Contacts of the helix formed by residues 35 - 42 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1305N OPC 5.9 7.6 - - - -
31Q ALA* 3.4 15.5 - - + +
32Q LEU* 3.6 20.0 - - + +
34Q ALA* 1.3 78.2 - - - +
36Q TYR* 1.3 66.7 + - + +
37Q PRO* 2.7 9.6 - - - +
38Q LEU* 2.6 16.8 + - + +
39Q VAL* 2.5 60.3 + - + +
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Residues in contact with TYR 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N PHE* 5.8 3.1 - + - -
32Q LEU 3.1 10.9 + - - +
33Q GLY* 4.5 1.1 - - - +
35Q LEU* 1.3 85.1 - - + +
37Q PRO* 1.3 66.3 - - + +
39Q VAL* 4.6 4.0 - - + -
40Q LYS* 2.8 77.7 + - + +
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Residues in contact with PRO 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N PHE* 3.2 46.6 - - + -
81N LEU* 6.3 3.6 - - + -
82N ILE* 5.8 1.3 - - + -
33Q GLY 2.7 22.2 - - - +
34Q ALA* 3.7 5.8 - - - -
35Q LEU 3.0 16.6 - - - +
36Q TYR* 1.3 95.7 - - + +
38Q LEU* 1.3 58.4 + - + +
40Q LYS* 3.3 3.5 - - - +
41Q TYR* 2.9 23.2 + - - +
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Residues in contact with LEU 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N ALA* 5.6 8.3 - - + -
53N ALA* 4.5 12.3 - - + -
82N ILE* 5.1 11.6 - - + +
1305N OPC 5.0 22.7 - - - -
34Q ALA 5.5 1.1 - - - +
35Q LEU* 2.6 20.6 + - + +
37Q PRO* 1.3 72.6 - - + +
39Q VAL* 1.3 64.2 + - + +
40Q LYS 3.0 1.3 - - - -
41Q TYR* 2.6 44.9 + - + +
42Q PHE* 3.2 34.0 + - + -
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Residues in contact with VAL 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q LEU* 2.5 51.9 + - + +
36Q TYR* 4.3 4.3 - - + +
38Q LEU* 1.3 77.3 - - + +
40Q LYS* 1.3 60.8 + - - +
42Q PHE* 3.7 12.8 + - + +
43Q ILE* 3.2 19.4 - - + +
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Residues in contact with LYS 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77N SER* 3.7 9.2 + - - -
78N PHE* 4.9 7.0 - - + -
36Q TYR* 2.8 70.4 + - + +
37Q PRO* 3.3 7.6 - - + +
39Q VAL* 1.3 77.1 - - - +
41Q TYR* 1.3 58.2 + - - +
43Q ILE* 2.8 40.7 - - + +
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Residues in contact with TYR 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N ALA* 2.4 40.5 + - + -
54N MET* 3.5 13.2 - - + +
57N TYR* 3.0 40.9 + + - +
72N ILE* 5.4 5.4 - - + +
76N VAL* 4.9 3.1 - - + +
77N SER* 2.6 42.9 + - - +
79N GLY* 4.4 11.0 - - - -
82N ILE* 3.8 30.3 - - + -
37Q PRO 2.9 12.3 + - - +
38Q LEU* 2.6 24.8 + - + +
40Q LYS* 1.3 66.3 - - - +
42Q PHE* 1.3 76.9 + + - -
43Q ILE 2.7 19.1 + - - +
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Residues in contact with PHE 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 4.5 8.6 - - + +
182A ARG* 3.3 25.9 + - - +
52N PHE* 3.7 23.8 - + - -
53N ALA* 3.7 28.0 - - + -
56N PHE* 3.2 49.6 - + - -
57N TYR* 3.6 4.9 - - - -
38Q LEU* 3.2 40.5 + - + -
39Q VAL* 4.3 8.7 - - - +
40Q LYS 3.6 0.4 - - - -
41Q TYR* 1.3 85.8 - + - +
43Q ILE* 1.3 59.3 + - + +
44Q PRO* 3.5 2.8 - - - +
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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