Contacts of the helix formed by residues 21 - 38 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I LEU* 2.7 46.5 + - + +
20I PRO* 1.3 76.6 - - + +
22I ALA* 1.3 57.9 + - - +
23I ASP 3.2 3.1 - - - -
24I GLN* 2.8 35.8 + - + +
25I VAL* 2.8 15.7 + - + +
147I ALA* 3.7 25.8 - - + +
148I VAL* 4.2 13.7 - - + -
151I CYS* 3.7 18.2 - - + -
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Residues in contact with ALA 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I LEU* 3.7 24.6 - - + +
18I LEU 3.2 1.4 + - - -
19I GLU* 2.8 18.0 + - - +
20I PRO 3.5 0.6 - - - -
21I VAL* 1.3 76.9 - - - +
23I ASP* 1.3 58.1 + - - +
25I VAL* 3.2 12.6 - - - +
26I ALA* 2.9 29.3 + - - +
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Residues in contact with ASP 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I PRO 5.3 1.3 + - - +
21I VAL 3.2 1.0 - - - -
22I ALA* 1.3 73.6 - - - +
24I GLN* 1.3 60.7 + - - +
26I ALA* 3.4 8.2 + - - +
27I HIS* 3.0 28.8 + - - +
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Residues in contact with GLN 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I VAL* 2.8 25.6 + - + +
23I ASP* 1.3 75.9 - - - +
25I VAL* 1.3 65.0 + - - +
27I HIS* 3.1 23.8 + - - +
28I MET* 2.9 27.9 + - - +
144I GLY* 2.7 38.0 + - - -
147I ALA* 3.9 20.3 - - + +
148I VAL* 4.4 6.5 - - + +
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Residues in contact with VAL 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ARG 6.0 0.9 - - - +
6I LEU* 4.0 26.2 - - + -
9I LEU* 4.6 11.0 - - + -
18I LEU* 5.5 1.3 - - + -
21I VAL* 2.8 28.6 + - + +
22I ALA* 3.2 21.1 - - - +
24I GLN* 1.3 72.5 - - - +
26I ALA* 1.3 63.6 + - - +
28I MET* 3.1 11.6 + - - +
29I GLY* 3.0 19.1 + - - -
50I LEU* 4.3 27.1 - - + -
145I TRP* 5.0 5.4 - - + -
148I VAL* 4.5 17.1 - - + +
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Residues in contact with ALA 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ARG* 5.0 15.7 - - + +
22I ALA 2.9 18.7 + - - +
23I ASP* 3.5 11.7 - - - +
25I VAL* 1.3 77.7 - - - +
27I HIS* 1.3 56.7 + - - +
29I GLY* 3.1 17.9 + - - -
30I GLN* 3.3 14.8 + - - +
33I ARG* 5.1 2.1 + - - -
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Residues in contact with HIS 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I ASP 3.0 14.5 + - - +
24I GLN* 3.3 26.7 - - - +
26I ALA* 1.3 72.4 - - - +
28I MET* 1.3 82.7 + - - +
30I GLN* 2.9 30.7 + - - +
31I PHE* 2.8 29.4 + - + +
143I LYS 4.8 5.7 + - - -
144I GLY* 5.5 1.3 - - - -
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Residues in contact with MET 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I GLN* 2.9 20.0 + - - +
25I VAL* 3.4 8.1 - - - +
27I HIS* 1.3 86.1 - - - +
29I GLY* 1.3 63.2 + - - +
31I PHE* 3.1 28.6 + - + +
32I LEU* 3.0 27.6 + - - +
143I LYS* 3.5 17.5 - - + +
144I GLY* 3.4 32.1 - - - +
145I TRP* 3.5 68.2 - - + +
148I VAL* 4.6 0.7 - - + -
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Residues in contact with GLY 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I VAL 3.0 12.2 + - - -
26I ALA* 3.1 7.1 + - - -
28I MET* 1.3 75.1 - - - +
30I GLN* 1.3 57.2 + - - +
