Contacts of the helix formed by residues 39 - 44 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M TRP* 4.0 9.0 - + - -
136M PRO 3.4 20.6 - - - -
137M LEU* 3.5 9.2 - - - -
138M ASN* 3.5 35.0 - - - -
139M VAL* 4.0 13.7 - - + -
142M TYR* 3.7 48.3 - + + -
271M ARG* 4.2 4.3 - - - -
33N LEU* 4.5 9.6 - - + +
36N GLY 3.0 24.5 + - - +
37N THR 4.0 3.6 - - - -
38N LYS* 1.3 77.7 - - - +
40N VAL* 1.3 88.8 + - + +
42N LEU* 2.8 18.4 + - - +
43N VAL* 3.0 22.9 + - + -
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Residues in contact with VAL 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271M ARG* 4.7 9.9 - - - +
37N THR 3.2 16.1 + - - +
38N LYS* 3.1 1.4 - - - -
39N PHE* 1.3 109.5 - - + +
41N ASN* 1.3 78.4 + - - +
42N LEU 3.1 1.6 + - - -
43N VAL* 3.2 23.9 + - + +
44N ASP* 4.1 4.3 - - - +
174N ARG* 4.5 0.9 + - - -
177N HIS* 6.3 2.2 - - + +
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Residues in contact with ASN 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N ALA 2.9 27.0 + - - +
9N GLY 4.2 0.6 + - - -
13N SER* 3.6 16.7 - - - +
38N LYS* 3.0 13.4 + - - +
39N PHE 2.9 1.0 + - - -
40N VAL* 1.3 87.8 - - - +
42N LEU* 1.3 58.4 + - - +
45N LEU* 3.4 9.4 - - - +
174N ARG* 2.8 56.9 + - + +
176N GLY 5.3 0.7 + - - -
177N HIS* 3.1 33.5 + - - -
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Residues in contact with LEU 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142M TYR* 3.3 34.8 + - + +
145M PHE* 5.5 0.7 - - - -
7N GLY 3.4 22.9 - - - +
8N ALA* 3.8 25.4 - - + -
13N SER* 4.8 0.2 - - - -
16N VAL* 4.8 2.0 - - + -
29N VAL* 4.1 25.6 - - + -
33N LEU* 5.2 2.9 - - + -
38N LYS 5.1 1.3 - - - +
39N PHE* 2.8 10.0 + - - +
41N ASN* 1.3 84.4 - - - +
43N VAL* 1.3 55.0 + - - +
44N ASP 3.2 2.2 - - - -
45N LEU* 2.7 44.7 + - + +
47N ILE* 4.4 16.3 - - + +
50N TYR* 4.7 8.1 - - + -
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Residues in contact with VAL 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131M ARG* 2.9 22.5 + - - -
134M GLU 4.9 1.4 - - - +
135M LYS* 4.0 24.5 - - + +
136M PRO* 3.6 49.5 - - + +
142M TYR* 4.1 11.0 - - + -
145M PHE* 4.3 6.3 - - + -
39N PHE* 3.0 22.3 + - + +
40N VAL* 3.2 22.6 + - + +
42N LEU* 1.3 77.1 - - - +
44N ASP* 1.3 64.1 + - + +
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Residues in contact with ASP 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M ARG* 3.5 10.5 + - - +
135M LYS* 4.5 17.5 - - + +
40N VAL 4.1 5.2 - - - +
41N ASN 4.2 0.3 - - - +
43N VAL* 1.3 80.5 - - + +
45N LEU* 1.3 68.6 + - - +
46N ASN* 5.2 2.6 + - - -
174N ARG* 3.0 43.2 + - - -
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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