Contacts of the helix formed by residues 22 - 36 (chain M) in PDB entry 1UW9
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 22 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20M PRO 4.6 3.6 - - - +
21M LEU* 1.3 76.1 - - - +
23M ASP* 1.3 59.7 + - - +
24M GLU* 3.5 10.4 + - - +
25M GLN* 2.9 44.6 + - - +
26M ILE* 2.9 27.4 + - - +
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Residues in contact with ASP 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M LEU 5.3 0.3 - - - +
22M THR* 1.3 74.3 - - - +
24M GLU* 1.3 56.2 + - - +
26M ILE* 3.4 16.7 + - - +
27M ALA* 2.9 29.9 + - - +
90M LEU* 5.6 1.2 - - - +
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Residues in contact with GLU 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M THR* 3.2 9.1 + - - +
23M ASP* 1.3 75.2 - - - +
25M GLN* 1.3 59.1 + - + +
27M ALA* 3.7 7.4 - - - +
28M ALA* 3.0 27.9 + - + +
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Residues in contact with GLN 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PRO* 5.0 2.2 + - - +
20M PRO 3.8 3.8 + - - -
21M LEU* 3.3 23.0 - - + +
22M THR* 2.9 55.4 + - - +
24M GLU* 1.3 74.5 - - + +
26M ILE* 1.3 65.1 + - - +
28M ALA* 3.4 7.9 + - - +
29M GLN* 3.1 28.3 + - - +
429R GLN* 3.7 20.9 + - - +
433R GLU* 4.1 14.4 - - - +
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Residues in contact with ILE 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M LEU* 3.8 31.2 - - + +
22M THR 2.9 20.3 + - - +
23M ASP* 3.7 17.5 - - - +
25M GLN* 1.3 73.1 - - - +
27M ALA* 1.3 65.6 + - - +
29M GLN* 3.0 10.9 + - - +
30M VAL* 3.0 26.4 + - + +
90M LEU* 4.3 17.7 - - + -
93M ILE* 4.6 12.1 - - + -
121M PHE* 4.2 15.3 - - + -
122M LEU 5.9 0.7 - - - +
123M VAL* 4.8 19.3 - - + +
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Residues in contact with ALA 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M ASP 2.9 18.3 + - - +
24M GLU* 3.7 8.7 - - + +
26M ILE* 1.3 76.1 - - - +
28M ALA* 1.3 56.5 + - - +
30M VAL* 3.2 9.6 + - - +
31M ASP* 2.9 36.1 + - - +
86M PRO* 5.5 0.3 - - - +
90M LEU* 4.4 22.9 - - + +
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Residues in contact with ALA 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M GLU* 3.0 17.6 + - + +
25M GLN* 3.6 8.7 - - - +
26M ILE 3.2 0.4 - - - -
27M ALA* 1.3 76.8 - - - +
29M GLN* 1.3 61.1 + - - +
31M ASP* 3.3 13.1 + - - +
32M TYR* 3.1 21.1 + - - +
432R ASN 4.4 4.9 - - - +
433R GLU* 4.0 28.2 - - + +
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Residues in contact with GLN 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M PHE* 3.5 20.6 - - + -
21M LEU* 4.5 6.5 - - + -
25M GLN 3.1 15.5 + - - +
26M ILE 3.0 8.3 + - - +
28M ALA* 1.3 72.1 - - - +
30M VAL* 1.3 65.7 + - - +
32M TYR* 3.2 8.1 + - - +
33M ILE* 3.1 26.6 + - - +
119M MET* 4.1 11.5 - - + +
121M PHE* 3.6 30.7 - - + -
429R GLN* 4.0 22.0 + - - +
432R ASN* 3.0 42.0 + - - +
433R GLU* 4.5 5.9 - - - +
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Residues in contact with VAL 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M ILE* 3.0 20.9 + - + +
27M ALA* 3.2 8.7 + - - +
29M GLN* 1.3 74.5 - - - +
31M ASP* 1.3 63.6 + - - +
33M ILE* 3.1 11.9 + - + +
34M VAL* 3.1 21.1 + - + +
86M PRO* 3.7 25.6 - - + +
89M VAL* 3.7 33.7 - - + -
90M LEU* 4.1 19.3 - - + -
93M ILE* 4.8 0.7 - - + -
107M LEU* 3.8 24.9 - - + -
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Residues in contact with ASP 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M ALA* 2.9 19.6 + - - +
28M ALA* 3.5 14.7 - - - +
30M VAL* 1.3 74.8 - - - +
32M TYR* 1.3 53.5 + - - +
34M VAL* 3.3 5.9 + - - +
35M ALA* 2.7 38.4 + - + +
86M PRO* 3.5 25.3 - - - +
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Residues in contact with TYR 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M ALA 3.1 8.6 + - - +
29M GLN* 3.3 15.7 - - - +
31M ASP* 1.3 77.9 - - - +
33M ILE* 1.3 63.9 + - - +
35M ALA* 3.5 5.3 + - + +
36M ASN* 2.9 51.7 + - - +
38M TRP* 3.4 29.4 - + - -
118M ILE 6.1 0.2 - - - -
119M MET* 5.2 10.5 - - + -
396R ASP* 5.2 0.5 + - - -
431R ARG* 3.5 23.7 + - - -
432R ASN* 3.2 68.1 + - + +
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Residues in contact with ILE 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M GLN 3.1 13.4 + - - +
30M VAL* 3.1 14.1 + - + +
32M TYR* 1.3 78.3 - - + +
34M VAL* 1.3 64.2 + - + +
36M ASN* 3.3 1.2 + - - -
37M GLY 3.2 3.6 + - - -
38M TRP* 3.1 52.6 + - + +
40M PRO* 3.9 19.7 - - + -
89M VAL* 5.5 0.2 - - + -
107M LEU* 3.9 26.2 - - + -
108M VAL 4.6 0.4 - - - +
109M ALA* 3.8 21.1 - - + -
119M MET* 3.5 42.2 - - + -
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Residues in contact with VAL 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M VAL* 3.1 15.2 + - + +
31M ASP* 3.8 5.2 - - - +
33M ILE* 1.3 78.8 - - + +
35M ALA* 1.3 67.5 + - - +
37M GLY* 3.0 14.7 + - - +
38M TRP 5.2 1.6 - - - +
40M PRO* 5.4 1.3 - - + -
83M CYS* 4.7 13.0 - - - +
84M ARG* 3.7 32.0 - - + +
85M ASP 4.4 6.1 - - - +
86M PRO* 4.0 34.8 - - + -
89M VAL* 5.1 2.5 - - + -
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Residues in contact with ALA 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M ASP* 2.7 23.0 + - + +
32M TYR* 3.8 8.3 - - + +
34M VAL* 1.3 75.2 - - - +
36M ASN* 1.3 64.6 + - - +
37M GLY 3.7 0.3 + - - -
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Residues in contact with ASN 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M TYR* 2.9 53.1 + - - +
34M VAL 3.1 0.6 - - - -
35M ALA* 1.3 82.1 - - - +
37M GLY* 1.3 62.9 + - - +
38M TRP* 3.3 44.5 + - + -
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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