32I LEU* 2.9 27.5 + - - +
33I ARG* 3.0 27.3 + - - +
145I TRP* 5.4 0.4 - - - -
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Residues in contact with GLN 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ALA* 3.3 7.5 + - - +
27I HIS* 2.9 42.3 + - - +
29I GLY* 1.3 72.6 - - - -
31I PHE* 1.3 61.4 + - - +
33I ARG* 3.3 29.2 - - - +
34I ALA* 3.0 25.3 + - - +
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Residues in contact with PHE 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I HIS* 2.8 24.3 + - + +
28I MET* 3.1 35.8 + - + +
30I GLN* 1.3 77.6 - - - +
32I LEU* 1.3 68.2 + - + +
34I ALA* 3.5 7.2 + - + +
35I GLU* 3.0 51.6 + - + +
140I HIS* 3.6 34.3 - + - -
143I LYS* 3.9 38.4 - - + -
145I TRP* 5.6 0.2 - + - -
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Residues in contact with LEU 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I MET 3.0 17.1 + - - +
29I GLY* 2.9 11.4 + - - +
31I PHE* 1.3 95.7 - - + +
33I ARG* 1.3 64.6 + - + +
35I GLU* 3.2 7.0 + - + +
36I ILE* 3.1 17.7 + - - +
42I TYR* 3.4 59.3 - - + +
49I VAL* 4.2 9.4 - - + -
131I THR* 4.0 29.8 - - + +
140I HIS* 4.3 2.0 - - + -
145I TRP* 4.3 11.9 - - + +
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Residues in contact with ARG 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I ALA 4.9 9.9 + - - -
26I ALA 5.1 1.8 + - - -
29I GLY* 3.0 28.0 + - - +
30I GLN* 3.3 32.1 - - - +
32I LEU* 1.3 73.2 - - + +
34I ALA* 1.3 60.9 + - - +
36I ILE* 3.1 13.8 + - + +
37I ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I GLN 3.0 20.1 + - - +
31I PHE* 3.5 9.9 - - + +
33I ARG* 1.3 75.2 - - - +
35I GLU* 1.3 59.0 + - + +
37I ALA* 3.7 7.3 - - - +
38I ALA* 2.8 30.8 + - - +
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Residues in contact with GLU 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I PHE* 3.0 48.8 + - + +
32I LEU* 3.3 13.5 - - - +
33I ARG 3.2 0.4 - - - -
34I ALA* 1.3 75.8 - - - +
36I ILE* 1.3 60.1 + - - +
38I ALA* 3.3 10.7 + - - +
39I GLY 3.3 0.3 + - - -
40I ARG* 2.5 75.4 + - - +
41I ARG 5.7 0.2 - - - -
42I TYR* 4.7 10.3 - - + +
133I ARG* 5.2 3.1 - - - +
140I HIS* 4.2 16.6 + - + -
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Residues in contact with ILE 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I LEU 3.1 11.3 + - - +
33I ARG* 3.1 13.0 + - + +
35I GLU* 1.3 72.8 - - - +
37I ALA* 1.3 58.7 + - - +
39I GLY* 2.7 27.2 + - - -
40I ARG 3.5 8.5 - - - +
41I ARG* 5.0 8.1 - - + -
42I TYR* 3.7 33.2 - - + +
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Residues in contact with ALA 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ARG 2.9 16.4 + - - +
34I ALA* 3.8 7.4 - - - +
36I ILE* 1.3 77.4 - - - +
38I ALA* 1.3 60.6 + - - +
39I GLY* 3.1 1.6 + - - -
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Residues in contact with ALA 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I ALA 2.8 19.8 + - - +
35I GLU* 3.4 11.0 - - - +
36I ILE 3.1 0.2 - - - -
37I ALA* 1.3 75.5 - - - +
39I GLY* 1.3 57.2 + - - +
40I ARG* 3.4 40.6 + - - +
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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