Contacts of the helix formed by residues 272 - 277 (chain E) in PDB entry 2W3S
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 SER 272 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E GLY 5.1 0.7 + - - -
61E ASN* 4.7 1.0 + - - -
130E ALA* 5.1 2.7 - - - -
131E GLY* 3.6 23.6 - - - +
271E ALA* 1.3 78.6 - - - +
273E GLU* 1.3 58.4 + - - +
274E GLN* 3.0 24.3 + - - +
275E VAL* 3.0 20.6 + - - +
276E ARG* 2.9 38.9 + - - +
359E GLN* 2.9 17.1 + - - +
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Residues in contact with GLU 273 (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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59E ALA* 5.4 5.4 - - + +
120E ARG* 5.3 4.4 + - - +
122E ARG* 5.4 6.4 + - - -
124E ASP* 5.5 0.5 - - - +
127E ASP* 3.9 20.9 + - - +
128E LEU* 3.9 38.2 + - + +
250E ALA* 4.1 4.7 - - - +
253E ARG* 4.3 7.8 + - - -
272E SER* 1.3 71.9 - - - +
274E GLN* 1.3 56.2 + - + +
276E ARG* 2.7 38.0 + - - +
277E GLN* 2.7 74.7 + - + +
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Residues in contact with GLN 274 (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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45E GLY* 4.5 0.4 - - - -
48E THR* 3.2 27.1 + - + +
59E ALA* 3.4 33.5 - - + +
60E VAL* 3.9 11.6 - - - -
61E ASN* 3.8 22.1 + - - +
113E SER* 3.3 7.1 + - - -
128E LEU 4.2 5.7 - - - +
131E GLY* 3.7 13.2 + - - -
132E ASN* 2.8 28.9 + - - -
272E SER* 3.0 20.0 + - - +
273E GLU* 1.3 79.6 + - + +
275E VAL* 1.3 61.5 + - - +
277E GLN* 3.5 7.6 - - - +
278E VAL* 3.3 16.6 - - - +
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Residues in contact with VAL 275 (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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42E GLY 4.3 0.4 - - - +
61E ASN* 3.6 20.0 - - - +
64E LEU* 3.8 10.5 - - + -
206E THR* 4.1 10.3 - - + -
270E PHE* 5.5 0.7 - - + -
271E ALA* 3.6 24.0 - - + -
272E SER* 3.0 13.6 + - - +
274E GLN* 1.3 73.2 - - - +
276E ARG* 1.3 62.9 + - - +
278E VAL* 2.9 8.3 + - - +
279E ALA* 2.9 35.0 + - + +
359E GLN* 4.1 2.0 - - - +
1465E FAD 3.7 47.3 - - + +
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Residues in contact with ARG 276 (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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127E ASP* 4.6 17.4 + - - +
130E ALA* 5.4 3.6 - - - +
248E THR* 3.6 2.3 - - - -
249E ILE* 3.4 34.7 + - + -
250E ALA* 3.0 35.0 + - + +
253E ARG* 3.9 18.9 - - - +
267E LEU 3.1 24.5 + - - -
268E ARG* 2.9 23.8 + - - -
270E PHE* 2.9 21.9 + - + +
271E ALA 3.8 6.9 + - - -
272E SER* 2.9 22.7 + - - +
273E GLU* 2.7 52.1 + - - +
275E VAL* 1.3 75.1 - - - +
277E GLN* 1.3 60.4 + - - +
278E VAL 3.2 1.6 + - - -
279E ALA* 3.8 1.8 - - - +
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Residues in contact with GLN 277 (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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58E ARG* 2.8 51.5 + - + +
59E ALA 3.8 19.5 - - - +
60E VAL* 4.0 8.1 - - + -
120E ARG* 5.0 8.7 + - - +
248E THR* 3.8 13.5 + - - +
250E ALA* 3.2 24.7 - - - +
273E GLU* 2.7 43.8 + - + +
274E GLN 3.5 9.2 - - - +
275E VAL 3.0 0.2 + - - -
276E ARG* 1.3 76.0 - - - +
278E VAL* 1.3 60.7 + - - +
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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