Contacts of the helix formed by residues 38 - 43 (chain E) in PDB entry 2NYM
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 GLN 38 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E GLN 2.8 22.9 + - - +
35E LYS* 2.4 25.1 + - + +
37E ARG* 1.3 69.0 - - - +
39E CYS* 1.3 62.9 + - - +
41E VAL* 3.0 22.0 - - - +
42E LEU* 3.2 7.1 + - - +
62E ALA* 4.8 7.4 - - + +
65E GLU* 5.1 10.3 - - - +
66E MSE 4.7 10.9 - - + +
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Residues in contact with CYS 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LYS 2.4 24.6 + - - +
36E LEU* 4.9 0.2 - - - -
38E GLN* 1.3 68.5 - - - +
40E CYS* 1.3 50.3 + - - +
41E VAL 2.8 4.5 - - - -
42E LEU* 2.7 10.5 + - - +
43E PHE* 2.6 35.3 + - - +
66E MSE 3.6 32.7 - - + -
82E TYR* 5.8 1.8 - - + -
84E GLU* 4.6 26.7 - - + +
85E VAL* 5.4 1.6 - - + +
88E MSE 4.2 8.7 - - + +
130E PHE* 5.9 0.4 - - + -
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Residues in contact with CYS 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LYS 4.3 0.2 + - - -
36E LEU 4.1 9.5 + - - +
37E ARG* 3.9 11.5 + - - +
38E GLN 3.4 0.6 - - - -
39E CYS* 1.3 78.0 - - - +
41E VAL* 1.3 60.8 + - - +
43E PHE* 3.4 20.6 - - - +
44E ASP* 4.0 7.3 + - - +
84E GLU* 4.1 18.7 + - - +
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Residues in contact with VAL 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ARG 3.5 11.8 + - - +
38E GLN* 3.0 18.1 + - - +
39E CYS 2.7 1.4 + - - -
40E CYS* 1.3 78.4 - - - +
42E LEU* 1.3 57.8 + - - +
43E PHE 3.0 5.3 + - - -
45E PHE* 3.9 16.6 + - - +
59E LYS* 4.9 2.0 - - - +
62E ALA* 5.4 6.1 - - + -
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Residues in contact with LEU 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E GLN 3.2 5.8 + - - +
39E CYS* 2.7 13.2 + - - +
41E VAL* 1.3 73.1 - - - +
43E PHE* 1.3 66.5 + - - +
59E LYS* 2.9 39.5 + - + -
62E ALA* 4.2 10.2 - - + +
63E LEU* 3.1 34.8 - - + -
66E MSE 5.1 1.6 - - - -
88E MSE 3.4 11.1 - - + +
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Residues in contact with PHE 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E CYS 2.6 17.5 + - - +
40E CYS* 3.4 18.2 - - - +
41E VAL 3.0 2.5 - - - -
42E LEU* 1.3 80.3 - - - +
44E ASP* 1.3 54.9 - - + +
45E PHE* 2.0 27.1 + - - +
46E VAL 4.0 1.2 + - - -
59E LYS* 3.9 2.1 + - - -
84E GLU 5.7 0.2 - - - +
87E HIS* 4.8 12.3 - - + +
88E MSE 3.8 28.9 - - + +
91E VAL* 5.3 5.8 - - + +
92E ASN* 4.3 8.0 - - - +
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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