Contacts of the helix formed by residues 29 - 46 (chain C) in PDB entry 5Z7R
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 29 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ASN* 3.6 5.2 + - - +
21C ARG* 3.7 25.8 - - - +
28C LEU* 1.3 77.7 - - - +
30C SER* 1.3 68.3 + - - +
31C ASP* 4.1 10.0 + - - +
32C THR* 2.3 43.2 + - - -
33C LEU* 2.9 28.7 + - - +
66C ALA* 5.8 0.4 - - - -
67C ASP* 3.7 16.0 + - + +
70C GLU* 3.6 22.0 + - - +
82C PHE* 5.7 2.2 - - - -
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Residues in contact with SER 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASN* 1.3 75.0 - - - +
31C ASP* 1.3 67.7 + - - +
33C LEU* 3.0 14.4 + - - +
34C LYS* 2.9 39.3 + - - +
70C GLU* 3.1 26.9 + - - +
82C PHE* 4.0 15.7 - - - -
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Residues in contact with ASP 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 5.2 1.4 - - - +
5C ASN* 4.2 10.6 + - - +
29C ASN* 3.3 13.9 + - - +
30C SER* 1.3 83.0 - - - +
32C THR* 1.3 57.5 + - - +
34C LYS* 3.2 13.6 + - - +
35C GLU* 2.9 38.9 + - - +
70C GLU* 4.8 2.0 + - - -
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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
----------------------------------------------------------
5C ASN* 2.6 33.3 + - + +
6C VAL* 4.3 7.9 - - + +
19C ILE* 4.2 18.2 - - + -
21C ARG* 3.6 5.5 - - - -
27C ALA 4.7 1.6 - - - +
28C LEU* 4.0 23.3 - - + -
29C ASN* 2.3 34.0 + - - -
30C SER 3.2 0.2 - - - -
31C ASP* 1.3 77.5 - - - +
33C LEU* 1.3 55.4 + - - +
35C GLU* 3.3 7.1 + - - +
36C MET* 2.9 31.2 + - + +
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 4.3 18.4 - - + -
29C ASN 2.9 21.7 + - - +
30C SER* 3.4 10.8 - - - +
32C THR* 1.3 76.2 - - - +
34C LYS* 1.3 57.8 + - + +
36C MET* 3.2 6.9 + - + +
37C ASP* 2.8 29.5 + - - +
82C PHE* 4.7 10.5 - - + +
85C LEU* 5.7 1.3 - - + -
86C GLY* 4.4 15.3 - - - +
89C VAL* 4.1 18.0 - - + +
90C PHE* 3.8 33.0 - - + -
115C ILE* 5.9 0.2 - - + -
143C PHE* 3.8 28.3 - - + -
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Residues in contact with LYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 4.6 17.0 - - + +
30C SER* 2.9 35.3 + - - +
31C ASP* 3.7 13.2 - - - +
33C LEU* 1.3 75.9 - - + +
35C GLU* 1.3 57.9 + - - +
37C ASP* 3.2 9.1 + - - +
38C TYR* 3.0 28.5 + - - +
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 4.2 16.1 - - + +
2C GLU 4.3 2.6 - - - +
3C LEU* 3.8 22.5 - - + +
4C ASN* 2.9 30.0 + - - +
5C ASN* 2.8 35.3 + - - +
6C VAL* 3.2 17.3 + - + -
31C ASP* 2.9 22.2 + - - +
32C THR 3.6 4.7 - - - +
34C LYS* 1.3 78.9 - - - +
36C MET* 1.3 61.6 + - - +
38C TYR* 3.3 7.4 + - - +
39C VAL* 3.0 30.1 + - - +
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Residues in contact with MET 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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6C VAL* 3.6 21.5 - - + +
17C VAL* 3.8 25.4 - - + -
19C ILE* 3.6 34.8 - - + -
28C LEU* 6.0 1.8 - - + -
32C THR* 2.9 18.6 + - + +
33C LEU* 3.2 8.5 + - + +
35C GLU* 1.3 76.0 - - - +
37C ASP* 1.3 58.5 + - - +
39C VAL* 3.2 8.3 + - - +
40C ILE* 2.8 51.7 + - + +
54C LEU* 4.4 9.2 - - - -
89C VAL* 4.3 10.5 - - + -
90C PHE* 5.9 0.2 - - + -
93C LEU* 5.8 5.4 - - + -
115C ILE* 4.5 16.6 - - + -
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Residues in contact with ASP 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU 2.8 13.8 + - - +
34C LYS* 3.2 13.4 + - - +
36C MET* 1.3 75.1 - - - +
38C TYR* 1.3 64.7 + - - +
40C ILE* 3.2 5.2 + - - +
