Contacts of the helix formed by residues 20 - 35 (chain V) in PDB entry 2ZJQ
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 ALA 20 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16V LYS* 3.5 18.6 - - + +
18V ILE 2.5 6.7 + - - -
19V ASP* 1.3 79.2 + - - +
21V ARG* 1.3 68.2 + - - +
22V LYS 3.1 1.8 - - - -
23V LYS* 2.8 29.6 + - + +
24V GLU* 3.0 11.8 + - - +
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Residues in contact with ARG 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V GLU* 2.9 48.3 + - - +
18V ILE 2.8 4.3 + - - +
20V ALA* 1.3 84.7 - - - +
22V LYS* 1.3 58.6 + - - +
23V LYS 3.1 0.2 - - - -
24V GLU* 3.4 14.9 + - - +
25V LEU* 2.8 30.4 + - - +
42V ARG* 5.8 1.6 - - - +
46V LEU* 3.9 18.8 - - + +
49V GLU* 2.7 41.5 + - - +
50V VAL* 3.5 26.5 - - + -
53V LEU* 3.6 9.9 - - - +
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Residues in contact with LYS 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q SER* 5.5 9.3 + - - +
4Q TYR* 3.5 21.7 - - + +
5Q ASP* 5.5 13.9 + - + +
18V ILE* 3.3 28.1 + - - +
19V ASP* 4.4 8.3 - - - +
20V ALA 3.1 1.0 - - - +
21V ARG* 1.3 76.4 - - - +
23V LYS* 1.3 57.5 + - - +
24V GLU 3.4 0.4 - - - -
25V LEU* 3.6 30.5 - - + +
26V MET* 3.8 11.0 + - - +
29V ARG* 5.3 1.0 + - - -
50V VAL* 4.4 17.7 - - + -
70X A 4.9 4.0 + - - +
71X A 3.6 25.2 + - - +
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Residues in contact with LYS 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q TYR* 3.1 59.0 + - + -
45Q ALA 5.6 1.6 + - - -
19V ASP 3.6 5.2 - - - +
20V ALA* 2.8 20.4 + - + +
22V LYS* 1.3 77.5 - - - +
24V GLU* 1.3 64.7 + - - +
26V MET* 4.0 6.1 - - - +
27V GLU* 3.6 21.0 + - + +
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Residues in contact with GLU 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V ALA 3.0 9.1 + - - +
21V ARG* 3.4 18.1 + - - +
23V LYS* 1.3 76.0 - - - +
25V LEU* 1.3 56.0 + - - +
26V MET 2.5 15.9 + - - -
27V GLU* 2.7 17.4 + - - -
28V LEU* 2.8 25.6 + - + +
42V ARG* 2.8 45.7 + - - +
46V LEU* 2.9 18.7 - - + +
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Residues in contact with LEU 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V ARG 2.8 18.5 + - - +
22V LYS* 3.6 29.6 - - + -
24V GLU* 1.3 74.4 - - - +
26V MET* 1.3 55.9 + - - +
28V LEU* 3.2 5.1 - - + +
29V ARG* 2.9 37.2 + - - +
43V VAL* 3.9 19.5 - - + -
46V LEU* 3.4 22.8 - - + +
47V ARG* 3.8 49.1 - - + +
50V VAL* 5.3 1.8 - - + -
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Residues in contact with MET 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q TYR* 3.8 25.8 - - + +
7Q LEU* 3.3 36.8 - - + -
45Q ALA* 5.0 4.3 - - + +
46Q PHE* 3.5 32.3 - - + -
22V LYS 3.8 14.5 + - - +
23V LYS 4.0 5.8 - - - +
24V GLU 2.5 5.7 + - - +
25V LEU* 1.3 71.7 - - - +
27V GLU* 1.3 95.9 + - + +
28V LEU 2.9 0.9 - - - -
29V ARG* 2.7 21.7 + - - +
30V PHE* 2.7 35.4 + - + +
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Residues in contact with GLU 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Q PHE* 4.4 2.8 - - - -
89Q GLU* 4.3 17.0 - - - +
91Q LEU* 4.3 20.4 - - - +
23V LYS* 3.6 15.7 + - + +
24V GLU* 2.7 10.3 + - - +
26V MET* 1.3 101.2 - - - +
28V LEU* 1.3 61.5 + - + +
30V PHE* 3.1 14.5 - - - +
31V GLN* 2.8 39.9 + - - +
