Contacts of the helix formed by residues 39 - 44 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TRP* 4.0 9.2 - + - -
136D PRO 3.3 19.1 - - - -
137D LEU* 3.4 10.3 - - - -
138D ASN* 3.3 36.8 - - - -
139D VAL* 3.8 14.6 - - + -
142D TYR* 3.6 45.0 - + + -
271D ARG* 4.3 2.2 - - - -
33E LEU* 4.4 9.4 - - + +
36E GLY 3.0 22.8 + - - +
37E THR 4.0 2.2 - - - -
38E LYS* 1.3 77.9 - - - +
40E VAL* 1.3 90.6 + - + +
42E LEU* 2.8 19.5 + - - +
43E VAL* 3.0 22.2 + - + -
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ARG* 4.5 11.4 - - - +
37E THR 3.2 15.9 - - - +
38E LYS* 3.1 1.6 - - - -
39E PHE* 1.3 109.4 - - + +
41E ASN* 1.3 78.5 + - - +
42E LEU 3.1 1.4 + - - -
43E VAL* 3.2 24.3 + - + +
44E ASP* 4.1 4.5 - - - +
174E ARG* 4.5 1.0 + - - -
176E GLY* 6.6 0.4 - - - -
177E HIS* 6.3 2.2 - - + +
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Residues in contact with ASN 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ALA 2.9 26.7 + - - +
9E GLY 4.2 0.6 + - - -
13E SER* 3.6 17.1 - - - +
38E LYS* 3.0 13.6 + - - +
39E PHE 2.9 1.0 + - - -
40E VAL* 1.3 89.6 - - - +
42E LEU* 1.3 58.2 + - - +
45E LEU* 3.4 9.7 - - - +
174E ARG* 2.8 58.1 + - + +
176E GLY 5.3 1.0 + - - -
177E HIS* 3.1 33.2 + - - -
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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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142D TYR* 3.4 35.3 + - + +
145D PHE* 5.6 0.5 - - - -
7E GLY 3.4 22.7 - - - +
8E ALA* 3.8 25.4 - - + -
13E SER* 4.8 0.2 - - - -
16E VAL* 4.7 2.2 - - + -
29E VAL* 4.1 26.7 - - + -
33E LEU* 5.3 3.4 - - + -
38E LYS 5.1 1.1 - - - +
39E PHE* 2.8 9.6 + - - +
41E ASN* 1.3 84.5 - - - +
43E VAL* 1.3 54.8 + - - +
44E ASP 3.2 3.1 - - - -
45E LEU* 2.8 45.5 + - + +
47E ILE* 4.4 16.3 - - + +
50E TYR* 4.7 6.7 - - + -
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Residues in contact with VAL 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D ARG* 3.0 21.8 + - - -
134D GLU 4.8 1.9 - - - +
135D LYS* 3.9 25.9 - - + +
136D PRO* 3.5 50.5 - - + +
142D TYR* 4.1 10.5 - - + -
145D PHE* 4.4 5.7 - - - -
39E PHE* 3.0 20.1 + - + +
40E VAL* 3.2 23.3 + - + +
42E LEU* 1.3 77.9 - - - +
44E ASP* 1.3 63.2 + - + +
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Residues in contact with ASP 44 (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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131D ARG* 3.6 8.5 + - - +
135D LYS* 4.4 18.3 + - + +
40E VAL 4.1 5.6 - - - +
43E VAL* 1.3 81.0 - - + +
45E LEU* 1.3 68.3 + - - +
46E ASN* 5.2 2.9 + - - -
174E ARG* 3.0 42.3 + - - -
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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