Contacts of the helix formed by residues 33 - 46 (chain A) in PDB entry 2DPD
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 TYR 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LEU* 1.3 74.3 - - - +
34A GLY* 1.3 68.6 + - - +
35A LEU* 4.0 0.2 - - + -
36A LYS* 3.4 41.2 + - + +
37A LEU* 3.1 20.5 + - - +
61A LEU* 4.7 3.6 - - - -
77A LYS* 4.2 27.7 - - + +
83A GLN* 5.0 1.9 + - - -
85A VAL* 3.4 20.6 - - + -
86A VAL 3.0 27.6 - - - +
87A LEU* 3.8 13.0 - - + -
88A TYR* 4.3 4.0 - - - -
3E A 2.5 44.4 + - - -
4E T 3.1 26.0 - - - +
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 1.3 77.0 - - - +
35A LEU* 1.3 58.4 + - - +
37A LEU* 3.2 3.0 + - - +
38A LEU* 2.9 28.6 + - - +
57A VAL* 3.8 9.2 - - - +
58A TYR* 3.7 20.0 - - - -
61A LEU* 3.9 18.7 - - - +
86A VAL 4.6 1.0 + - - -
88A TYR* 4.8 1.0 - - - -
4E T 3.3 9.2 + - - -
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TYR* 4.0 1.1 - - + -
34A GLY* 1.3 68.7 - - - +
36A LYS* 1.3 67.2 + - - +
38A LEU* 4.3 16.2 - - + -
39A GLU* 3.2 36.4 + - + +
54A HIS* 4.6 11.0 - - + -
58A TYR* 3.0 31.6 - - + +
2E T 5.6 1.6 - - + -
3E A 3.5 45.4 + - + +
4E T 2.9 32.6 + - + +
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Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 4.9 7.3 - - - +
31A ARG 4.8 2.8 + - - +
32A LEU* 3.5 30.5 - - + +
33A TYR* 3.4 44.2 + - + +
34A GLY 3.3 0.4 - - - -
35A LEU* 1.3 74.6 - - - +
37A LEU* 1.3 69.2 + - - +
39A GLU* 2.9 17.6 + - + +
40A VAL* 2.9 30.0 + - + +
77A LYS* 5.2 9.5 - - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 4.4 1.1 - - + -
23A MET* 3.5 58.8 - - + +
26A MET* 4.1 24.2 - - - -
32A LEU* 4.1 20.8 - - + +
33A TYR 3.1 10.8 + - - +
34A GLY 3.6 4.9 - - - +
36A LYS* 1.3 78.0 - - - +
38A LEU* 1.3 57.3 + - - +
40A VAL* 3.2 5.3 + - - +
41A LEU* 2.8 55.4 + - + +
57A VAL* 3.6 22.9 - - + -
61A LEU* 4.8 2.0 - - + -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY 2.9 16.7 + - - +
35A LEU* 3.9 17.7 - - + +
36A LYS 3.1 0.2 + - - -
37A LEU* 1.3 76.6 - - - +
39A GLU* 1.3 60.6 + - - +
41A LEU* 3.2 4.3 + - - +
42A ARG* 2.7 60.9 + - + +
52A PRO* 3.1 35.4 - - + +
53A ASN 3.7 12.3 - - - +
54A HIS* 3.6 32.3 - - + +
57A VAL* 4.1 15.5 - - + -
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.2 26.4 + - + +
36A LYS* 2.9 9.6 + - + +
38A LEU* 1.3 82.6 - - - +
40A VAL* 1.3 57.4 + - + +
42A ARG* 3.7 37.0 + - - +
43A SER* 3.0 31.0 + - - -
3E A 5.7 2.0 - - - +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET* 4.5 18.8 - - + -
32A LEU* 5.4 4.0 - - + -
36A LYS* 2.9 40.1 + - + +
37A LEU* 3.5 9.0 - - - +
39A GLU* 1.3 78.2 - - + +
41A LEU* 1.3 56.8 + - + +
43A SER* 3.8 4.6 + - - -
44A GLU* 2.9 44.7 + - + +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.5 32.1 - - + -
22A TYR* 3.8 38.6 - - + -
26A MET* 5.1 2.7 - - - -
37A LEU* 2.8 44.5 + - + +
38A LEU* 3.5 3.6 - - - +
40A VAL* 1.3 73.6 - - - +
42A ARG* 1.3 68.2 + - - +
44A GLU* 3.2 9.8 + - - +
45A PHE* 2.9 45.8 + - + +
50A PHE* 5.5 1.6 - - + -
52A PRO* 4.3 14.8 - - + -
57A VAL* 4.7 4.5 - - + -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 2.7 42.1 + - + +
39A GLU* 3.4 34.9 + - - +
41A LEU* 1.3 73.2 - - - +
43A SER* 1.3 57.2 + - - +
45A PHE* 4.2 0.2 - - - -
46A LYS* 3.0 30.4 + - - +
50A PHE 4.3 3.8 - - - +
51A LYS* 4.8 13.3 + - + +
52A PRO* 3.0 36.1 + - + +
53A ASN* 3.7 16.6 - - - +
54A HIS* 4.3 3.4 + - - +
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU 3.0 17.1 + - - -
40A VAL* 3.8 4.7 + - - -
42A ARG* 1.3 74.0 - - - +
44A GLU* 1.3 68.9 + - - +
45A PHE 2.8 2.4 + - - -
46A LYS* 2.9 22.6 + - - +
47A GLU 4.8 0.5 + - - -
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR* 3.8 10.0 - - - -
26A MET* 3.7 23.7 - - - +
40A VAL* 2.9 30.2 + - + +
41A LEU* 3.2 12.5 + - - +
43A SER* 1.3 74.3 + - - +
45A PHE* 1.3 65.4 + - + +
47A GLU* 5.9 0.9 - - - +
48A ILE* 5.7 0.7 - - - +
116B LYS* 2.9 49.7 + - - +
120B ASP* 2.9 17.7 - - - +
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Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.7 25.1 - + - -
22A TYR* 3.3 33.2 - + - -
41A LEU* 2.9 39.6 + - + +
43A SER 2.8 1.2 + - - -
44A GLU* 1.3 81.5 - - + +
46A LYS* 1.3 55.3 + - - +
47A GLU 2.7 18.0 + - - -
48A ILE* 2.8 21.1 + - + +
49A GLY 3.0 7.4 + - - +
50A PHE* 3.3 40.2 - + + +
113B LEU* 3.6 29.2 - - + -
116B LYS* 3.5 34.1 - - + -
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG 3.0 16.1 + - - +
43A SER* 2.9 18.1 + - - +
45A PHE* 1.3 72.4 - - - +
47A GLU* 1.3 64.6 + - - +
49A GLY* 3.3 14.2 + - - +
50A PHE 4.3 3.1 + - - -
51A LYS* 6.3 1.1 - - - -
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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