Contacts of the helix formed by residues 15 - 26 (chain S) 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 HIS 15 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A PRO* 4.4 16.0 - - + +
296A ASP* 2.4 28.6 + - - +
322A PRO* 5.8 3.4 - - + -
324A ARG* 5.2 13.4 + - - -
12S SER* 2.8 33.5 + - - +
13S GLY 2.9 7.4 + - - +
14S ILE* 1.3 76.4 + - - +
16S ALA* 1.3 78.9 + - + +
18S PRO* 3.3 10.2 - - - +
19S ALA* 3.2 13.7 + - - -
51S MET* 4.7 6.9 + - - +
54S GLY* 4.1 24.6 - - - -
55S ILE 3.5 20.4 + - - -
56S GLN* 5.2 2.6 - - + +
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Residues in contact with ALA 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TYR* 3.5 31.2 - - + -
296A ASP* 2.7 23.9 + - - +
12S SER* 5.4 3.8 - - - +
15S HIS* 1.3 80.1 - - + +
17S ARG* 1.3 68.0 + - + +
18S PRO* 4.2 4.5 - - + -
19S ALA* 3.1 7.8 + - - +
20S THR* 3.0 12.5 + - - -
51S MET* 4.8 0.7 - - - +
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Residues in contact with ARG 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 3.0 38.9 - - - +
84A ASP* 4.0 5.7 + - - +
295A TYR* 3.6 22.8 - - + +
69D ASP* 4.6 8.1 + - - +
99D ASP* 3.6 21.8 + - - -
16S ALA* 1.3 78.5 - - + +
18S PRO* 1.3 55.7 - - + +
20S THR* 2.6 30.1 + - - -
21S THR* 2.7 22.6 + - + +
84S GLU* 3.9 5.2 - - - +
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Residues in contact with PRO 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S SER* 5.7 4.0 - - - +
15S HIS 3.3 11.0 - - - +
16S ALA* 3.6 3.6 - - + -
17S ARG* 1.3 93.6 - - + +
19S ALA* 1.3 55.6 + - - +
21S THR* 2.9 15.2 + - - -
22S LEU* 2.9 19.2 + - - +
84S GLU* 3.0 32.5 - - + +
86S LEU* 3.3 35.6 - - + +
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Residues in contact with ALA 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14S ILE* 3.5 34.5 - - + +
15S HIS* 3.2 18.1 + - - +
16S ALA 3.1 11.9 + - - +
18S PRO* 1.3 78.9 - - - +
20S THR* 1.3 54.1 + - - +
22S LEU* 4.0 2.1 - - - +
23S VAL* 2.6 40.7 + - + +
47S ILE* 5.2 0.7 - - - -
50S VAL* 4.7 2.2 - - + -
51S MET* 4.3 16.2 - - + -
86S LEU* 4.6 0.2 - - - +
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Residues in contact with THR 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP* 4.3 9.2 - - + +
85A ILE* 3.2 35.7 - - + -
88A MSE 3.2 18.6 - - + +
295A TYR* 2.6 30.0 + - + +
16S ALA 3.0 11.0 + - - -
17S ARG 2.6 14.0 + - - -
19S ALA* 1.3 71.0 - - - +
21S THR* 1.3 60.5 + - - -
23S VAL* 3.6 3.3 - - - +
24S GLN* 2.9 33.6 + - - +
47S ILE* 3.8 8.1 - - + -
51S MET* 4.8 1.2 - - - +
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Residues in contact with THR 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S ARG* 2.7 24.9 + - + +
18S PRO 2.9 11.4 + - - -
20S THR* 1.3 73.3 - - - +
22S LEU* 1.3 52.1 + - - +
24S GLN* 3.0 12.8 + - - +
25S ALA* 2.7 37.2 + - - +
80S THR* 3.8 10.5 - - - +
84S GLU* 2.8 41.3 + - - +
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Residues in contact with LEU 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S ILE* 5.0 13.9 - - + -
18S PRO 2.9 13.7 + - - +
19S ALA* 4.2 2.9 - - - +
21S THR* 1.3 78.7 + - - +
23S VAL* 1.3 62.0 + - + +
24S GLN 2.8 5.8 + - - -
25S ALA* 3.5 6.8 + - - -
26S ALA* 3.5 11.8 + - - +
35S LEU* 5.6 1.6 - - + -
44S LEU* 3.5 32.6 - - + +
50S VAL* 5.6 1.1 - - + -
61S ILE* 5.8 0.4 - - + -
63S ILE* 6.0 2.5 - - + -
77S LEU* 4.1 19.6 - - + +
80S THR* 3.9 22.7 - - + -
81S MET* 3.3 50.7 - - + +
86S LEU* 4.2 10.8 - - + -
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Residues in contact with VAL 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A MSE 5.1 6.6 - - + +
19S ALA* 2.6 30.2 + - + +
20S THR 3.6 3.8 - - - +
21S THR 3.3 0.2 - - - -
22S LEU* 1.3 75.9 - - + +
24S GLN* 1.3 59.5 + - - +
26S ALA 4.6 0.9 - - - -
27S SER* 3.8 15.4 + - - -
44S LEU* 3.8 12.7 - - + +
45S LYS* 3.8 26.8 - - - +
46S SEP 3.9 0.4 - - - -
47S ILE* 3.8 35.9 - - + +
50S VAL* 3.7 35.9 - - + -
51S MET* 5.7 0.2 - - + -
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Residues in contact with GLN 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP 5.0 1.2 - - - +
88A MSE 3.0 45.6 - - + +
20S THR* 2.9 18.0 + - - +
21S THR* 3.2 13.3 - - - +
22S LEU 2.8 0.6 - - - -
23S VAL* 1.3 79.4 - - - +
25S ALA* 1.3 58.6 + - - +
26S ALA 3.1 1.8 - - - -
27S SER* 2.6 35.2 + - - -
28S LYS* 3.4 24.3 + - - +
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Residues in contact with ALA 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21S THR 2.7 18.2 + - - +
22S LEU 4.1 4.0 - - - +
24S GLN* 1.3 73.4 - - - +
26S ALA* 1.3 55.7 + - - +
28S LYS* 3.2 32.3 - - + +
29S PHE* 3.3 19.4 - - + -
76S ALA* 5.3 4.9 - - + +
77S LEU* 4.3 7.4 - - + -
80S THR* 3.2 28.7 - - - +
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Residues in contact with ALA 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22S LEU 3.5 4.5 + - - +
23S VAL 5.4 0.2 - - - +
24S GLN 3.1 0.8 - - - -
25S ALA* 1.3 76.0 - - - +
27S SER* 1.3 58.6 + - - +
28S LYS 3.0 6.1 - - - -
29S PHE* 3.5 14.2 + - - +
33S ILE* 3.8 9.2 - - + +
44S LEU* 3.2 25.4 - - + +
45S LYS* 2.8 24.5 - - + +
77S LEU* 3.0 34.5 - - + -
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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
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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