Contacts of the helix formed by residues 228 - 239 (chain A) in PDB entry 3KMU
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 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ASP 3.6 4.9 + - - -
227A TRP* 1.3 84.8 - - - +
229A THR* 1.3 64.1 + - - +
230A ARG* 3.5 8.4 + - - +
231A LYS* 3.1 29.2 + - - +
232A SER* 3.0 23.1 + - - -
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Residues in contact with THR 229 (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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228A SER* 1.3 74.2 - - - +
230A ARG* 1.3 56.9 - - - +
232A SER* 3.3 7.3 + - - -
233A ARG* 2.8 31.7 + - + +
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Residues in contact with ARG 230 (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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228A SER* 3.3 8.6 + - - +
229A THR* 1.3 78.2 - - - +
231A LYS* 1.3 60.4 + - + +
233A ARG* 3.4 25.2 + - - +
234A ASP* 2.9 44.7 + - - +
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Residues in contact with LYS 231 (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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224A VAL* 4.4 4.6 - - + +
225A ARG 3.3 14.5 + - - -
226A ASP* 3.0 34.8 + - - +
227A TRP* 3.7 25.9 - - + -
228A SER* 3.1 16.4 + - - +
230A ARG* 1.3 78.7 - - + +
232A SER* 1.3 59.3 + - - +
234A ASP* 3.3 10.1 + - - +
235A PHE* 2.8 28.6 + - - +
344A PHE* 3.8 33.3 + - + +
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Residues in contact with SER 232 (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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227A TRP* 3.4 16.1 - - - -
228A SER 3.0 16.3 + - - -
229A THR* 3.6 8.5 - - - -
231A LYS* 1.3 71.4 - - - +
233A ARG* 1.3 67.3 + - - +
235A PHE* 3.2 2.5 + - - +
236A ASN* 3.0 40.4 + - - +
259A SER 2.6 34.2 + - - -
260A PRO* 4.0 8.1 + - - +
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Residues in contact with ARG 233 (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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229A THR* 2.8 20.3 + - + +
230A ARG* 3.5 27.5 - - - +
232A SER* 1.3 74.0 - - - +
234A ASP* 1.3 91.9 + - - +
236A ASN* 3.1 12.2 + - - +
237A GLU* 3.0 41.2 + - + +
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Residues in contact with ASP 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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230A ARG* 2.9 33.2 + - - +
231A LYS* 3.6 9.6 - - - +
233A ARG* 1.3 104.2 + - - +
235A PHE* 1.3 63.2 + - - +
237A GLU* 3.1 5.3 + - - +
238A GLU* 2.9 46.4 + - - +
343A SER* 3.8 12.7 + - - +
344A PHE* 4.9 1.6 - - + -
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Residues in contact with PHE 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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222A LEU* 3.8 13.5 - - + -
227A TRP* 4.0 7.2 - + + -
231A LYS 2.8 15.1 + - - +
232A SER 3.2 7.8 + - - +
234A ASP* 1.3 76.3 - - - +
236A ASN* 1.3 72.8 + - - +
238A GLU* 3.2 4.7 + - - +
239A CYS* 2.9 63.4 + - - -
256A ALA* 4.2 3.6 - - + -
257A CYS 3.6 20.6 - - - -
258A GLN* 4.9 1.8 - - - -
259A SER 5.2 0.9 - - - -
265A PRO* 3.5 21.3 - - + -
266A THR 3.7 24.9 - - - -
267A LEU* 3.8 4.9 - - + -
342A PHE* 3.6 21.1 - + - -
344A PHE* 3.6 28.4 - + + -
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Residues in contact with ASN 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 SER* 3.0 30.4 + - - +
233A ARG* 3.6 7.7 - - - +
235A PHE* 1.3 89.5 - - - +
237A GLU* 1.3 64.5 - - - +
239A CYS* 4.7 2.9 - - - +
240A PRO* 3.0 24.2 - - - +
258A GLN* 3.2 57.6 - - - +
260A PRO 5.3 1.0 + - - -
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Residues in contact with GLU 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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233A ARG* 3.0 36.7 + - - +
234A ASP* 3.1 8.3 + - - +
236A ASN* 1.3 82.6 - - - +
238A GLU* 1.3 62.9 + - + +
240A PRO* 3.5 11.4 - - - +
241A ARG* 4.3 10.6 - - - +
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Residues in contact with GLU 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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234A ASP* 2.9 29.9 + - - +
235A PHE* 3.9 0.4 - - - +
237A GLU* 1.3 79.9 - - + +
239A CYS* 1.3 65.1 + - - +
241A ARG* 3.4 21.4 + - - +
242A LEU* 3.9 8.5 - - - +
316A PRO* 5.9 1.3 - - + -
317A ARG* 3.1 23.7 + - - +
342A PHE* 3.2 29.2 - - + +
343A SER* 2.5 46.8 + - - -
344A PHE* 5.4 0.2 - - - -
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Residues in contact with CYS 239 (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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235A PHE* 2.9 52.4 + - - +
236A ASN* 4.7 2.5 - - - +
238A GLU* 1.3 76.0 - - - +
240A PRO* 1.4 73.3 - - + +
242A LEU* 2.9 27.8 + - - +
243A ARG* 3.7 9.1 - - + +
253A VAL* 5.1 3.3 - - + +
256A ALA* 3.5 27.6 - - + +
267A LEU* 3.6 10.5 - - + -
342A PHE* 3.8 3.6 - - - -
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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