Contacts of the helix formed by residues 21 - 37 (chain M) in PDB entry 2ZHX
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 VAL 21 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M LEU* 2.9 39.8 + - + +
20M PRO* 1.3 80.7 - - + +
22M ALA* 1.3 54.6 + - - +
23M ASP 3.1 3.1 - - - -
24M GLN* 2.6 39.3 + - + +
25M VAL* 2.7 20.8 + - + +
147M ALA* 4.1 13.2 - - + +
148M VAL* 4.2 18.4 - - + -
151M CYS* 3.5 28.7 - - + -
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Residues in contact with ALA 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M ARG 5.4 1.4 - - - +
6M LEU* 3.6 23.3 - - + +
18M LEU 3.5 1.4 + - - -
19M GLU* 2.9 17.4 + - - +
20M PRO 3.4 0.8 - - - -
21M VAL* 1.3 77.7 - - - +
23M ASP* 1.3 60.5 + - - +
25M VAL* 3.1 24.5 - - - +
26M ALA* 3.2 13.3 + - - +
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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
----------------------------------------------------------
20M PRO 5.1 2.0 + - - +
21M VAL* 3.1 1.0 - - - -
22M ALA* 1.3 80.0 - - - +
24M GLN* 1.3 58.9 + - - +
26M ALA* 3.9 6.1 - - - +
27M HIS* 3.0 26.2 + - - +
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Residues in contact with GLN 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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21M VAL* 2.6 32.9 + - + +
23M ASP* 1.3 73.2 - - - +
25M VAL* 1.3 63.7 + - - +
27M HIS* 3.3 26.9 - - - +
28M MET* 3.2 21.7 + - - +
144M GLY* 2.6 39.0 + - - -
147M ALA* 4.0 19.3 - - + +
148M VAL* 4.5 5.1 - - + +
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Residues in contact with VAL 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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4M ARG 5.8 2.7 - - - +
6M LEU* 4.2 20.0 - - + -
9M LEU* 4.5 13.9 - - + -
18M LEU* 6.5 0.2 - - + -
21M VAL* 2.7 22.0 + - + +
22M ALA* 3.1 27.8 - - - +
24M GLN* 1.3 69.9 - - - +
26M ALA* 1.3 61.0 + - + +
28M MET* 2.9 13.9 + - - +
29M GLY* 2.9 23.9 + - - -
50M LEU* 4.4 29.2 - - + -
145M TRP* 5.2 5.2 - - + -
148M VAL* 4.6 18.2 - - + +
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Residues in contact with ALA 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M ARG* 4.6 20.6 - - + +
22M ALA 3.2 14.9 + - - +
23M ASP* 3.9 8.7 - - - +
25M VAL* 1.3 79.6 - - - +
27M HIS* 1.3 66.5 + - - +
29M GLY* 3.0 12.8 + - - +
30M GLN* 3.1 11.6 + - - +
33M ARG* 5.2 0.2 + - - -
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Residues in contact with HIS 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M ASP 3.0 16.3 + - - +
24M GLN* 3.3 28.9 - - - +
26M ALA* 1.3 74.7 - - - +
28M MET* 1.3 81.5 + - - +
30M GLN* 3.0 26.5 + - + +
31M PHE* 3.1 13.3 + - + +
143M LYS 5.1 3.0 + - - -
144M GLY* 5.2 3.0 - - - -
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Residues in contact with MET 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M GLN* 3.3 14.6 - - - +
25M VAL* 2.9 10.2 + - - +
27M HIS* 1.3 85.9 - - - +
29M GLY* 1.3 59.0 + - - +
31M PHE* 2.7 47.8 + - + +
32M LEU* 2.9 20.0 + - + +
143M LYS 3.1 28.3 - - - +
144M GLY* 3.5 21.3 - - - +
145M TRP* 3.5 62.1 - - + +
148M VAL* 4.8 0.9 - - + -
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Residues in contact with GLY 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M ALA 5.9 2.2 - - - -
