Contacts of the helix formed by residues 230 - 239 (chain A) in PDB entry 1KXM
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 LEU 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A HEM 3.6 35.4 - - + -
2A BZI 3.8 15.9 + - + -
147A ALA* 4.0 7.0 - - + +
175A HIS* 3.8 6.1 - - + -
180A THR* 4.3 1.1 - - + -
187A TYR* 3.4 44.6 - - + -
220A GLN* 5.0 0.4 - - - -
221A TRP* 4.4 0.9 - - - -
228A MET* 3.7 15.7 - - + -
229A MET* 1.3 74.8 - - - +
231A PRO* 1.3 64.8 - - + +
232A THR* 3.7 16.6 - - - +
233A ASP* 2.8 40.7 + - - +
234A TYR* 2.9 11.8 + - - +
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Residues in contact with PRO 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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147A ALA 3.3 17.5 - - - +
148A ASP* 4.1 15.7 - - + -
149A LYS 3.5 12.1 - - - +
150A ASP* 5.2 0.2 - - - -
187A TYR* 4.0 10.3 - - + +
211A LEU* 5.9 0.4 - - + -
219A GLU* 3.4 33.0 - - + +
220A GLN* 4.4 2.7 - - - -
221A TRP* 4.1 17.9 - - + +
229A MET 4.3 2.5 - - - +
230A LEU* 1.3 82.4 - - + +
232A THR* 1.3 60.3 + - - +
234A TYR* 3.4 2.1 + - - +
235A SER* 3.0 23.2 + - - -
238A GLN* 4.7 2.6 + - - -
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Residues in contact with THR 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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1A HEM 3.5 25.9 - - + +
146A ASP 3.4 20.2 - - - +
147A ALA 3.1 19.5 + - - +
149A LYS* 3.5 19.3 - - + +
153A TYR* 4.6 0.7 - - + -
154A VAL* 3.7 24.8 - - + +
172A MET* 4.8 4.3 - - - +
230A LEU* 3.7 9.9 - - - +
231A PRO* 1.3 76.3 - - - +
233A ASP* 1.3 66.0 + - - +
235A SER* 3.0 19.0 + - - -
236A LEU* 3.9 9.0 - - - +
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Residues in contact with ASP 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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2A BZI 2.5 34.1 + - - -
172A MET* 3.8 6.2 - - - +
175A HIS* 2.8 23.7 + - - -
200A PHE* 3.5 18.9 - - + -
204A LEU* 3.8 8.4 - - - +
229A MET* 3.7 15.0 - - - -
230A LEU* 2.8 33.9 + - - +
232A THR* 1.3 74.6 + - - +
234A TYR* 1.3 64.3 + - - +
236A LEU* 3.0 26.9 + - - +
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Residues in contact with TYR 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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204A LEU* 4.2 10.1 - - + -
209A TRP* 3.8 24.1 + + + +
221A TRP* 3.3 84.4 - + + +
229A MET* 4.6 2.2 - - + +
230A LEU 2.9 7.7 + - - +
231A PRO 3.8 3.1 - - - +
233A ASP* 1.3 77.7 - - - +
235A SER* 1.3 57.2 + - - +
236A LEU 3.0 0.4 - - - -
237A ILE* 2.9 55.5 + - + +
238A GLN* 3.3 31.1 + - + -
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Residues in contact with SER 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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150A ASP* 3.8 6.6 - - - -
151A ALA* 3.4 35.8 + - - +
154A VAL* 4.0 6.6 - - - +
231A PRO 3.0 16.9 + - - -
232A THR 3.0 14.1 + - - -
233A ASP 3.1 0.6 - - - -
234A TYR* 1.3 77.2 - - - +
236A LEU* 1.3 66.9 + - - +
238A GLN* 3.4 18.8 - - - +
239A ASP* 3.0 28.6 + - - +
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Residues in contact with LEU 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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154A VAL* 4.8 2.0 - - + -
168A VAL* 4.9 1.1 - - + -
169A VAL* 4.5 19.5 - - + -
172A MET* 3.7 44.9 - - + -
200A PHE* 3.9 16.2 - - + -
204A LEU* 4.3 2.9 - - + -
232A THR 3.9 5.8 - - - +
233A ASP 3.0 14.7 + - - +
235A SER* 1.3 83.9 - - - +
237A ILE* 1.3 58.3 + - - +
242A TYR* 3.3 39.9 - - + -
243A LEU* 3.0 28.2 + - - -
246A VAL* 3.7 16.3 - - + +
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Residues in contact with ILE 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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204A LEU* 3.6 46.9 - - + +
205A LEU* 4.2 7.4 - - + -
209A TRP* 4.7 1.6 - - + -
234A TYR* 2.9 51.1 + - + +
236A LEU* 1.3 81.8 - - - +
238A GLN* 1.3 62.9 + - - +
239A ASP 3.5 2.0 - - - -
243A LEU* 3.8 38.5 - - + +
246A VAL* 4.0 11.9 - - + -
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Residues in contact with GLN 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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150A ASP* 5.3 8.1 - - - +
151A ALA* 5.4 2.0 - - + +
221A TRP* 4.3 7.2 - - - +
231A PRO 4.7 2.6 + - - -
234A TYR* 3.5 38.2 - - + +
235A SER* 3.1 29.6 + - - +
237A ILE* 1.3 79.0 - - - +
239A ASP* 1.3 61.8 + - - +
240A PRO* 3.7 6.2 - - - +
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Residues in contact with ASP 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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151A ALA* 3.4 25.2 - - + +
155A ARG* 2.9 42.1 + - - -
235A SER 3.0 8.5 + - - +
236A LEU 3.7 0.3 - - - +
238A GLN* 1.3 77.1 - - - +
240A PRO* 1.3 66.2 - - - +
241A LYS* 2.9 30.1 + - - +
242A TYR* 3.0 11.3 + - + +
243A LEU* 2.8 30.4 + - - +
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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