Contacts of the helix formed by residues 23 - 39 (chain C) 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 ASN 23 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C LEU 6.1 0.2 - - - +
20C PRO* 5.9 4.9 - - + +
22C VAL* 1.3 84.7 + - - +
24C SER* 1.3 52.6 + - - +
25C GLY* 2.8 20.4 + - - -
26C VAL* 2.6 42.2 + - + +
27C LEU* 2.7 14.3 + - - +
106C MET* 3.1 19.2 - - + -
18I ARG* 5.4 0.4 + - - -
609X U 5.7 2.4 + - - -
610X G 5.4 3.8 + - - -
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Residues in contact with SER 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 4.5 2.2 - - - +
23C ASN* 1.3 70.4 + - - +
25C GLY* 1.3 61.8 + - - +
27C LEU* 2.6 12.3 + - - +
28C HIS* 2.3 36.4 + - - +
14I LYS 4.9 2.8 + - - -
15I ASP* 2.7 34.0 - - - +
16I ARG* 4.0 12.4 + - - +
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Residues in contact with GLY 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASN* 2.8 12.3 + - - -
24C SER* 1.3 81.1 + - - +
26C VAL* 1.3 57.8 + - - +
28C HIS* 3.3 3.3 - - - +
29C GLU* 2.9 22.0 + - - +
16I ARG 3.7 2.4 + - - -
17I LYS 3.4 21.5 - - - +
18I ARG* 3.3 26.0 + - - -
21I ARG* 4.3 0.3 - - - -
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Residues in contact with VAL 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASN* 2.6 35.4 + - + +
25C GLY* 1.3 69.7 - - - -
27C LEU* 1.3 61.4 + - - +
28C HIS 3.0 1.1 - - - -
29C GLU* 3.4 1.5 + - - +
30C VAL* 2.7 30.8 + - + +
99C VAL* 3.7 24.5 - - + -
102C LEU* 4.5 12.8 - - + +
103C GLY* 6.4 0.2 - - - -
106C MET* 3.8 17.7 - - + -
18I ARG* 2.9 24.0 - - - +
609X U 4.0 12.1 - - - +
610X G 4.4 15.3 - - - +
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 3.5 10.5 - - + -
23C ASN 2.7 48.3 + - - +
24C SER* 2.6 14.6 + - - +
26C VAL* 1.3 71.8 - - - +
28C HIS* 1.3 62.1 + - - +
30C VAL* 3.3 14.9 - - - +
31C VAL* 2.8 23.6 + - - +
102C LEU 5.7 0.2 - - - +
103C GLY* 5.4 2.2 - - - +
106C MET* 3.3 22.2 - - + -
107C ALA* 4.1 27.1 - - + +
110C SER* 4.8 3.1 - - - +
177C VAL* 4.9 7.2 - - + +
181C LEU* 3.8 32.8 - - + -
15I ASP* 3.9 4.3 - - - +
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Residues in contact with HIS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C SER 2.3 28.2 + - - +
25C GLY 3.3 5.6 - - - +
27C LEU* 1.3 65.2 - - - +
29C GLU* 1.3 69.2 + - - +
30C VAL 2.6 7.1 + - - +
31C VAL* 2.8 21.8 - - + +
32C THR* 3.3 20.6 + - - -
15I ASP* 2.7 29.8 + - + +
16I ARG 3.4 7.9 - - - +
17I LYS* 2.9 32.1 + - + -
21I ARG* 2.7 25.5 + - - +
1257X U 2.9 45.7 + - - -
1258X G 3.7 1.5 - - - -
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Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLY 2.9 11.3 + - - +
26C VAL* 3.5 9.2 - - - +
28C HIS* 1.3 78.3 - - - +
30C VAL* 1.3 67.2 + - - +
32C THR* 4.2 2.0 - - - -
33C TRP* 3.7 5.7 + - - +
93C TYR* 3.7 7.6 + - - +
95C LEU* 3.3 41.3 - - + +
99C VAL* 4.2 14.5 - - + +
18I ARG* 2.8 17.8 + - - +
21I ARG* 3.8 18.5 + - - +
608X G 4.5 5.3 + - - -
609X U 2.6 33.5 + - - +
672X C 4.2 14.2 + - - +
673X G 5.2 2.9 - - - +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL* 2.7 27.4 - - + +
27C LEU* 3.3 11.4 - - - +
28C HIS 2.6 5.4 + - - -
29C GLU* 1.3 76.6 - - - +
31C VAL* 1.3 65.3 + - - +
32C THR 2.4 19.8 + - - -
33C TRP* 2.5 34.8 + - + +
34C GLN* 4.6 2.9 - - + -
95C LEU* 4.0 9.2 - - + -
99C VAL* 4.2 19.5 - - + +
100C ARG* 5.6 4.3 - - - -
103C GLY* 4.3 15.7 - - - -
177C VAL* 3.8 31.0 - - + -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU 2.8 21.8 - - - +
