Contacts of the helix formed by residues 27 - 40 (chain Q) in PDB entry 5IY8
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 27 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25Q PHE 3.8 1.6 + - - -
26Q TYR* 1.3 79.0 - - - +
28Q ILE* 1.3 61.2 + - - -
29Q GLU* 3.4 3.4 - - - -
30Q HIS* 3.2 11.8 + - - +
31Q ALA* 2.9 24.1 + - - +
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Residues in contact with ILE 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Q GLY* 1.3 70.0 - - - -
29Q GLU* 1.3 69.3 + - + +
31Q ALA* 3.7 10.1 - - + -
32Q LEU* 2.9 37.0 + - + +
190R LEU* 4.0 29.4 - - + -
191R PHE 4.1 11.7 - - - +
192R VAL* 3.6 26.7 - - + -
205R ASP* 5.3 6.5 - - - +
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Residues in contact with GLU 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Q GLY 3.4 0.6 - - - -
28Q ILE* 1.3 85.4 - - + +
30Q HIS* 1.3 70.3 + - - +
32Q LEU* 4.3 3.3 + - - -
33Q ALA* 4.3 8.1 + - - +
54Q PHE* 4.3 21.5 - - + -
58Q GLN* 3.3 23.0 + - + +
62Q VAL* 4.2 12.7 - - + +
192R VAL* 5.4 7.9 - - + -
193R ASN* 5.0 10.5 + - - +
194R ARG* 3.5 25.0 + - - +
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Residues in contact with HIS 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Q TYR* 4.0 26.5 - + + -
27Q GLY* 3.2 14.2 + - - +
28Q ILE 3.2 0.4 - - - -
29Q GLU* 1.3 86.4 - - + +
31Q ALA* 1.3 53.0 + - - +
33Q ALA* 3.4 6.1 + - - +
34Q LEU* 2.8 38.9 + - + +
58Q GLN* 5.9 3.4 - - - -
61Q SER 5.1 0.6 + - - -
62Q VAL* 3.9 43.0 - - + +
65Q ASN* 3.0 33.3 + - - +
66Q LEU* 5.1 3.6 - - + -
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Residues in contact with ALA 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q LYS* 5.2 0.5 + - - -
22Q ILE* 4.2 22.4 - - + +
23Q ARG* 6.0 1.3 - - - -
26Q TYR* 4.8 4.2 - - + +
27Q GLY 2.9 17.4 + - - +
28Q ILE* 3.2 13.6 + - + +
30Q HIS* 1.3 74.0 - - - +
32Q LEU* 1.3 56.6 + - + +
34Q LEU* 3.3 10.8 - - + +
35Q ASP* 2.6 35.7 + - - +
205R ASP* 6.2 0.9 - - - +
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Residues in contact with LEU 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Q ILE* 2.9 19.1 + - + +
29Q GLU 4.7 0.2 - - - +
30Q HIS 3.4 0.4 - - - -
31Q ALA* 1.3 73.3 - - + +
33Q ALA* 1.3 66.4 + - - +
35Q ASP* 3.4 20.7 + - + +
36Q ILE* 3.6 12.6 + - - +
52Q LEU* 4.4 5.3 - - + +
54Q PHE* 3.8 29.4 - - + -
190R LEU* 5.1 7.9 - - + -
192R VAL* 3.6 37.5 - - + -
203R PHE* 4.2 35.7 - - + -
204R ASN 5.0 8.7 - - - +
205R ASP* 5.8 1.1 - - - +
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Residues in contact with ALA 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q GLU 4.3 6.1 + - - +
30Q HIS 3.4 8.7 + - - +
32Q LEU* 1.3 78.3 - - - +
34Q LEU* 1.3 62.7 + - - +
36Q ILE* 3.0 16.8 + - - +
37Q LEU* 3.0 18.6 + - + +
48Q MET* 3.8 17.1 - - + +
52Q LEU* 4.1 21.8 - - + +
54Q PHE* 4.8 2.4 - - + -
59Q LEU* 4.3 12.8 - - + -
62Q VAL* 4.4 14.4 - - + -
63Q LEU* 5.1 0.9 - - + -