41C GLY* 3.0 18.2 + - - -
88C LYS* 5.4 10.4 + - - -
89C VAL* 3.9 26.4 - - + +
92C ARG* 2.8 45.2 + - - -
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Residues in contact with TYR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.7 56.0 + - + -
3C LEU* 4.1 22.2 - - + -
8C LEU* 5.8 1.6 - - + -
34C LYS 3.0 13.5 + - - +
35C GLU 3.5 7.2 - - - +
36C MET 3.2 0.2 - - - -
37C ASP* 1.3 77.9 - - - +
39C VAL* 1.3 62.5 + - + +
41C GLY* 3.0 5.9 + - - -
42C GLU* 2.9 63.7 + - + +
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 4.5 10.8 - - + -
6C VAL* 4.0 20.2 - - + -
8C LEU* 4.4 20.2 - - + -
17C VAL* 4.1 24.0 - - + -
35C GLU 3.0 16.9 + - - +
36C MET* 3.7 12.1 - - - +
38C TYR* 1.3 84.5 - - + +
40C ILE* 1.3 72.7 + - + +
42C GLU* 3.7 5.2 - - - +
43C ILE* 3.0 39.1 + - + +
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Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C MET* 2.8 31.6 + - + +
37C ASP* 3.7 5.6 - - - +
39C VAL* 1.3 80.9 - - + +
41C GLY* 1.3 57.9 + - - +
43C ILE* 3.3 9.3 + - + +
44C GLU* 2.9 34.1 + - - +
89C VAL* 3.7 37.0 - - + +
92C ARG* 3.9 28.7 - - + +
93C LEU* 3.9 28.7 - - + +
96C LEU* 4.0 21.0 - - + +
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Residues in contact with GLY 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASP 3.0 11.4 + - - -
38C TYR* 3.0 5.6 + - - -
40C ILE* 1.3 74.8 - - - +
42C GLU* 1.3 65.4 + - - +
44C GLU* 3.1 8.3 + - - +
45C ASN* 3.1 31.7 + - - -
92C ARG* 3.4 23.8 - - - +
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 4.4 17.3 - - + -
10C LYS* 5.3 5.8 + - - +
38C TYR* 2.9 63.9 + - + +
39C VAL* 3.3 9.4 + - - +
41C GLY* 1.3 74.7 - - - +
43C ILE* 1.3 62.1 + - + +
45C ASN* 3.3 14.0 + - - +
46C ASP* 3.3 23.7 + - - +
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Residues in contact with ILE 43 (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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8C LEU* 4.3 9.0 - - + -
10C LYS* 5.9 1.8 - - - -
15C ALA* 4.1 19.7 - - + -
17C VAL* 3.9 28.7 - - + -
39C VAL* 3.0 26.5 + - + +
40C ILE* 3.6 7.6 - - + +
42C GLU* 1.3 75.7 - - + +
44C GLU* 1.3 57.0 + - - +
46C ASP* 3.4 12.5 + - - +
49C VAL* 3.9 21.9 - - + +
52C VAL* 4.0 10.5 - - + -
93C LEU* 6.5 0.4 - - + -
96C LEU* 3.9 23.8 - - + -
98C LYS* 2.8 38.9 + - + -
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ILE* 2.9 16.6 + - - +
41C GLY* 3.1 8.9 + - - +
43C ILE* 1.3 78.9 - - - +
45C ASN* 1.3 67.3 + - - +
46C ASP 3.3 0.9 + - - -
47C SER* 5.7 0.2 - - - -
92C ARG* 2.9 54.7 + - - +
96C LEU* 3.9 20.1 - - + +
97C GLU 6.0 0.2 - - - +
98C LYS* 3.8 10.6 + - - +
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Residues in contact with ASN 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLY* 3.1 21.8 + - - +
42C GLU* 3.3 14.5 + - - +
43C ILE 3.3 0.4 - - - -
44C GLU* 1.3 83.8 - - - +
46C ASP* 1.3 56.3 + - - +
47C SER* 3.3 8.9 + - - -
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Residues in contact with ASP 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LYS* 3.7 24.0 + - - +
42C GLU 3.3 15.5 + - - +
43C ILE* 3.6 3.3 - - - +
44C GLU 3.3 2.0 - - - -
45C ASN* 1.3 74.6 - - - +
47C SER* 1.3 57.7 + - - +
48C GLU* 2.8 32.3 + - - +
49C VAL* 3.0 41.4 + - + +
98C LYS* 3.0 17.7 + - - -
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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
------------------------------------------------------------
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