Contacts of the helix formed by residues 55 - 59 (chain S) in PDB entry 2WPM
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 ALA 55 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54S THR* 1.3 87.2 + - - +
56S ALA* 1.3 65.5 + - - +
57S HIS* 4.0 9.9 - - - +
58S CYS* 3.0 24.6 + - - +
59S VAL* 3.9 1.9 + - - +
102S ASP* 3.5 22.2 - - - +
104S ALA* 4.0 1.8 - - - -
196S GLY* 3.3 23.6 - - - +
212S ILE* 4.0 4.0 - - + -
213S ILE 3.9 10.8 - - - +
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Residues in contact with ALA 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55S ALA* 1.3 71.6 - - - +
57S HIS* 1.3 57.0 + - - +
58S CYS 3.0 5.9 + - - -
59S VAL* 3.0 14.1 + - - +
60S GLU* 3.5 13.2 + - - +
90S PRO* 4.1 9.6 - - + +
94S PHE* 3.5 34.9 - - + -
102S ASP* 2.9 9.4 + - - +
103S ILE 3.3 28.4 - - - +
104S ALA* 3.6 13.2 - - + -
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Residues in contact with HIS 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L GLY* 4.1 4.5 - - - -
3L ARG* 1.5 36.3 + - - -
42S CYS* 5.3 0.2 - - - -
55S ALA* 4.0 4.6 - - + +
56S ALA* 1.3 74.9 - - - +
58S CYS* 1.3 62.2 + - - +
59S VAL 3.4 0.2 - - - -
60S GLU* 3.6 29.1 - - - +
94S PHE* 3.7 8.2 - - + -
99S TYR* 3.8 22.4 - + + -
102S ASP* 2.6 31.8 + - - +
195S SER* 2.9 24.2 - - - -
214S SER 3.0 19.9 + - - -
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Residues in contact with CYS 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S LEU* 5.0 0.4 - - + -
41S PHE* 3.1 27.6 - - + -
42S CYS* 2.0 52.7 - - + -
54S THR* 4.3 4.9 - - - +
55S ALA* 3.0 19.4 + - - +
56S ALA 3.0 0.8 - - - -
57S HIS* 1.3 82.8 - - - +
59S VAL* 1.3 63.7 + - + +
60S GLU 3.8 0.8 + - - -
61S THR* 5.7 0.5 + - - -
63S ILE* 5.5 0.5 - - - +
195S SER* 3.4 25.4 - - - -
196S GLY 4.3 0.2 - - - -
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Residues in contact with VAL 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S LEU* 4.5 14.6 - - + -
41S PHE* 4.6 6.5 - - + -
54S THR* 4.5 2.0 - - + -
55S ALA 4.0 4.3 - - - +
56S ALA* 3.0 10.0 + - - +
58S CYS* 1.3 91.3 - - + +
60S GLU* 1.3 62.5 + - - +
61S THR* 3.5 11.8 + - - +
63S ILE* 4.7 9.2 - - + -
88S ILE* 3.6 41.2 - - + +
90S PRO* 5.5 5.6 - - + +
104S ALA* 3.9 20.6 - - + -
106S LEU* 4.3 16.2 - - + -
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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