Contacts of the helix formed by residues 34 - 45 (chain D) in PDB entry 2RFQ
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 PRO 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D ARG* 5.6 4.5 - - + +
26D GLU* 4.8 16.2 - - + +
27D THR* 3.2 34.5 - - + +
30D LEU* 3.9 20.2 - - + -
32D ARG 3.6 5.2 - - - +
33D ILE* 1.3 94.6 - - + +
35D ASP* 1.3 65.4 + - - +
36D ASP* 4.3 8.5 - - + +
37D SER* 3.0 25.5 + - - +
38D MSE 3.2 9.9 + - - +
79D THR* 5.5 0.2 - - - +
144D HIS* 4.4 0.2 - - - -
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Residues in contact with ASP 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 5.3 0.4 - - - +
32D ARG* 5.7 2.1 + - - +
33D ILE 3.4 1.4 + - - -
34D PRO* 1.3 70.9 - - - +
36D ASP* 1.3 65.8 + - - +
38D MSE 3.2 3.7 + - - +
39D LYS* 2.9 24.3 + - - +
144D HIS* 3.3 26.3 + - - -
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Residues in contact with ASP 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ARG* 3.4 30.6 + - - +
34D PRO* 3.2 6.6 - - + +
35D ASP* 1.3 80.8 - - - +
37D SER* 1.3 58.4 + - - +
39D LYS* 3.4 6.5 + - - +
40D ALA* 2.9 30.0 + - - +
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Residues in contact with SER 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 5.9 0.2 - - - -
19D THR* 5.8 1.2 - - - +
20D LEU* 3.7 27.0 - - - +
23D ARG* 5.1 11.8 + - - +
27D THR* 5.0 1.9 + - - -
33D ILE* 3.7 16.4 - - - -
34D PRO* 3.0 24.3 + - - +
36D ASP* 1.3 75.8 - - - +
38D MSE 1.3 61.8 + - - +
40D ALA* 3.3 5.6 + - - +
41D LEU* 2.9 36.5 + - - +
79D THR* 4.9 5.2 + - - -
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Residues in contact with MSE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ILE* 3.6 27.8 - - + -
34D PRO 3.2 0.6 + - - +
35D ASP* 3.2 7.0 + - - +
37D SER* 1.3 77.5 - - - +
39D LYS* 1.3 58.9 + - - +
41D LEU* 3.4 11.4 + - - +
42D GLN* 2.9 29.6 + - - +
47D PHE* 3.5 34.0 - - + -
79D THR* 5.7 0.2 - - - -
82D VAL* 4.2 21.1 - - + -
83D SER* 5.5 0.4 - - - -
86D ILE* 4.8 3.8 - - + -
112D ARG* 3.7 32.4 + - - +
144D HIS* 3.5 45.5 - - + +
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Residues in contact with LYS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ASP 2.9 15.9 + - - +
36D ASP* 3.8 7.2 - - - +
38D MSE 1.3 78.8 - - - +
40D ALA* 1.3 56.9 + - - +
42D GLN* 3.3 21.6 + - - +
43D GLU* 2.9 66.1 + - + +
112D ARG* 5.9 1.1 - - - +
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.6 32.5 - - + -
36D ASP 2.9 18.1 + - - +
37D SER* 3.8 4.9 - - - +
39D LYS* 1.3 75.8 - - - +
41D LEU* 1.3 63.7 + - - +
43D GLU* 3.1 8.5 + - - +
44D THR* 3.1 24.6 + - - +
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.7 26.2 - - + -
16D LEU* 4.0 12.3 - - + +
20D LEU* 4.8 3.8 - - + -
37D SER* 2.9 25.5 + - - +
38D MSE 3.7 18.4 - - - +
40D ALA* 1.3 76.3 - - - +
42D GLN* 1.3 61.9 + - - +
44D THR* 2.7 24.6 + - - -
46D PHE* 3.5 12.6 + - + +
47D PHE* 3.7 15.3 - - + -
72D ILE* 3.8 22.7 - - + -
79D THR* 3.6 20.6 - - + -
83D SER* 3.3 20.6 - - - +
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Residues in contact with GLN 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D MSE 2.9 17.8 + - - +
39D LYS* 3.3 23.6 + - - +
41D LEU* 1.3 75.0 - - - +
43D GLU* 1.3 76.8 + - - +
45D GLY* 3.0 21.8 + - - -
47D PHE* 3.7 15.7 + - + +
48D ARG* 5.7 2.1 + - - +
110D ASP* 3.5 44.0 + - + +
112D ARG* 2.8 34.9 + - - +
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Residues in contact with GLU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 4.4 9.0 + - - -
39D LYS* 2.9 52.9 + - + +
40D ALA* 3.1 7.6 + - - +
42D GLN* 1.3 96.2 + - - +
44D THR* 1.3 62.6 + - - +
45D GLY* 3.3 0.9 + - - -
110D ASP* 5.4 0.2 - - - +
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Residues in contact with THR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.5 13.2 - - - +
12D ARG* 3.1 57.1 + - + +
13D LEU* 3.7 26.2 - - + +
16D LEU* 3.9 12.8 - - + -
40D ALA 3.1 14.8 + - - +
41D LEU 2.7 16.7 + - - +
43D GLU* 1.3 77.6 - - - +
45D GLY* 1.3 56.7 + - - +
46D PHE* 3.1 17.3 + - - +
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Residues in contact with GLY 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.1 9.6 - - - +
12D ARG* 4.8 1.3 - - - -
42D GLN 3.0 14.5 + - - -
43D GLU 3.1 1.8 + - - -
44D THR* 1.3 77.4 - - - +
46D PHE* 1.3 66.0 + - - +
47D PHE 3.3 2.5 - - - -
48D ARG* 2.9 31.7 + - - +
49D LEU 3.5 3.3 + - - -
58D TYR* 3.7 14.1 - - - -
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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