Contacts of the helix formed by residues 30 - 45 (chain C) in PDB entry 1RZR
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 LYS 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C VAL* 1.3 68.3 - - - +
31C PRO* 1.3 65.9 - - + +
32C SER* 3.0 23.3 - - - +
33C THR* 2.8 36.6 + - + +
34C ARG* 2.6 35.3 + - - +
700R C 4.2 7.2 + - - +
701R T 3.3 17.9 + - - +
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Residues in contact with PRO 31 (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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29C VAL 3.2 6.5 - - - +
30C LYS* 1.3 92.0 - - + +
32C SER* 1.3 61.1 + - - +
34C ARG* 4.0 7.4 - - + -
35C LYS* 3.0 36.0 + - + +
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Residues in contact with SER 32 (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 LYS* 3.0 22.4 - - - +
31C PRO* 1.3 79.6 - - - +
33C THR* 1.3 63.4 + - - +
35C LYS* 3.9 1.9 - - - +
36C LYS* 2.9 26.0 + - - +
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Residues in contact with THR 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 5.4 8.7 - - - +
29C VAL* 4.1 2.3 - - - +
30C LYS* 2.8 49.4 + - + +
32C SER* 1.3 77.7 - - - +
34C ARG* 1.3 59.6 + - - +
36C LYS* 3.4 12.8 - - + +
37C VAL* 3.3 24.3 + - - +
701R T 3.3 24.0 + - - +
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Residues in contact with ARG 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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21C ARG 4.7 1.6 + - - -
22C VAL* 4.5 17.5 + - + +
25C GLY* 3.8 11.9 - - - -
26C ASN* 2.9 43.2 + - - +
28C ASN* 4.6 0.8 - - - +
29C VAL* 3.3 43.9 + - + +
30C LYS 2.6 20.1 + - - +
31C PRO* 4.4 5.2 - - - +
33C THR* 1.3 71.4 - - - +
35C LYS* 1.3 84.6 + - + +
36C LYS 2.9 4.5 - - - -
37C VAL* 2.9 24.6 - - - +
38C LEU* 2.9 18.9 + - + +
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Residues in contact with LYS 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 PRO* 3.0 24.0 + - + +
32C SER* 3.9 2.7 - - - +
34C ARG* 1.3 94.3 - - - +
36C LYS* 1.3 58.5 + - - +
38C LEU* 3.8 30.9 - - + +
39C GLU* 2.8 38.5 + - - +
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Residues in contact with LYS 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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11C GLU 3.5 7.4 + - - -
12C ALA* 2.6 42.3 + - + +
13C SER* 4.2 5.9 + - - -
14C VAL* 5.9 1.3 - - + -
32C SER 2.9 19.8 + - - +
33C THR* 3.4 15.3 - - + +
35C LYS* 1.3 80.7 - - - +
37C VAL* 1.3 61.9 + - - +
39C GLU* 2.9 24.9 - - - +
40C THR* 3.3 14.8 + - + +
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 4.3 5.4 - - + -
12C ALA* 3.2 34.1 - - + -
14C VAL* 4.4 10.5 - - + -
19C VAL* 3.8 28.5 - - + -
22C VAL* 3.1 27.8 - - + -
33C THR 3.4 12.8 - - - +
34C ARG 2.9 15.9 - - - +
36C LYS* 1.3 77.3 - - - +
38C LEU* 1.3 64.9 + - - +
39C GLU 2.6 14.8 + - - -
40C THR* 2.8 15.8 + - - -
41C ILE* 2.9 13.7 + - + +
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Residues in contact with LEU 38 (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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22C VAL* 5.1 11.4 - - + +
34C ARG* 2.9 19.2 + - + +
35C LYS* 3.8 35.4 - - + +
37C VAL* 1.3 80.3 - - + +
39C GLU* 1.3 61.6 + - - +
41C ILE* 3.4 30.1 - - + +
42C GLU* 2.9 38.9 + - + +
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Residues in contact with GLU 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 LYS* 2.8 31.6 + - - +
36C LYS* 2.9 16.9 - - - +
37C VAL 2.6 0.6 + - - -
38C LEU* 1.3 80.1 - - - +
40C THR* 1.3 61.9 + - + +
41C ILE 3.0 4.6 + - - -
42C GLU* 3.6 2.8 + - - +
43C ARG* 3.4 26.5 + - + +
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Residues in contact with THR 40 (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 VAL* 4.4 3.3 - - - +
11C GLU* 2.8 53.0 - - - +
12C ALA* 3.4 15.0 + - - +
36C LYS* 3.3 15.0 + - + +
37C VAL 2.8 14.2 + - - -
39C GLU* 1.3 72.3 - - + +
41C ILE* 1.3 61.6 + - - +
43C ARG* 3.3 19.4 - - - +
44C LEU* 2.9 30.8 - - - +
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Residues in contact with ILE 41 (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 VAL* 3.5 26.7 - - + -
19C VAL* 3.9 22.2 - - + -
22C VAL* 3.9 11.7 - - + -
23C VAL* 4.7 7.9 - - + -
37C VAL 2.9 12.5 + - - +
38C LEU* 3.4 29.8 - - + +
39C GLU 3.0 0.4 - - - -
40C THR* 1.3 73.8 - - - +
42C GLU* 1.3 76.3 + - + +
43C ARG 3.0 1.1 - - - -
44C LEU* 3.1 14.6 + - - +
45C GLY 3.5 10.4 + - - -
46C TYR* 4.0 29.9 + - + +
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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
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38C LEU* 2.9 37.2 + - + +
39C GLU* 3.6 2.7 + - - +
41C ILE* 1.3 84.7 - - + +
43C ARG* 1.3 68.9 + - - +
44C LEU 3.2 7.3 + - - +
45C GLY* 4.0 3.9 + - - +
46C TYR 6.2 0.2 - - - -
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Residues in contact with ARG 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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11C GLU* 3.7 19.7 - - - -
39C GLU* 3.4 22.0 + - + +
40C THR* 3.3 20.2 - - - +
41C ILE 3.0 0.4 - - - -
42C GLU* 1.3 78.1 - - - +
44C LEU* 1.3 71.2 + - + +
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Residues in contact with LEU 44 (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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3C VAL* 4.0 35.2 - - + -
7C ASP 5.9 1.3 - - - +
8C VAL* 5.4 5.2 - - + -
11C GLU* 3.7 28.0 - - + +
40C THR 2.9 24.7 - - - +
41C ILE* 3.1 7.1 + - - +
42C GLU 3.6 3.0 - - - +
43C ARG* 1.3 90.7 - - + +
45C GLY* 1.3 60.6 + - - +
46C TYR* 4.0 6.1 - - + +
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Residues in contact with GLY 45 (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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1C MSE 3.3 26.3 + - - +
3C VAL* 5.3 1.0 - - - +
41C ILE 3.5 3.5 + - - -
42C GLU* 4.5 4.7 - - - -
44C LEU* 1.3 77.6 - - - +
46C TYR* 1.3 71.7 + - - +
47C ARG* 3.4 7.3 + - - +
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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