3 + - + +
24X HIS* 3.7 3.4 - - - +
25X GLY* 2.8 33.6 + - - -
66X THR* 4.4 19.8 + - + +
69X LEU* 4.0 15.6 - - + +
70X THR* 4.5 21.8 - - - +
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Residues in contact with ALA 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X ASP* 3.4 5.1 + - - +
21X ILE* 1.3 85.4 - - + +
23X GLY* 1.3 55.8 + - - +
25X GLY* 3.5 1.1 + - - -
26X GLN* 3.0 30.1 + - - +
62X LYS* 3.7 34.9 - - + +
66X THR* 3.5 17.9 - - - +
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Residues in contact with GLY 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X ASP* 3.2 24.5 + - - -
22X ALA* 1.3 74.6 - - - +
24X HIS* 1.3 63.8 + - - +
26X GLN* 4.0 10.5 + - - +
27X GLU* 3.1 31.0 + - - +
62X LYS* 5.7 2.5 - - - -
118X LYS* 4.4 8.5 - - - -
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Residues in contact with HIS 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X LYS 3.3 23.4 + - - -
17X VAL* 3.7 24.1 + - + +
20X ASP* 2.5 41.2 + - + +
21X ILE 3.7 1.1 - - - +
23X GLY* 1.3 74.4 - - - +
25X GLY* 1.3 59.5 + - - +
27X GLU* 3.3 2.3 + - - +
28X VAL* 2.9 33.9 + - + +
69X LEU* 3.6 17.0 - - + -
114X VAL* 4.2 8.7 - - + +
115X LEU* 4.5 6.7 - - + -
118X LYS* 3.7 33.3 - - + +
119X HIS* 3.0 29.9 + + - -
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Residues in contact with GLY 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ILE 2.8 19.0 + - - -
22X ALA 3.9 0.9 - - - -
23X GLY 3.4 0.2 - - - -
24X HIS* 1.3 72.9 - - - +
26X GLN* 1.3 57.5 + - - +
28X VAL* 3.6 3.9 + - - +
29X LEU* 3.0 32.4 + - - +
65X GLY* 3.7 24.1 - - - -
69X LEU* 3.3 18.8 - - - +
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Residues in contact with GLN 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X ALA 3.0 17.7 + - - +
23X GLY* 4.0 10.3 + - - +
25X GLY* 1.3 73.4 - - - +
27X GLU* 1.3 65.1 + - + +
29X LEU* 3.2 2.5 + - - +
30X ILE* 3.0 44.8 + - + +
55X MET 4.3 1.4 - - - +
56X LYS* 3.0 48.3 + - - +
58X SER 4.1 6.1 - - - +
61X LEU* 4.2 11.4 - - + +
62X LYS* 3.9 40.1 + - - +
65X GLY* 4.2 2.3 - - - -
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Residues in contact with GLU 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X GLY 3.1 14.1 + - - +
24X HIS 3.3 3.3 + - - +
26X GLN* 1.3 81.0 - - + +
28X VAL* 1.3 67.3 + - - +
30X ILE* 3.8 7.1 - - + +
31X ARG* 2.9 26.0 + - - +
56X LYS* 5.8 4.3 - - - +
114X VAL* 3.8 17.6 - - + +
117X SER* 4.4 9.2 + - - -
118X LYS* 2.3 51.3 + - - +
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Residues in contact with VAL 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X HIS* 2.9 26.6 + - + +
25X GLY* 3.6 7.4 - - - +
27X GLU* 1.3 74.0 - - - +
29X LEU* 1.3 64.2 + - + +
31X ARG* 3.3 2.6 + - - +
32X LEU* 3.0 21.7 + - - +
68X VAL* 5.9 0.7 - - + -
69X LEU* 4.3 14.1 - - + -
107X ILE* 3.5 36.8 - - + +
110X ALA* 3.8 4.8 - - + +
111X ILE* 3.6 30.7 - - + -
114X VAL* 3.7 25.5 - - + +
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Residues in contact with LEU 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X GLY 3.0 20.5 + - - +
26X GLN 3.2 3.8 + - - +
28X VAL* 1.3 75.1 - - + +
