Contacts of the helix formed by residues 39 - 44 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84R TRP* 3.9 10.1 - + - -
136R PRO 3.4 20.2 - - - -
137R LEU* 3.4 10.1 - - - -
138R ASN* 3.4 35.7 - - - -
139R VAL* 3.9 15.0 - - + -
142R TYR* 3.8 39.8 - + + -
271R ARG* 4.1 3.6 - - - -
33S LEU* 4.4 10.5 - - + +
36S GLY 3.0 23.6 + - - +
37S THR 4.0 3.1 - - - -
38S LYS* 1.3 78.1 - - - +
40S VAL* 1.3 89.9 + - + +
42S LEU* 2.8 19.3 + - - +
43S VAL* 3.0 27.2 + - + -
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Residues in contact with VAL 40 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271R ARG* 4.5 11.2 - - - +
37S THR 3.2 16.2 - - - +
38S LYS* 3.1 1.8 - - - -
39S PHE* 1.3 108.4 - - + +
41S ASN* 1.3 78.9 + - - +
42S LEU 3.1 1.7 + - - -
43S VAL* 3.2 23.9 + - + +
44S ASP* 4.1 4.3 - - - +
174S ARG* 4.5 1.0 + - - -
177S HIS* 6.3 1.6 - - + +
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Residues in contact with ASN 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S ALA 2.9 27.1 + - - +
9S GLY 4.2 0.4 + - - -
13S SER* 3.6 17.2 - - - +
38S LYS* 3.0 13.4 + - - +
39S PHE 2.9 1.0 + - - -
40S VAL* 1.3 88.5 - - - +
42S LEU* 1.3 58.9 + - - +
45S LEU* 3.4 10.0 - - - +
174S ARG* 2.8 57.0 + - + +
176S GLY 5.3 0.7 + - - -
177S HIS* 3.1 32.2 + - - -
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Residues in contact with LEU 42 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142R TYR* 3.4 35.4 + - + +
145R PHE* 5.6 0.5 - - - -
7S GLY 3.4 22.7 - - - +
8S ALA* 3.8 25.6 - - + -
13S SER* 4.9 0.2 - - - -
16S VAL* 4.7 2.2 - - + -
29S VAL* 4.1 27.1 - - + -
33S LEU* 5.3 3.6 - - + -
38S LYS 5.1 0.9 - - - +
39S PHE* 2.8 8.5 + - - +
41S ASN* 1.3 84.0 - - - +
43S VAL* 1.3 56.7 + - - +
44S ASP 3.1 2.5 - - - -
45S LEU* 2.8 46.2 + - + +
47S ILE* 4.4 15.0 - - + -
50S TYR* 4.7 6.7 - - + -
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Residues in contact with VAL 43 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131R ARG* 3.0 21.3 + - - -
134R GLU 4.9 1.7 - - - +
135R LYS* 4.0 21.6 - - + +
136R PRO* 3.6 50.4 - - + +
142R TYR* 4.2 10.8 - - + -
145R PHE* 4.4 6.3 - - + -
39S PHE* 3.0 21.2 + - + +
40S VAL* 3.2 22.6 + - + +
42S LEU* 1.3 76.8 - - - +
44S ASP* 1.3 67.8 + - + +
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Residues in contact with ASP 44 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131R ARG* 3.6 8.1 + - - +
135R LYS* 4.5 17.0 - - + +
20S ASN* 5.0 0.2 - - - +
40S VAL 4.1 5.4 - - - +
41S ASN 4.2 0.3 - - - +
43S VAL* 1.3 80.7 - - + +
45S LEU* 1.3 69.8 + - - +
46S ASN* 5.2 3.1 + - - -
174S ARG* 3.0 42.4 + - - -
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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