Contacts of the helix formed by residues 35 - 42 (chain D) in PDB entry 2D2C
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 LEU 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D ALA* 3.4 15.3 - - + +
32D LEU* 3.6 20.9 - - + +
34D ALA* 1.3 79.5 - - - +
36D TYR* 1.3 65.7 + - + +
37D PRO* 2.8 10.6 - - - +
38D LEU* 2.5 15.6 + - + +
39D VAL* 2.5 59.9 + - + +
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Residues in contact with TYR 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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78A PHE* 5.8 2.9 - + - -
32D LEU 3.1 10.7 + - - +
33D GLY* 4.5 0.9 - - - +
35D LEU* 1.3 86.1 - - + +
37D PRO* 1.3 67.3 - - + +
39D VAL* 4.6 3.6 - - + -
40D LYS* 2.8 77.0 + - + +
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Residues in contact with PRO 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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78A PHE* 2.8 48.2 - - + -
81A LEU* 5.9 7.6 - - + -
82A ILE* 5.5 0.9 - - + -
33D GLY 2.8 22.0 - - - +
34D ALA* 3.7 5.4 - - - -
35D LEU 3.0 15.9 - - - +
36D TYR* 1.3 96.2 - - + +
38D LEU* 1.3 63.9 + - + +
40D LYS* 3.4 0.2 - - - +
41D TYR* 3.0 13.0 + - - +
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Residues in contact with LEU 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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49A ALA* 5.4 11.7 - - + -
50A THR* 6.0 0.7 - - - +
53A ALA* 4.5 6.3 - - + -
82A ILE* 4.3 18.4 - - + +
34D ALA 5.5 0.4 - - - -
35D LEU* 2.5 20.9 + - + +
37D PRO* 1.3 74.8 - - + +
39D VAL* 1.3 63.3 + - + +
41D TYR* 2.6 45.9 + - + +
42D PHE* 3.2 34.2 + - + -
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Residues in contact with VAL 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 LEU* 2.5 52.4 + - + +
36D TYR* 4.3 4.3 - - + +
38D LEU* 1.3 77.9 - - + +
40D LYS* 1.3 60.2 + - - +
41D TYR 3.3 0.3 + - - -
42D PHE* 3.7 13.2 + - - +
43D ILE* 3.2 19.3 + - + +
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Residues in contact with LYS 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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77A SER* 2.8 25.0 + - - +
78A PHE* 4.1 9.9 - - + -
36D TYR* 2.8 70.0 + - + +
37D PRO 3.4 5.4 - - - +
39D VAL* 1.3 76.7 - - - +
41D TYR* 1.3 56.9 + - - +
43D ILE* 2.7 37.7 - - + +
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Residues in contact with TYR 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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53A ALA* 3.4 29.3 + - + -
54A MET* 3.6 22.0 - - - +
57A TYR* 3.3 25.1 + + - +
72A ILE* 4.5 6.1 - - + +
76A VAL* 3.7 17.4 - - + +
77A SER* 2.8 25.6 + - - +
79A GLY* 3.6 23.1 - - - -
82A ILE* 3.0 42.5 - - + +
37D PRO 3.0 8.9 + - - +
38D LEU* 2.6 25.2 + - + +
40D LYS* 1.3 66.4 - - - +
42D PHE* 1.3 84.3 + + - -
43D ILE 2.7 24.8 + - - +
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Residues in contact with PHE 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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52A PHE* 4.2 15.5 - + - -
53A ALA* 3.0 47.8 - - + -
56A PHE* 3.5 41.3 - + + -
57A TYR* 2.7 20.8 + - - -
38D LEU* 3.2 40.6 + - + -
39D VAL* 4.3 7.6 - - - +
40D LYS 3.6 0.4 - - - -
41D TYR* 1.3 83.4 - + - +
43D ILE* 1.3 57.7 + - + +
44D PRO* 3.5 2.6 - - - +
168N LEU* 5.4 4.6 - - + +
182N ARG* 3.4 15.7 + - - +
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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