Contacts of the helix formed by residues 33 - 47 (chain C) in PDB entry 1REP
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 ARG 33 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A T 3.2 30.3 + - - +
14A G 3.2 38.0 + - - -
32C SER* 1.3 73.0 - - - +
34C ASP* 1.3 77.1 + - - +
36C LYS* 2.6 25.6 + - - +
37C ARG* 2.7 55.2 + - - +
73C LEU* 5.6 0.6 - - - +
81C ASP* 4.5 2.0 + - - -
157C ILE 3.4 18.6 + - - +
158C THR* 3.2 37.4 + - - +
160C PRO* 4.1 7.3 - - + +
163C MET* 3.7 24.2 - - - +
252C MG 4.4 5.1 - - - -
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Residues in contact with ASP 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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13A T 4.3 9.0 + - - -
32C SER* 3.4 4.4 + - - +
33C ARG* 1.3 108.2 + - - +
35C GLN* 1.3 61.1 + - - +
37C ARG* 3.8 9.2 + - - +
38C MET* 3.1 33.1 + - + +
67C TYR* 4.0 9.2 - - - +
81C ASP* 3.4 39.8 - - + +
84C GLN* 5.5 2.3 + - - -
85C ALA* 4.1 15.3 - - + -
252C MG 4.1 2.1 - - - -
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Residues in contact with GLN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 3.4 18.6 - - + +
32C SER* 3.0 43.2 + - - +
34C ASP* 1.3 77.6 - - - +
36C LYS* 1.3 58.5 + - - +
38C MET* 3.4 7.5 - - - +
39C LEU* 3.1 24.6 + - - +
85C ALA* 3.2 25.3 + - + +
88C SER* 2.8 49.9 + - - -
89C PHE* 3.5 21.5 - - + +
92C LYS* 3.1 17.8 + - - +
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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
----------------------------------------------------------
29C TYR* 2.8 32.2 + - + +
31C LEU* 4.0 20.2 - - + +
32C SER 2.8 21.9 + - - +
33C ARG 2.6 10.0 + - - +
35C GLN* 1.3 69.2 - - - +
37C ARG* 1.3 64.8 + - - +
38C MET 3.0 1.8 - - - -
39C LEU* 3.0 10.6 + - - +
40C TYR* 3.0 38.2 + - - -
160C PRO* 4.3 11.9 - - + +
163C MET* 3.6 29.2 - - + -
164C ARG* 3.6 20.5 - - + +
167C GLU* 3.1 29.3 + - - -
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A G 5.3 1.4 + - - -
33C ARG* 2.7 74.1 + - + +
34C ASP* 3.9 5.0 + - - +
36C LYS* 1.3 73.2 - - - +
38C MET* 1.3 62.4 + - - +
40C TYR* 3.4 25.0 + - + +
41C LEU* 3.5 7.8 + - - +
67C TYR* 3.6 24.1 + - - +
71C PHE* 3.6 61.3 + - + +
73C LEU* 4.5 15.2 - - - +
81C ASP* 4.8 0.6 + - - -
154C THR 5.4 1.9 + - - +
155C LYS* 3.1 25.3 + - - +
156C GLU* 5.2 0.8 - - - +
157C ILE 4.3 3.4 + - - -
163C MET* 4.8 8.0 - - + +
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Residues in contact with MET 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASP 3.1 24.2 + - - +
35C GLN* 3.4 8.1 - - - +
37C ARG* 1.3 76.7 - - - +
39C LEU* 1.3 64.4 + - - +
41C LEU* 3.4 7.2 + - - +
42C PHE* 3.1 52.7 + - + -
62C ILE* 4.5 9.2 - - + -
67C TYR* 4.1 23.6 - - + +
81C ASP 4.4 0.9 - - - +
82C ILE* 3.8 33.7 - - + +
85C ALA* 3.9 13.7 - - + -
86C LEU* 3.8 28.5 - - - -
89C PHE* 4.8 5.2 - - + -
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Residues in contact with LEU 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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24C LEU* 4.5 13.5 - - + -
29C TYR* 5.1 5.8 - - - +
31C LEU* 4.1 12.8 - - + -
35C GLN 3.1 13.0 + - - +
36C LYS* 3.0 13.9 + - + +
38C MET* 1.3 73.2 - - - +
40C TYR* 1.3 69.1 + - + +
42C PHE* 3.0 22.3 + - + +
43C VAL* 2.9 35.6 + - + +
89C PHE* 5.3 4.5 - - + -
114C TRP* 3.4 45.8 - - + -
131C ILE* 5.0 2.5 - - + -
139C PHE* 4.1 17.5 - - + -
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Residues in contact with TYR 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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18C ILE* 4.1 13.4 - - + +
20C GLN* 4.6 6.3 - - - -
36C LYS* 3.0 22.5 + - - -
37C ARG* 3.4 15.9 - - + +
38C MET 3.3 0.2 - - - -
39C LEU* 1.3 81.4 - - + +
41C LEU* 1.3 59.8 + - + +
43C VAL* 3.0 6.8 + - + +
44C ASP* 2.9 26.2 + - - +