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Residues in contact with LEU 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q ILE* 3.5 38.6 - - + -
26Q TYR* 4.2 15.7 - - + -
30Q HIS* 2.8 24.1 + - + +
31Q ALA* 3.2 10.7 + - - +
33Q ALA* 1.3 77.8 - - - +
35Q ASP* 1.3 50.3 + - - +
37Q LEU* 3.2 14.1 + - + +
38Q ILE* 2.7 40.1 + - + +
66Q LEU* 3.8 25.8 - - + +
71Q PHE* 3.5 38.1 - - + -
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Residues in contact with ASP 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q LYS* 2.9 36.7 + - - +
22Q ILE* 6.3 0.2 - - - -
31Q ALA 2.6 19.3 + - - +
32Q LEU* 3.4 15.3 - - + +
34Q LEU* 1.3 75.2 - - - +
36Q ILE* 1.3 62.5 + - + +
38Q ILE* 3.2 18.3 - - - +
39Q ARG 3.4 4.2 + - - -
161R ARG* 3.1 36.7 + - - -
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Residues in contact with ILE 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q LEU 3.8 7.6 - - - +
33Q ALA 3.0 6.8 + - - +
35Q ASP* 1.3 73.9 - - + +
37Q LEU* 1.3 62.8 + - + +
39Q ARG* 2.9 60.8 + - - +
40Q ASN* 3.5 2.6 + - - -
41Q SER 5.0 1.6 + - - -
43Q VAL* 5.8 9.9 - - + -
48Q MET* 4.5 17.0 - - + -
51Q LEU* 4.1 17.3 - - + -
52Q LEU* 3.5 44.6 - - + -
161R ARG* 5.3 0.4 - - - +
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Residues in contact with LEU 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q ALA* 3.0 15.5 + - + +
34Q LEU* 3.2 17.7 + - + +
36Q ILE* 1.3 76.3 - - + +
38Q ILE* 1.3 58.3 + - - +
40Q ASN* 2.8 19.6 + - - +
41Q SER 5.8 2.7 - - - +
43Q VAL* 5.8 5.6 - - + -
48Q MET* 4.0 22.9 - - + -
63Q LEU* 5.1 2.5 - - + -
66Q LEU* 3.6 31.4 - - + -
71Q PHE* 3.6 17.9 - - + -
72Q ILE* 3.9 26.0 - - + -
96Q TYR* 5.6 7.9 - - + +
97Q ARG* 5.8 1.3 - - - -
98Q THR* 3.0 26.8 + - - +
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Residues in contact with ILE 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q LYS* 3.7 37.1 - - + +
18Q ALA* 3.8 30.5 - - + -
19Q LYS* 4.3 30.3 - - + +
22Q ILE* 5.2 6.5 - - + -
34Q LEU* 2.7 25.1 + - + +
35Q ASP* 3.2 17.9 - - - +
36Q ILE 3.1 0.2 - - - -
37Q LEU* 1.3 77.4 - - - +
39Q ARG* 1.3 61.8 + - - +
40Q ASN* 3.1 5.2 + - - +
71Q PHE* 5.0 13.2 - - + -
161R ARG* 5.3 3.1 - - - +
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Residues in contact with ARG 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q LYS* 5.9 3.6 - - - +
35Q ASP 3.8 2.0 - - - +
36Q ILE* 2.9 48.2 + - - +
38Q ILE* 1.3 78.9 - - - +
40Q ASN* 1.3 69.2 + - - +
41Q SER* 4.2 12.1 + - - +
43Q VAL* 5.9 4.6 - - - +
51Q LEU* 3.7 23.2 - - - +
158R HIS 3.5 19.7 - - - +
159R ASP* 3.0 41.8 + - - +
160R GLN 5.9 0.2 - - - -
161R ARG* 3.5 40.5 + - - +
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Residues in contact with ASN 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q ILE 3.5 0.6 + - - -
37Q LEU* 2.8 19.9 + - - +
38Q ILE 4.0 4.9 - - - +
39Q ARG* 1.3 87.0 - - - +
41Q SER* 1.3 66.5 + - - +
97Q ARG* 4.9 2.8 - - - +
98Q THR* 3.2 39.0 + - + +
100Q VAL* 4.4 16.7 - - + +
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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