Contacts of the helix formed by residues 17 - 31 (chain A) in PDB entry 2CZ6
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 PRO 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLN 3.8 1.5 - - - +
16A ALA* 1.3 87.9 - - + +
18A VAL* 1.3 66.6 + - - +
19A SER* 3.3 4.3 - - - +
20A ASP* 3.0 43.1 + - - +
21A ARG* 3.1 9.2 + - - +
99B ALA 5.3 0.2 - - - +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA 3.4 2.0 + - - -
17A PRO* 1.3 70.9 - - - +
19A SER* 1.3 60.1 + - - +
21A ARG* 3.1 22.8 + - - +
22A ALA* 2.8 27.9 + - - +
32B TRP* 3.6 42.6 - - + +
74B GLU* 3.6 36.6 - - + +
77B VAL* 5.1 4.9 - - + -
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 3.3 4.1 - - - +
18A VAL* 1.3 81.3 - - - +
20A ASP* 1.3 62.1 + - - +
22A ALA* 3.4 0.3 + - - -
23A TRP* 3.0 50.2 + - - -
32B TRP* 3.8 26.1 - - - -
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Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 4.7 1.1 - - + -
17A PRO* 3.0 39.9 + - + +
19A SER* 1.3 80.6 + - - +
21A ARG* 1.3 57.8 + - - +
23A TRP* 4.2 2.9 - - - +
24A ALA* 3.0 29.5 + - - +
27A ARG* 5.1 1.2 + - - -
98B LEU 4.8 1.3 - - - +
99B ALA* 3.5 27.4 - - - +
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 3.4 28.6 + - - +
16A ALA* 2.7 35.4 + - + +
17A PRO 3.1 9.5 + - - +
18A VAL* 3.5 23.5 - - - +
20A ASP* 1.3 74.6 - - - +
22A ALA* 1.3 64.4 + - - +
24A ALA* 3.3 0.9 + - - +
25A LEU* 3.0 20.1 + - - +
74B GLU* 2.8 42.8 + - - +
77B VAL* 4.3 4.5 - - + +
78B ILE* 4.0 13.7 - - - +
99B ALA* 4.1 5.4 - - + -
102B PRO 3.7 16.2 - - - +
103B PHE* 3.3 51.4 - - + +
104B PRO* 5.6 0.4 + - - +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL 2.8 19.5 + - - +
19A SER 3.9 0.2 - - - +
21A ARG* 1.3 74.7 - - - +
23A TRP* 1.3 61.3 + - - +
25A LEU* 3.3 7.1 + - - +
26A PHE 3.1 16.5 + - - -
32B TRP* 3.8 40.4 - - + +
35B LEU* 3.7 18.0 - - + +
39B LEU* 4.9 0.2 - - - +
77B VAL* 3.9 21.2 - - + +
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Residues in contact with TRP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A SER* 3.0 41.5 + - - +
20A ASP* 4.4 2.7 - - - +
22A ALA* 1.3 73.7 - - - +
24A ALA* 1.3 60.1 + - - +
26A PHE* 3.2 32.2 + + - +
27A ARG* 2.8 51.5 + - + +
40A VAL* 5.5 2.2 - - + -
31B GLU* 3.6 27.1 - - + +
32B TRP* 3.7 16.2 - - + +
34B HIS* 4.2 13.2 - + - -
35B LEU* 3.6 26.9 - - + -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASP 3.0 20.1 + - - +
21A ARG 3.5 5.8 - - - +
22A ALA 3.3 0.2 - - - -
23A TRP* 1.3 77.1 - - - +
25A LEU* 1.3 56.7 - - - +
27A ARG* 3.7 6.3 - - - +
28A ALA* 2.8 32.9 + - - +
95B LEU* 3.7 12.1 - - - +
98B LEU* 3.7 16.5 - - + +
99B ALA* 3.5 28.9 - - + +
103B PHE* 4.7 2.5 - - + -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG 3.0 13.2 + - - +
22A ALA* 3.3 9.8 + - - +
24A ALA* 1.3 76.9 - - - +
26A PHE* 1.3 62.3 + - - +
28A ALA* 3.4 1.0 + - - +
29A LEU* 3.2 38.5 + - + +
35B LEU* 6.3 0.7 - - + -
36B PRO* 5.7 3.1 - - + -
39B LEU* 3.9 17.9 - - + -
77B VAL* 3.9 32.8 - - + +
80B VAL* 4.0 19.7 - - + -
81B ALA* 3.8 24.2 - - + +
84B MET* 4.4 3.8 - - + -
90B LEU* 3.8 21.1 - - + -
95B LEU* 3.7 10.0 - - + +
103B PHE* 4.8 3.4 - - + -
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA 3.1 12.4 + - - +
23A TRP* 3.2 36.5 + + + +
25A LEU* 1.3 78.8 - - - +
27A ARG* 1.3 64.3 + - + +
29A LEU* 3.7 1.7 - - - +
30A ASP* 2.8 66.2 + - + +
35A VAL* 4.3 13.5 - - + -
40A VAL* 3.8 38.6 - - + -
41A GLU* 5.0 8.1 - - - -
35B LEU* 4.1 10.1 - - + -
39B LEU* 3.8 18.7 - - + +
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASP 5.1 1.2 + - - -
23A TRP* 2.8 45.9 + - + +
24A ALA* 3.9 5.8 - - - +
26A PHE* 1.3 84.5 - - + +
28A ALA* 1.3 60.7 + - - +
30A ASP* 4.4 3.4 - - - -
31A GLY* 2.8 28.9 + - - -
98B LEU* 3.0 58.1 + - + +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA 2.8 19.3 + - - +
25A LEU 3.8 4.3 - - - +
27A ARG* 1.3 76.6 - - - +
29A LEU* 1.3 62.6 + - - +
31A GLY* 4.3 0.5 - - - -
32A LYS* 3.4 29.4 + - - +
90B LEU* 3.8 26.9 - - + -
94B GLU* 4.7 9.2 - - + -
95B LEU* 4.1 7.2 - - + -
98B LEU* 3.6 18.3 - - + +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.2 32.3 + - + +
26A PHE 3.8 0.7 - - - +
28A ALA* 1.3 76.3 - - - +
30A ASP* 1.3 65.1 + - - +
32A LYS* 3.1 10.9 + - - +
34A LEU* 3.2 30.3 + - + +
35A VAL* 3.8 15.7 - - + -
39B LEU* 4.0 24.7 - - + -
42B ALA* 6.0 1.6 - - + -
47B LEU* 4.6 3.8 - - + -
84B MET* 3.9 40.8 - - + -
89B ILE* 4.0 10.3 - - + -
90B LEU* 4.0 24.0 - - + -
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 2.8 53.4 + - + +
27A ARG* 4.1 3.8 - - - +
29A LEU* 1.3 73.4 - - - +
31A GLY* 1.3 58.9 + - - +
33A GLY* 3.0 19.8 + - - -
35A VAL* 3.6 30.8 - - + +
36A PRO 5.3 0.2 - - - +
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG 2.8 18.4 + - - -
28A ALA 4.3 0.7 - - - -
30A ASP* 1.3 77.6 + - - +
32A LYS* 1.3 59.7 + - - +
33A GLY 3.4 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
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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