Contacts of the helix formed by residues 39 - 44 (chain R) in PDB entry 2X86
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 PHE 39 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Q TRP* 3.7 12.3 - + - -
136Q PRO 3.4 20.9 - - - -
137Q LEU 3.2 10.1 - - - -
138Q ASN* 3.2 36.1 - - - -
139Q VAL* 3.7 18.4 - - + -
142Q TYR* 3.8 36.2 - + + -
271Q ARG* 3.9 2.7 - - - -
33R LEU* 4.5 9.9 - - + +
36R GLY 3.0 23.6 + - - +
37R THR 4.0 2.2 - - - -
38R LYS* 1.3 77.6 - - - +
40R VAL* 1.3 92.1 - - + +
42R LEU* 2.8 19.6 + - - +
43R VAL* 3.0 26.4 + - + -
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Residues in contact with VAL 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271Q ARG* 4.1 12.6 - - - +
37R THR 3.2 16.2 - - - +
38R LYS* 3.1 1.8 - - - -
39R PHE* 1.3 109.1 - - + +
41R ASN* 1.3 78.5 + - - +
42R LEU 3.1 1.4 + - - -
43R VAL* 3.2 24.8 + - + +
44R ASP* 4.1 4.9 - - - +
174R ARG* 4.5 1.0 + - - -
177R HIS* 6.3 1.3 - - + -
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Residues in contact with ASN 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ALA 2.9 27.0 + - - +
9R GLY 4.2 0.6 + - - -
13R SER* 3.6 17.3 - - - +
38R LYS* 3.0 13.9 + - - +
39R PHE 2.9 1.4 + - - -
40R VAL* 1.3 88.6 - - - +
42R LEU* 1.3 58.0 + - - +
45R LEU* 3.4 9.4 - - - +
174R ARG* 2.8 57.5 + - + +
176R GLY 5.3 0.9 + - - -
177R HIS* 3.1 32.6 + - - -
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Residues in contact with LEU 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142Q TYR* 3.5 35.9 + - + +
145Q PHE* 5.7 0.2 - - - -
7R GLY 3.4 22.2 - - - +
8R ALA* 3.8 25.6 - - + -
16R VAL* 4.7 2.2 - - + -
29R VAL* 4.1 27.1 - - + -
33R LEU* 5.3 3.1 - - + -
38R LYS 5.4 0.7 - - - +
39R PHE* 2.8 10.3 + - - +
41R ASN* 1.3 83.0 - - - +
43R VAL* 1.3 55.0 + - - +
44R ASP 3.2 2.7 - - - -
45R LEU* 2.8 45.3 + - + +
47R ILE* 4.4 15.2 - - + +
50R TYR* 4.7 7.0 - - + -
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Residues in contact with VAL 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131Q ARG* 3.3 20.3 + - - -
134Q GLU 4.9 0.9 - - - +
135Q LYS* 3.9 26.9 - - + +
136Q PRO* 3.3 51.9 - - + +
142Q TYR* 4.2 9.6 - - + -
145Q PHE* 4.6 6.1 - - + -
39R PHE* 3.0 21.5 + - + +
40R VAL* 3.2 22.8 + - + +
42R LEU* 1.3 77.1 - - - +
44R ASP* 1.3 63.2 + - + +
45R LEU 4.2 0.2 - - - +
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Residues in contact with ASP 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Q ARG* 3.8 8.1 + - - +
135Q LYS* 4.3 25.9 + - + +
40R VAL 4.1 5.2 - - - +
41R ASN 4.2 0.2 - - - +
43R VAL* 1.3 75.6 - - + +
45R LEU* 1.3 68.1 + - - +
46R ASN* 5.2 2.9 + - - -
174R ARG* 3.0 41.9 + - - -
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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