30X ILE* 1.3 57.8 + - - +
32X LEU* 3.3 15.6 + - + +
33X PHE* 2.9 59.5 + - + -
43X PHE* 5.1 3.1 - - + -
46X PHE* 4.6 2.5 - - + -
61X LEU* 3.6 19.3 - - + +
64X HIS* 3.6 26.2 - - + -
65X GLY* 3.6 27.8 - - - +
68X VAL* 4.8 6.7 - - + -
107X ILE* 4.1 24.2 - - + -
154X MNH 6.1 1.3 - - + -
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Residues in contact with ILE 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X GLN* 3.0 33.3 + - + +
27X GLU* 3.9 7.6 - - + +
29X LEU* 1.3 73.6 - - - +
31X ARG* 1.3 63.5 + - - +
33X PHE* 3.5 0.7 + - - -
34X THR* 2.8 37.3 + - + +
52X GLU* 4.1 27.1 - - + +
55X MET* 3.7 24.0 - - + -
56X LYS* 3.8 44.0 - - + +
61X LEU* 4.0 8.1 - - + -
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Residues in contact with ARG 31 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27X GLU 2.9 18.3 + - - +
28X VAL 3.6 4.0 - - - +
30X ILE* 1.3 77.5 - - - +
32X LEU* 1.3 61.4 + - - +
34X THR* 3.5 6.3 + - - -
35X GLY* 3.1 27.0 + - - +
36X HIS* 5.0 0.9 - - - -
110X ALA* 3.8 15.7 - - + +
113X HIS* 4.0 42.8 + - + -
114X VAL* 4.4 6.5 - - + -
159X SO4 2.7 49.1 + - - +
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Residues in contact with LEU 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X VAL 3.0 12.4 + - - +
29X LEU* 3.4 13.5 - - + +
31X ARG* 1.3 76.7 - - - +
33X PHE* 1.3 75.4 + - + +
36X HIS* 3.0 35.6 + - + +
39X THR* 3.6 28.7 - - + +
103X TYR 4.5 2.0 - - - +
106X PHE* 3.6 28.0 - - + -
107X ILE* 4.0 23.3 - - + +
110X ALA* 4.1 8.8 - - + +
154X MNH 4.1 24.9 - - + -
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Residues in contact with PHE 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X LEU* 2.9 38.6 + - + +
30X ILE 3.5 0.2 + - - -
32X LEU* 1.3 87.1 - - + +
34X THR* 1.3 58.6 + - - +
36X HIS 3.9 0.2 - - - -
37X PRO* 3.2 30.2 - - - +
39X THR* 3.4 21.5 - - - -
40X LEU* 3.5 30.6 - - + +
43X PHE* 3.6 41.3 - + - -
46X PHE* 3.9 11.2 - + - -
55X MET* 3.9 25.6 - - + +
61X LEU* 3.8 29.6 - - + -
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Residues in contact with THR 34 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30X ILE* 2.8 27.3 + - + +
31X ARG* 3.5 8.5 + - - -
33X PHE* 1.3 76.6 - - - +
35X GLY* 1.3 65.4 + - - +
36X HIS 3.3 0.2 - - - -
37X PRO* 4.1 10.0 - - - +
52X GLU* 3.7 25.4 + - + +
55X MET* 3.6 28.5 - - + -
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Residues in contact with GLY 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X ARG* 3.1 21.1 + - - -
34X THR* 1.3 77.4 + - - +
36X HIS* 1.3 79.3 + - - +
37X PRO* 3.7 5.0 - - - +
159X SO4 5.7 3.4 - - - -
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Residues in contact with HIS 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X ARG 5.0 0.7 - - - -
32X LEU* 3.0 19.5 + - + +
33X PHE 3.6 3.1 - - - +
34X THR 3.3 0.2 - - - -
35X GLY* 1.3 90.4 + - - +
37X PRO* 1.3 59.5 - - - +
38X GLU* 3.2 15.0 + - - +
39X THR* 2.5 40.4 + - + -
106X PHE* 3.5 65.6 - + + -
159X SO4 3.7 23.0 + - - -
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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