71C PHE* 5.1 4.5 - + - -
149C PHE* 3.6 24.0 - + - -
151C LEU* 3.8 30.3 - - + -
154C THR* 3.3 28.6 + - - +
163C MET* 3.4 32.1 - - + +
167C GLU* 2.3 38.5 + - - +
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Residues in contact with LEU 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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16C PRO* 5.4 1.1 - - + -
18C ILE* 5.6 0.2 - - + -
37C ARG 3.5 9.6 + - - +
38C MET* 3.4 8.0 + - - +
39C LEU 3.2 0.4 - - - -
40C TYR* 1.3 81.4 - - + +
42C PHE* 1.3 62.9 + - - +
44C ASP* 3.7 11.8 - - + +
45C GLN* 3.0 29.7 + - - +
62C ILE* 4.2 20.0 - - + -
66C LYS* 4.2 21.5 - - - +
67C TYR* 4.0 28.7 - - + -
70C ILE* 4.3 17.5 - - + -
71C PHE* 4.1 11.9 - - + -
151C LEU* 3.7 30.5 - - + -
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Residues in contact with PHE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C MET* 3.1 44.2 + - + -
39C LEU* 3.0 27.0 + - + +
41C LEU* 1.3 73.5 - - - +
43C VAL* 1.3 66.4 + - - +
45C GLN* 4.1 2.6 - - - +
46C ILE* 2.9 36.7 + - + +
60C CYS* 3.9 17.7 - - + -
61C GLU 5.2 0.2 - - - -
62C ILE* 3.2 34.8 - - + -
86C LEU* 4.9 0.2 - - + -
89C PHE* 4.7 5.4 - + - -
115C PHE* 4.0 21.3 - + - -
129C VAL* 3.6 27.8 - - + -
131C ILE* 3.6 20.4 - - + -
139C PHE* 5.8 0.2 - - + -
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Residues in contact with VAL 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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18C ILE* 4.4 12.6 - - + -
19C VAL 4.4 9.0 - - - +
20C GLN* 4.7 14.1 - - + +
24C LEU* 5.1 7.0 - - + -
39C LEU* 2.9 31.3 + - + +
40C TYR* 3.6 6.5 - - + +
42C PHE* 1.3 73.4 - - - +
44C ASP* 1.3 72.0 + - - +
46C ILE* 2.8 11.4 + - + +
47C ARG* 2.8 32.4 + - + +
139C PHE* 3.6 40.2 - - + +
140C ILE* 5.1 0.4 - - + -
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Residues in contact with ASP 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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16C PRO* 3.7 30.3 - - - +
17C ARG 4.9 6.9 + - - +
18C ILE* 4.2 17.4 - - + +
40C TYR 2.9 15.1 + - - +
41C LEU* 3.7 11.6 - - + +
43C VAL* 1.3 80.0 - - - +
45C GLN* 1.3 63.6 + - - +
47C ARG* 2.9 16.9 + - - +
48C LYS* 2.9 45.6 + - - +
66C LYS* 5.3 6.8 + - - -
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Residues in contact with GLN 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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41C LEU* 3.0 18.0 + - - +
42C PHE* 4.1 5.4 - - - +
44C ASP* 1.3 79.8 - - - +
46C ILE* 1.3 60.4 + - - +
48C LYS* 3.3 21.0 - - - +
49C SER* 2.8 25.7 - - - +
56C HIS* 5.8 2.0 - - - +
60C CYS* 3.1 21.4 - - - +
61C GLU* 2.9 53.7 + - - +
62C ILE* 5.0 1.7 - - - +
66C LYS* 5.8 4.9 + - - +
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Residues in contact with ILE 46 (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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42C PHE* 2.9 32.8 + - + +
43C VAL* 2.8 16.7 + - - +
45C GLN* 1.3 70.4 - - - +
47C ARG* 1.3 69.9 + - - +
49C SER* 2.9 24.2 + - - -
56C HIS* 3.9 19.8 - - + +
60C CYS* 3.4 26.9 - - - -
131C ILE* 4.7 6.7 - - + -
136C ILE* 4.2 33.9 - - + -
139C PHE* 4.3 21.8 - - + -
140C ILE* 4.7 10.3 - - + -
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Residues in contact with ARG 47 (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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17C ARG 5.9 1.3 - - - -
18C ILE* 6.0 0.4 - - - +
19C VAL* 2.6 61.4 + - - +
43C VAL* 2.8 28.6 + - + +
44C ASP* 3.3 9.2 - - - +
46C ILE* 1.3 75.1 - - - +
48C LYS* 1.3 59.3 + - + +
49C SER* 2.7 15.9 + - - -
139C PHE 4.0 1.0 + - - -
140C ILE* 3.3 33.3 - - + +
141C GLY* 3.2 30.5 - - - +
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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