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Residues in contact with LEU 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24V GLU* 2.8 38.2 + - + +
25V LEU* 3.2 12.6 - - + +
26V MET 2.8 0.2 + - - -
27V GLU* 1.3 78.4 - - + +
29V ARG* 1.3 64.0 + - - +
31V GLN* 2.9 24.2 + - - +
32V ALA* 2.8 21.6 + - - +
37V LEU* 5.2 8.0 - - + +
39V GLN* 4.4 14.8 - - + +
42V ARG* 3.9 27.1 - - + -
43V VAL* 4.6 19.3 - - + -
46V LEU* 4.1 13.9 - - + -
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Residues in contact with ARG 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q TYR 4.7 2.2 + - - -
5Q ASP* 6.2 0.2 - - - +
7Q LEU* 3.7 17.1 + - - +
8Q GLN* 2.7 65.9 + - - +
9Q ALA* 4.6 2.3 - - + +
22V LYS 5.3 1.4 + - - -
25V LEU* 2.9 19.7 + - - +
26V MET* 2.7 40.5 + - - +
28V LEU* 1.3 72.9 - - - +
30V PHE* 1.3 65.4 + - - +
32V ALA* 2.9 22.1 - - + +
33V ALA* 3.2 7.4 + - - +
37V LEU* 6.0 0.2 - - - -
43V VAL* 5.8 2.4 - - - +
59X G 5.3 8.5 - - - -
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Residues in contact with PHE 30 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q LEU* 3.2 34.1 - - + -
9Q ALA* 3.5 4.5 - - - -
10Q PRO* 3.2 39.1 - - + +
27Q PHE* 3.9 23.1 - + - -
46Q PHE* 3.9 25.6 - + - -
91Q LEU* 5.3 13.7 - - + -
26V MET* 2.7 26.7 + - + +
27V GLU* 3.1 26.9 - - - +
29V ARG* 1.3 73.5 - - - +
31V GLN* 1.3 73.1 + - - +
32V ALA 2.7 2.1 + - - -
33V ALA* 2.8 10.9 + - - +
34V ALA* 2.9 12.8 + - + +
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Residues in contact with GLN 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V GLU* 2.8 20.9 + - + +
28V LEU* 2.9 26.5 - - - +
30V PHE* 1.3 75.7 - - - +
32V ALA* 1.3 71.6 + - - +
34V ALA* 2.6 12.1 + - - -
35V GLY* 2.6 21.4 + - - -
36V GLN* 4.2 25.8 - - + +
37V LEU* 4.6 8.9 - - + +
38V ALA 5.4 0.2 + - - -
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Residues in contact with ALA 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V LEU 2.8 9.7 + - - +
29V ARG* 2.9 21.3 - - + +
30V PHE 2.7 2.4 + - - -
31V GLN* 1.3 68.0 - - - +
33V ALA* 1.3 55.3 + - - +
34V ALA 2.7 0.3 + - - -
35V GLY* 2.4 34.1 + - - -
36V GLN 4.2 0.2 + - - -
37V LEU* 3.5 39.5 + - + +
60X A 5.4 2.7 - - - +
61X U 5.5 3.6 - - - +
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Residues in contact with ALA 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q ALA* 4.3 21.3 - - + -
10Q PRO* 4.5 9.2 - - + +
12Q ILE* 3.7 26.6 - - + +
29V ARG 4.2 4.7 - - - +
30V PHE 2.8 7.2 + - - +
32V ALA* 1.3 75.8 - - - +
34V ALA* 1.3 55.7 + - - +
35V GLY 3.3 2.0 - - - -
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Residues in contact with ALA 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q PRO* 4.8 8.1 - - + -
12Q ILE* 4.8 9.3 - - + +
94Q GLN* 4.3 20.6 - - - +
30V PHE* 2.9 11.9 + - + +
31V GLN* 2.6 20.9 + - - +
33V ALA* 1.3 73.6 - - - +
35V GLY* 1.3 65.7 + - - +
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Residues in contact with GLY 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31V GLN 2.6 2.5 + - - +
32V ALA 2.4 26.3 + - - -
33V ALA 3.3 1.2 - - - -
34V ALA* 1.3 76.4 - - - +
36V GLN* 1.3 68.9 + - - +
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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