Contacts of the helix formed by residues 233 - 238 (chain A) in PDB entry 3SN6
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 LYS 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A GLU 4.9 1.4 + - - -
231A ARG 3.2 0.6 - - - -
232A ARG* 1.3 89.2 - - + +
234A TRP* 1.3 62.7 + - - +
235A ILE 3.5 0.3 + - - -
236A GLN* 3.5 37.1 + - - +
237A CYS* 4.4 1.6 + - - -
59B TYR* 4.5 4.7 + - - -
101B MET* 4.8 4.2 - - - +
145B TYR* 3.2 20.9 - - + +
186B ASP* 3.9 6.7 + - - +
188B MET* 3.5 22.4 - - + +
204B CYS* 3.4 35.2 - - - -
228B ASP* 3.9 12.4 + - - -
230B ASN* 3.2 17.6 - - - +
246B ASP* 3.1 32.7 + - - -
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Residues in contact with TRP 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 4.5 10.1 - - + -
224A VAL* 3.5 46.0 - - + -
227A GLN* 3.5 29.3 - - + +
228A ARG 3.6 10.2 + - - -
230A GLU 3.2 24.5 + - - -
231A ARG* 3.2 39.5 - - + -
233A LYS* 1.3 75.1 - - - +
235A ILE* 1.3 79.5 + - + +
236A GLN 3.0 2.9 - - - -
237A CYS* 2.9 33.9 + - - +
238A PHE* 3.8 10.4 - + - -
101B MET* 4.9 1.3 - - - -
117B LEU* 3.6 24.5 - - + -
145B TYR* 3.9 24.9 - + + -
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Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 4.8 10.9 - - + +
46A LEU* 5.1 3.8 - - + -
231A ARG* 2.8 35.3 + - + +
232A ARG* 3.6 15.7 - - - +
234A TRP* 1.3 95.4 - - + +
236A GLN* 1.3 67.7 + - + +
237A CYS 3.3 0.3 + - - -
238A PHE* 3.7 19.9 + - - +
244A ILE* 5.7 0.4 - - + -
272A LEU* 5.5 1.3 - - + -
276A ILE* 3.6 30.1 - - + -
279A ASN* 5.2 9.4 - - + +
282A LEU* 3.6 34.1 - - + +
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Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ARG* 3.0 24.6 + - - +
233A LYS* 3.6 36.8 - - - +
234A TRP 3.0 0.2 - - - -
235A ILE* 1.3 81.1 - - + +
237A CYS* 1.3 63.5 + - - +
238A PHE 3.1 2.2 + - - -
239A ASN* 3.6 19.2 + - - +
279A ASN* 5.5 2.7 - - - +
281A TRP* 3.8 29.3 + - + +
282A LEU* 5.7 1.8 - - - -
59B TYR* 4.0 8.6 + - - +
314B ARG* 3.1 30.0 + - - -
332B TRP* 3.8 15.8 - - + -
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Residues in contact with CYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A TRP* 2.9 23.5 + - - +
236A GLN* 1.3 78.9 - - - +
238A PHE* 1.3 61.1 + - + +
57B LYS* 3.0 11.8 + - - -
59B TYR* 3.5 21.5 - - - -
75B GLN* 2.8 28.8 + - - +
99B TRP* 3.8 4.8 + - + -
101B MET* 3.5 36.6 - - - -
117B LEU* 3.6 26.7 - - + -
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Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 5.7 1.6 - - - +
43A LEU 5.5 0.2 - - - -
44A LEU* 3.4 40.8 - - + -
222A PHE* 3.4 35.7 - + + -
224A VAL* 4.1 0.2 - - + -
234A TRP* 3.8 23.6 - + - -
235A ILE 3.8 9.6 - - - +
236A GLN 3.1 3.1 - - - -
237A CYS* 1.3 75.8 - - - +
239A ASN* 1.3 59.4 + - - +
240A ASP* 4.1 2.5 - - - +
241A VAL* 3.6 30.2 - - + +
244A ILE* 5.2 0.3 - - - +
282A LEU* 3.1 23.7 - - - +
57B LYS* 4.5 0.7 - - - +
99B TRP* 3.0 48.0 - + - +
117B LEU* 3.6 14.1 - - + -
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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