Contacts of the helix formed by residues 31 - 40 (chain D) in PDB entry 2DFS
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 GLU 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A TYR* 3.9 8.7 + - - -
19D PHE* 3.3 30.9 - - + +
21D LYS* 4.0 10.9 + - - -
27D ILE* 4.5 8.5 - - + -
28D THR* 3.0 29.5 + - + +
30D LYS* 1.3 73.9 - - - +
32D LEU* 1.4 57.2 + - - +
33D GLY 3.3 1.8 - - - -
34D THR* 2.6 49.2 + - - +
35D VAL* 3.0 20.8 + - - +
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Residues in contact with LEU 32 (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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28D THR 3.8 2.4 + - - -
29D THR* 3.4 16.0 + - - +
30D LYS 3.3 2.0 - - - -
31D GLU* 1.4 77.2 - - - +
33D GLY* 1.3 61.5 + - - +
35D VAL* 3.3 9.1 - - + +
36D MET* 3.1 47.8 + - + +
48D LEU* 3.5 18.2 - - + +
51D MET* 5.2 3.1 - - + -
52D ILE* 3.4 32.5 - - + +
63D ILE* 3.4 31.9 - - + -
67D GLU* 5.2 5.4 - - - +
68D PHE* 3.8 18.8 - - + -
71D MET* 5.7 7.2 - - + -
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Residues in contact with GLY 33 (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 LYS 4.5 2.6 + - - -
31D GLU* 3.3 1.0 - - - +
32D LEU* 1.3 77.2 - - - +
34D THR* 1.3 57.0 + - - +
36D MET* 3.6 3.0 + - - +
37D ARG* 3.0 51.0 + - - +
48D LEU* 3.4 34.9 - - - +
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Residues in contact with THR 34 (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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831A VAL* 4.0 25.4 - - + +
835A TYR* 5.9 1.3 - - + -
19D PHE* 3.7 10.6 - - - -
30D LYS 4.7 2.4 + - - +
31D GLU* 2.6 45.5 + - - +
33D GLY* 1.3 73.2 - - - +
35D VAL* 1.4 50.3 + - - -
37D ARG* 3.6 10.3 - - - +
38D SER* 2.7 34.8 + - - -
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Residues in contact with VAL 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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15D ALA* 4.8 2.5 - - + +
16D PHE* 4.5 11.0 - - + +
19D PHE* 3.8 31.9 - - + -
27D ILE* 4.0 18.4 - - + -
31D GLU 3.0 17.4 + - - +
32D LEU* 3.3 23.3 - - + +
34D THR* 1.4 71.6 - - - +
36D MET* 1.4 66.6 + - - +
38D SER* 3.2 2.7 + - - -
39D LEU* 3.1 26.4 + - + +
68D PHE* 3.5 38.1 - - + -
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Residues in contact with MET 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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32D LEU* 3.1 41.5 + - + +
33D GLY 3.8 1.1 - - - +
35D VAL* 1.4 72.7 - - - +
37D ARG* 1.3 61.4 + - - +
39D LEU* 3.2 20.5 + - - +
40D GLY 3.3 5.9 + - - -
41D GLN* 3.4 33.7 + - - +
43D PRO* 3.7 23.3 - - + -
48D LEU* 3.8 18.4 - - - -
51D MET* 3.4 42.0 - - + +
68D PHE* 3.9 20.9 - - + -
71D MET* 5.0 2.9 - - + -
72D MET* 5.2 3.6 - - + +
79D THR* 5.6 0.2 - - - -
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Residues in contact with ARG 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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824A LYS* 3.8 6.6 - - - +
827A ARG* 4.0 8.5 - - - +
828A MET* 4.0 24.2 - - + +
831A VAL* 3.3 21.8 - - + -
832A ARG* 2.7 34.3 + - - +
33D GLY* 3.0 30.5 + - - +
34D THR* 3.9 6.7 - - - +
36D MET* 1.3 74.4 - - - +
38D SER* 1.3 58.7 + - - +
41D GLN 3.3 15.3 - - - +
43D PRO* 2.7 43.5 + - + +
44D THR 3.2 10.3 + - - -
45D GLU* 2.6 45.7 + - - +
48D LEU* 4.0 9.5 - - - +
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Residues in contact with SER 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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831A VAL* 3.8 4.4 - - - +
832A ARG* 3.6 19.9 - - - +
835A TYR* 3.9 21.1 - - - +
15D ALA* 5.0 11.2 - - - +
18D LEU* 6.2 0.3 - - - +
19D PHE* 3.6 25.2 - - - -
34D THR 2.7 22.3 + - - -
35D VAL* 3.2 7.2 + - - -
37D ARG* 1.3 71.5 - - - +
39D LEU* 1.3 63.2 + - - +
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Residues in contact with LEU 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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832A ARG* 4.7 1.2 - - - -
10D ALA* 3.0 41.9 - - + +
12D PHE* 3.6 53.2 - - + +
15D ALA* 4.1 13.7 - - + -
35D VAL* 3.1 9.9 + - + +
36D MET* 3.2 9.9 - - - +
38D SER* 1.3 77.9 - - - +
40D GLY* 1.3 56.8 + - - +
41D GLN* 4.4 13.9 - - - +
68D PHE* 4.1 22.9 - - + -
72D MET* 4.1 20.2 - - + -
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Residues in contact with GLY 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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832A ARG* 2.8 40.1 + - - -
10D ALA* 5.5 2.5 - - - -
36D MET 3.3 1.4 + - - -
37D ARG 3.8 0.6 + - - -
38D SER 3.5 1.6 - - - -
39D LEU* 1.3 78.5 - - - +
41D GLN* 1.3 62.1 + - - +
42D ASN* 2.9 6.4 - - - +
83D GLU* 3.4 21.7 - - - +
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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