28C HIS* 2.8 23.6 - - + +
30C VAL* 1.3 83.1 - - - +
32C THR* 1.3 57.5 + - - +
34C GLN* 2.4 46.4 + - - +
35C LEU* 3.1 14.4 + - + -
177C VAL* 4.9 6.1 - - + +
178C TYR* 4.0 37.5 - - + +
181C LEU* 5.3 10.1 - - + -
12I SER* 6.1 0.9 - - - +
15I ASP* 4.1 6.1 - - - +
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C HIS* 3.3 30.4 + - - -
29C GLU* 4.2 3.8 - - - -
30C VAL 2.4 8.7 + - - -
31C VAL* 1.3 76.0 - - - +
33C TRP* 1.3 65.6 + - - +
35C LEU* 3.5 12.7 + - - +
36C ALA* 2.8 27.0 + - + +
91C TYR* 4.2 17.7 - - - +
93C TYR* 4.8 5.6 - - + +
21I ARG* 3.7 11.2 + - - +
455X A 4.8 1.0 + - - +
1257X U 5.0 0.2 + - - -
1258X G 4.3 26.7 - - - +
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Residues in contact with TRP 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLU 3.7 4.3 - - - +
30C VAL* 2.5 30.3 + - + +
32C THR* 1.3 75.1 - - - +
34C GLN* 1.3 108.0 + - + +
36C ALA* 3.0 3.6 - - - +
37C SER* 2.9 24.3 + - - -
92C ASP* 5.0 2.6 + - - -
93C TYR* 2.8 60.0 + + - +
94C THR* 4.2 1.9 - - + +
95C LEU* 3.4 35.8 - - + +
100C ARG* 3.6 41.1 - - + -
627X A 4.0 26.5 - - - -
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Residues in contact with GLN 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 4.6 2.7 - - + -
31C VAL* 2.4 31.6 + - - +
33C TRP* 1.3 89.2 - - + +
35C LEU* 1.3 60.2 + - + +
37C SER* 2.4 42.1 + - - -
38C ARG* 2.8 17.2 + - - +
176C ASN* 2.3 29.8 + - - +
177C VAL* 4.1 9.1 + - - +
178C TYR* 3.2 31.3 - - - +
627X A 2.1 36.5 + - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 3.7 20.4 - - + +
32C THR* 3.8 13.2 - - - +
34C GLN* 1.3 71.3 - - - +
36C ALA* 1.3 53.3 + - - +
38C ARG* 2.5 32.7 + - - +
39C ARG 2.4 35.8 + - - -
178C TYR* 3.9 34.1 - - + +
455X A 3.1 25.4 - - + +
1216X G 5.4 13.9 - - - +
1258X G 6.0 2.5 - - - +
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C THR* 2.8 26.0 + - + +
33C TRP* 3.0 12.3 - - - +
35C LEU* 1.3 73.1 - - - +
37C SER* 1.3 55.9 + - - +
39C ARG* 3.3 19.5 - - - +
90C SER 3.9 0.2 - - - +
91C TYR* 2.6 58.2 - - + +
92C ASP* 4.9 0.2 - - - -
93C TYR* 4.1 6.3 - - + -
455X A 3.5 8.6 - - - +
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Residues in contact with SER 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TRP* 2.9 19.8 + - - -
34C GLN* 2.4 34.0 + - - -
36C ALA* 1.3 69.4 - - - +
38C ARG* 1.3 66.2 + - - +
39C ARG 3.1 8.3 + - - +
90C SER 5.0 0.5 - - - +
92C ASP* 4.1 32.9 - - - +
93C TYR 5.7 0.2 - - - -
627X A 4.1 11.8 + - - -
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Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLN* 2.9 29.9 + - - +
35C LEU* 2.5 33.5 + - - +
37C SER* 1.3 80.9 + - - +
39C ARG* 1.3 64.3 + - - +
40C ARG* 3.0 8.1 + - - +
176C ASN* 3.4 13.1 + - - +
178C TYR* 3.3 53.4 - - - +
179C ASP* 5.4 1.2 + - - -
626X A 4.0 26.0 + - - -
627X A 4.4 6.7 + - - +
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU 2.4 25.0 + - - +
36C ALA* 3.3 18.6 - - - +
37C SER 3.1 9.1 - - - +
38C ARG* 1.3 66.8 - - - +
40C ARG* 1.3 81.2 + - - +
41C GLY* 5.1 2.4 - - - -
89C ARG* 4.3 22.6 - - - +
90C SER* 4.0 10.4 - - - +
91C TYR* 3.3 40.1 - - + +
455X A 3.0 65.9 + - + +
456X C 3.6 21.0 + - - -
1259X A 4.1 17.5 + - - -
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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
------------------------------------------------------------
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