Contacts of the helix formed by residues 36 - 48 (chain A) in PDB entry 2D8M
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASN* 1.3 86.0 - - + +
37A PHE* 1.3 66.7 + - + +
39A SER* 2.9 9.5 + - - -
40A GLU* 2.8 24.7 + - + +
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Residues in contact with PHE 37 (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 PHE* 3.6 33.4 - + + -
34A GLN 3.2 13.0 - - - +
35A ASN 3.1 0.4 - - - -
36A PRO* 1.3 80.9 - - + +
38A ARG* 1.3 57.5 + - - +
40A GLU* 3.1 20.0 + - + +
41A LEU* 2.8 40.8 + - + +
44A LYS* 5.9 0.2 - - - -
66A ALA* 5.8 0.2 - - + -
86A LYS* 3.3 39.0 - - + -
90A LEU* 4.8 19.3 - - + -
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Residues in contact with ARG 38 (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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30A LEU* 3.8 13.7 - - + +
33A PHE* 3.5 32.1 - - + +
34A GLN* 3.1 14.8 + - - +
35A ASN* 3.2 35.1 + - + +
37A PHE* 1.3 78.4 - - - +
39A SER* 1.3 64.2 + - - +
41A LEU* 3.7 1.9 + - - +
42A ARG* 3.1 49.3 + - - +
52A TYR* 4.2 10.3 + - - -
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Residues in contact with SER 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 ASN* 3.9 12.6 - - - +
36A PRO* 2.9 13.6 + - - -
38A ARG* 1.3 79.6 + - - +
40A GLU* 1.3 67.0 + - - +
42A ARG* 3.2 13.2 + - - +
43A ASP* 3.0 24.2 + - - +
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Residues in contact with GLU 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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36A PRO* 2.8 16.3 + - + +
37A PHE* 3.6 22.7 - - + +
39A SER* 1.3 73.3 - - - +
41A LEU* 1.3 64.6 + - - +
43A ASP* 3.4 6.2 + - - +
44A LYS* 3.2 54.0 + - + +
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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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30A LEU* 3.2 23.3 - - + -
33A PHE* 3.2 46.9 - - + -
37A PHE* 2.8 30.2 + - + +
38A ARG 3.8 4.3 - - - +
40A GLU* 1.3 74.2 - - - +
42A ARG* 1.3 65.3 + - - +
44A LYS* 3.3 8.9 + - + +
45A ALA* 3.1 17.5 + - + +
64A ILE* 4.0 4.7 - - + -
86A LYS* 4.6 9.0 - - + -
89A VAL* 3.9 29.8 - - + -
90A LEU* 4.4 17.5 - - + -
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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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30A LEU* 3.6 11.0 - - + +
38A ARG* 3.1 36.1 + - - +
39A SER* 3.2 13.8 + - - +
41A LEU* 1.3 77.5 - - - +
43A ASP* 1.3 67.4 + - - +
45A ALA* 2.8 19.3 + - - +
46A LEU* 3.0 26.1 + - + +
52A TYR* 3.1 68.0 + - + -
128A SER* 5.9 3.2 + - - -
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Residues in contact with ASP 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 SER 3.0 9.1 + - - +
40A GLU* 3.6 10.5 - - - +
42A ARG* 1.3 77.4 - - - +
44A LYS* 1.3 57.1 + - + +
46A LEU* 2.7 39.8 + - - +
47A GLU* 2.5 49.5 + - - +
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Residues in contact with LYS 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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37A PHE* 5.9 1.2 - - - -
40A GLU* 3.2 49.2 + - + +
41A LEU* 3.5 8.3 - - - +
43A ASP* 1.3 77.6 - - + +
45A ALA* 1.3 63.5 + - - +
47A GLU* 3.1 21.9 + - - +
48A LEU* 3.3 16.3 + - - +
89A VAL* 4.1 8.7 - - + -
90A LEU* 3.6 35.0 - - + +
93A HIS* 3.7 41.5 - - + +
94A ARG 6.1 0.2 - - - +
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Residues in contact with ALA 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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28A VAL* 3.6 28.7 - - + -
30A LEU* 6.0 3.4 - - + -
41A LEU* 3.1 11.8 + - + +
42A ARG* 2.8 19.3 + - - +
44A LYS* 1.3 73.0 - - - +
46A LEU* 1.3 61.1 + - + +
48A LEU* 3.6 10.7 + - - +
50A ALA* 3.2 27.4 + - - +
52A TYR* 5.5 2.9 - - + -
64A ILE* 6.3 0.4 - - + -
89A VAL* 4.0 17.8 - - + +
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Residues in contact with LEU 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 24.4 + - + +
43A ASP* 2.7 34.9 + - - +
45A ALA* 1.3 69.8 - - - +
47A GLU* 1.3 57.7 + - - +
49A GLY* 2.8 26.2 + - - -
50A ALA 3.9 15.5 - - - +
51A LYS* 5.5 0.2 - - - -
52A TYR* 4.1 24.0 - - + +
126A PRO* 5.2 20.6 - - + +
128A SER* 4.4 18.8 - - - +
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Residues in contact with GLU 47 (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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16A PRO* 3.6 26.6 - - + +
19A LEU* 3.1 22.9 - - + +
20A GLY* 2.8 31.2 + - - -
43A ASP* 2.5 57.9 + - - +
44A LYS* 3.1 13.4 + - - +
46A LEU* 1.3 80.0 - - - +
48A LEU* 1.3 51.5 + - - +
49A GLY 2.8 4.0 + - - -
93A HIS* 3.2 15.8 + - + +
126A PRO* 6.2 1.3 - - - -
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Residues in contact with LEU 48 (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* 2.5 28.4 - - + +
20A GLY* 3.1 4.0 - - - +
22A ILE* 3.9 22.9 - - + -
23A LEU* 2.8 54.7 + - + +
44A LYS 3.3 14.5 + - - +
45A ALA* 3.7 6.7 - - - +
46A LEU 3.3 0.2 - - - -
47A GLU* 1.3 75.6 - - - +
49A GLY* 1.3 56.8 + - - +
89A VAL* 4.0 22.9 - - + +
92A CYS* 3.6 45.8 - - + +
93A HIS* 3.8 6.1 - - - +
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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