Contacts of the helix formed by residues 15 - 26 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291C VAL* 5.7 5.1 - - - +
293C PRO* 5.1 10.0 - - + +
296C ASP* 2.7 27.7 + - - +
322C PRO 6.0 2.2 - - - -
12T SER* 2.6 34.9 - - - +
13T GLY 3.0 5.9 + - - +
14T ILE* 1.3 83.9 + - - +
16T ALA* 1.3 78.2 + - + +
18T PRO* 3.0 18.0 - - - +
19T ALA* 3.1 10.9 + - - +
51T MET* 4.8 7.0 - - - +
54T GLY* 4.1 24.7 + - - -
55T ILE 3.4 19.0 + - - -
56T GLN* 5.1 1.9 - - - -
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Residues in contact with ALA 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C TYR* 3.2 46.9 - - + +
296C ASP* 3.2 11.1 + - - +
12T SER* 5.8 4.0 - - - -
15T HIS* 1.3 85.8 - - + +
17T ARG* 1.3 69.6 + - + +
18T PRO* 3.8 6.1 - - + -
19T ALA* 3.2 6.4 + - - +
20T THR* 3.3 8.0 + - - +
51T MET* 5.3 0.5 - - - +
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Residues in contact with ARG 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ARG* 3.0 29.7 - - - +
84C ASP* 3.7 16.4 - - - +
295C TYR* 3.4 15.2 - - + +
69G ASP* 2.4 41.2 + - - +
71G SER* 4.8 2.6 + - - -
99G ASP* 3.4 17.0 + - - -
16T ALA* 1.3 77.6 - - + +
18T PRO* 1.3 60.2 - - + +
20T THR* 2.6 27.1 + - - +
21T THR* 2.7 21.4 + - - +
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Residues in contact with PRO 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T SER* 5.7 6.5 - - - -
13T GLY 4.6 11.4 - - - +
15T HIS 3.0 13.5 - - - +
16T ALA* 3.2 5.8 - - + -
17T ARG* 1.3 95.1 - - + +
19T ALA* 1.3 57.0 + - - +
21T THR* 3.4 7.7 + - - +
22T LEU* 3.0 28.5 + - - +
84T GLU* 5.0 11.4 - - + +
86T LEU* 4.1 30.1 - - + +
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Residues in contact with ALA 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14T ILE* 3.8 30.9 - - + +
15T HIS* 3.1 16.5 + - - +
16T ALA 3.7 7.2 - - - +
18T PRO* 1.3 75.9 - - - +
20T THR* 1.3 65.1 + - - +
22T LEU* 3.5 6.0 - - - +
23T VAL* 2.8 33.4 + - + +
50T VAL* 4.3 10.3 - - + -
51T MET* 4.7 11.0 - - + -
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Residues in contact with THR 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASP* 4.8 4.9 - - + +
85C ILE* 3.8 27.4 - - + -
295C TYR* 3.1 35.5 + - + +
299C ALA* 4.9 2.9 - - + -
16T ALA 3.3 8.9 + - - +
17T ARG* 2.6 20.1 + - - +
19T ALA* 1.3 72.4 - - + +
21T THR* 1.3 54.8 + - - -
23T VAL* 4.3 5.6 - - - -
24T GLN* 2.6 57.3 + - - +
47T ILE* 4.7 8.3 - - + -
51T MET* 5.5 1.6 - - - -
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Residues in contact with THR 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17T ARG* 2.7 30.0 + - - +
18T PRO 3.8 3.7 + - - -
20T THR* 1.3 75.9 + - - +
22T LEU* 1.3 56.5 + - - +
24T GLN* 4.2 9.1 - - + +
25T ALA* 2.9 25.3 + - - +
80T THR* 4.0 5.9 + - - +
84T GLU* 3.3 31.4 + - + +
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Residues in contact with LEU 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ILE* 4.9 11.4 - - + -
18T PRO 3.0 16.3 + - - +
19T ALA* 3.5 6.1 - - - +
20T THR 3.0 0.4 - - - -
21T THR* 1.3 77.9 - - - +
23T VAL* 1.3 56.8 + - + +
25T ALA* 3.1 1.3 + - - +
26T ALA* 2.7 32.6 + - - +
35T LEU* 5.8 2.0 - - + -
44T LEU* 4.3 18.6 - - + -
61T ILE* 5.9 1.1 - - + -
63T ILE* 5.0 3.6 - - + -
77T LEU* 3.1 40.2 - - + +
80T THR* 3.3 21.8 - - + -
81T MET* 3.8 30.3 - - + -
86T LEU* 3.9 12.3 - - + -
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Residues in contact with VAL 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C MSE 4.4 2.0 - - + -
19T ALA* 2.8 26.6 + - + +
20T THR 3.7 0.7 - - - +
22T LEU* 1.3 73.5 - - - +
24T GLN* 1.3 57.7 + - - +
26T ALA* 2.4 26.6 + - - -
27T SER* 2.6 19.5 + - - +
44T LEU* 3.3 30.7 - - + +
45T LYS 3.3 26.2 - - - +
46T SEP 3.8 0.4 - - - +
47T ILE* 3.4 31.2 - - + -
50T VAL* 4.2 21.8 - - + -
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Residues in contact with GLN 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ASP* 4.4 7.5 + - - +
87C THR* 5.5 3.2 - - - +
88C MSE 3.2 51.0 - - - +
20T THR* 2.6 44.0 + - - +
21T THR* 4.2 8.7 - - + +
23T VAL* 1.3 71.6 - - - +
25T ALA* 1.3 56.0 + - - +
27T SER* 2.8 31.2 + - - -
28T LYS* 3.3 13.4 + - - +
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Residues in contact with ALA 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T THR 2.9 21.3 + - - +
22T LEU* 3.1 7.6 + - - +
23T VAL 3.1 0.4 - - - -
24T GLN* 1.3 79.1 - - - +
26T ALA* 1.3 57.1 + - - +
28T LYS* 3.0 29.2 + - - +
29T PHE* 3.3 16.1 - - - -
76T ALA* 5.1 2.8 - - + +
77T LEU* 3.8 11.7 - - + +
80T THR* 3.8 19.3 - - + +
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Residues in contact with ALA 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T LEU 2.7 4.6 + - - +
23T VAL 2.4 15.1 + - - +
25T ALA* 1.3 71.9 - - - +
27T SER* 1.3 57.3 + - - +
28T LYS 3.4 2.2 - - - -
29T PHE* 4.3 7.8 + - - -
33T ILE* 3.6 12.7 - - + +
44T LEU* 3.3 28.9 - - + +
45T LYS* 3.1 26.6 - - - +
77T LEU* 3.2 28.3 - - + -
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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