25M VAL 2.9 12.7 + - - -
26M ALA* 3.0 7.7 + - - -
28M MET* 1.3 75.7 - - - +
30M GLN* 1.3 63.0 + - - +
32M LEU* 3.6 9.8 + - - +
33M ARG* 2.9 39.7 + - - +
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Residues in contact with GLN 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M ALA 3.1 6.8 + - - +
27M HIS* 3.0 18.7 + - + +
29M GLY* 1.3 74.8 - - - +
31M PHE* 1.3 51.6 + - - +
33M ARG* 3.1 25.6 + - - +
34M ALA* 2.8 35.0 + - - +
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Residues in contact with PHE 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 HIS* 3.1 16.0 + - + +
28M MET* 2.7 42.9 + - + +
30M GLN* 1.3 71.2 - - - +
32M LEU* 1.3 73.4 + - + +
34M ALA* 3.0 14.3 + - + +
35M GLU* 2.9 49.8 + - + +
131M THR* 5.1 0.2 - - - -
140M HIS* 4.2 27.8 - + - -
143M LYS* 3.9 41.5 - - + -
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Residues in contact with LEU 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M MET* 2.9 19.4 + - + +
29M GLY* 4.1 8.1 - - - +
31M PHE* 1.3 82.9 - - + +
33M ARG* 1.3 55.8 + - + +
35M GLU* 2.7 32.4 + - + +
36M ILE* 3.0 11.1 + - - +
42M TYR* 3.4 49.0 - - + +
49M VAL* 4.4 10.8 - - + -
131M THR* 3.5 38.8 - - + +
140M HIS* 4.8 5.2 - - + -
145M TRP* 4.5 13.0 - - + +
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Residues in contact with ARG 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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3M ALA 5.3 6.7 + - - -
26M ALA 5.2 0.6 + - - -
29M GLY* 2.9 38.7 + - - +
30M GLN* 3.1 24.6 + - - +
32M LEU* 1.3 71.4 - - + +
34M ALA* 1.3 60.1 + - - +
35M GLU 3.0 4.7 - - - -
36M ILE* 4.2 13.2 - - + +
37M ALA* 3.1 28.4 + - - +
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Residues in contact with ALA 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 GLN 2.8 16.6 + - - +
31M PHE* 3.2 20.9 - - + +
33M ARG* 1.3 72.0 - - - +
35M GLU* 1.3 60.6 + - - +
37M ALA* 4.3 4.7 - - - +
38M ALA* 3.4 20.3 + - - +
40M ARG* 5.4 0.5 + - - -
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Residues in contact with GLU 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 PHE* 2.9 42.3 + - + +
32M LEU* 2.7 18.0 + - - +
34M ALA* 1.3 78.8 - - - +
36M ILE* 1.3 63.5 + - - +
37M ALA 3.2 1.1 - - - -
38M ALA* 2.8 19.1 + - - +
39M GLY 3.5 0.9 + - - -
40M ARG* 2.5 66.3 + - - +
41M ARG 5.3 1.9 - - - +
42M TYR* 5.0 9.4 - - + +
133M ARG* 5.0 5.5 - - - +
140M HIS* 3.9 19.1 + - + +
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Residues in contact with ILE 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 LEU 3.0 13.8 + - - +
33M ARG* 4.2 14.4 - - + +
35M GLU* 1.3 73.8 - - - +
37M ALA* 1.3 59.5 + - - +
39M GLY* 2.9 24.1 + - - -
40M ARG 3.3 11.4 + - - +
41M ARG* 4.9 9.0 - - + -
42M TYR* 3.8 34.5 - - + +
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Residues in contact with ALA 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M ARG 3.1 18.2 + - - +
34M ALA* 4.6 4.7 - - - +
36M ILE* 1.3 79.7 - - - +
38M ALA* 1.3 60.0 + - - +
39M GLY* 3.1 1.7 + - - -
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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
------------------------------------------------------------
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