Contacts of the helix formed by residues 230 - 246 (chain B) in PDB entry 2KAI
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 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU* 2.9 41.0 + - - +
129B PRO* 4.8 3.4 - - + -
178B GLU* 2.8 26.7 + - - +
179B SER* 2.9 25.7 + - - +
180B MET 3.9 8.9 + - - +
181B LEU* 3.6 32.1 - - + -
210B GLN* 4.5 2.2 - - - +
228B TYR 3.3 1.6 + - - -
229B THR* 1.3 67.8 - - - +
231B LEU* 1.3 67.0 + - - +
232B ILE* 3.1 17.1 + - + +
233B PHE* 3.1 27.4 + - - +
234B TYR* 3.7 7.0 - - - -
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.8 22.0 - - + -
103B LEU* 4.3 11.0 - - + -
123B LEU* 3.5 33.2 - - + -
124B PRO* 3.8 16.2 - - + -
209B TRP* 3.5 25.8 - - + +
210B GLN 3.1 25.4 + - - +
211B GLY 4.7 2.2 - - - -
212B ILE* 4.0 21.1 - - + -
229B THR* 3.2 7.4 + - + +
230B LYS* 1.3 71.3 - - - +
232B ILE* 1.3 57.5 + - - +
234B TYR* 2.9 24.2 + - - +
235B LEU* 3.5 8.9 + - - +
238B ILE* 4.5 6.7 - - + -
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Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 4.1 13.8 - - + +
125B THR 4.2 6.7 - - - +
127B GLN* 3.6 39.5 - - - +
128B GLU* 3.3 29.6 - - + +
210B GLN* 4.3 5.5 + - - +
230B LYS* 3.1 15.8 + - + +
231B LEU* 1.3 79.0 - - - +
233B PHE* 1.3 64.8 + - - +
234B TYR 3.1 0.4 + - - -
235B LEU* 3.5 37.8 + - + +
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Residues in contact with PHE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A HIS* 6.0 0.4 - - - -
101B HIS* 4.5 10.8 - + - -
178B GLU* 3.8 28.3 - - + -
179B SER* 3.7 32.8 - - - -
230B LYS* 3.1 21.2 + - - +
231B LEU 3.0 0.8 + - - -
232B ILE* 1.3 82.1 - - - +
234B TYR* 1.3 87.6 + + + +
235B LEU 3.5 0.7 + - - -
236B ASP* 4.9 5.2 + - - +
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Residues in contact with TYR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A HIS* 3.6 31.6 - + - -
101B HIS* 2.8 46.8 + - - -
103B LEU* 3.3 27.1 - - + -
179B SER* 3.4 25.6 + - - -
229B THR* 3.5 25.7 - - + +
230B LYS 3.7 14.1 - - - -
231B LEU* 2.9 9.5 + - - +
233B PHE* 1.3 104.3 - + - +
235B LEU* 1.3 62.6 + - - +
236B ASP 3.2 3.2 + - - -
237B TRP* 3.4 7.9 + - + +
238B ILE* 3.0 28.1 + - + +
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Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 3.6 41.7 - - + -
124B PRO* 3.8 14.6 - - + +
125B THR* 5.6 0.9 - - - -
231B LEU 3.5 4.0 + - - +
232B ILE* 3.5 42.0 - - + +
233B PHE 3.5 1.2 - - - -
234B TYR* 1.3 76.0 - - - +
236B ASP* 1.3 58.0 + - - +
238B ILE* 3.5 5.7 + - + +
239B ASP* 3.0 41.0 + - - +
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Residues in contact with ASP 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PHE 4.9 4.9 + - - +
234B TYR 3.2 1.2 - - - -
235B LEU* 1.3 74.7 - - - +
237B TRP* 1.3 56.9 + - - +
239B ASP* 3.0 6.1 + - - +
240B ASP* 2.8 55.1 + - - +
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Residues in contact with TRP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 4.5 1.3 - - + -
89A PHE* 3.3 33.0 - - + -
90A PRO 4.0 1.3 + - - -
91A HIS* 3.6 43.5 - + + +
92A PRO* 3.7 19.2 - - + +
103B LEU* 3.6 31.0 - - + -
104B MET* 4.3 2.5 - - - -
105B LEU* 4.0 25.8 - - + -
234B TYR* 3.4 10.6 + - + +
236B ASP* 1.3 79.4 + - - +
238B ILE* 1.3 80.0 + - + +
240B ASP* 3.3 7.2 + - + +
241B THR* 2.8 58.4 + - + -
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 4.5 8.5 - - + -
53A LEU* 4.1 25.8 - - + -
103B LEU* 4.6 1.3 - - + -
105B LEU* 4.1 7.2 - - + +
123B LEU* 3.7 32.3 - - + -
231B LEU* 4.5 12.8 - - + -
234B TYR* 3.0 35.6 + - + +
235B LEU* 3.6 5.6 - - - +
237B TRP* 1.3 98.2 - - + +
239B ASP* 1.3 65.4 + - - +
241B THR* 4.0 1.2 - - - -
242B ILE* 3.1 43.3 + - + +
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 4.6 10.7 - - - +
235B LEU* 3.0 21.5 + - - +
236B ASP* 3.0 5.7 + - - +
238B ILE* 1.3 87.5 - - - +
240B ASP* 1.3 68.3 + - - +
242B ILE* 3.2 13.6 + - + +
243B THR* 2.9 30.5 + - - +
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Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ASP* 2.8 42.7 + - - +
237B TRP* 3.9 6.1 + - + +
239B ASP* 1.3 77.3 - - - +
241B THR* 1.3 58.5 + - - +
243B THR* 3.1 4.4 + - - -
244B GLU* 2.8 56.3 + - - +
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Residues in contact with THR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TRP* 4.2 2.7 - - + -
89A PHE* 3.9 35.6 - - + +
105B LEU* 3.4 28.5 - - + -
237B TRP* 2.8 37.2 + - + -
240B ASP* 1.3 77.2 - - - +
242B ILE* 1.3 59.1 + - - +
243B THR 3.0 5.2 + - - -
244B GLU* 5.0 2.6 + - - -
245B ASN* 2.9 34.0 + - - +
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.3 19.3 - - + +
48A ASN* 4.4 10.8 - - + +
51A TRP* 3.4 61.6 + - + +
105B LEU* 4.0 7.9 - - + -
238B ILE* 3.1 30.5 + - + +
239B ASP* 3.2 14.1 + - - +
241B THR* 1.3 76.8 - - - +
243B THR* 1.3 61.3 + - - +
245B ASN 4.3 6.9 + - - +
246B PRO* 5.3 2.1 - - - +
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Residues in contact with THR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ASP* 2.9 20.5 + - - +
240B ASP* 3.7 4.7 - - - -
241B THR 3.0 0.2 - - - -
242B ILE* 1.3 85.0 - - - +
244B GLU* 1.3 65.3 + - + +
245B ASN 3.0 18.0 - - - +
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Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ASP* 2.8 42.9 + - - +
241B THR* 5.0 2.2 + - - -
243B THR* 1.3 80.2 - - + +
245B ASN* 1.3 70.5 + - - +
246B PRO 4.9 0.2 - - - +
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Residues in contact with ASN 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TRP* 4.1 11.0 - - + -
89A PHE* 3.5 34.1 - - - -
107B ARG* 4.1 4.6 - - - +
241B THR* 2.9 28.7 + - - +
242B ILE 4.3 4.5 - - - +
243B THR 3.0 15.1 - - - +
244B GLU* 1.3 87.7 + - - +
246B PRO* 1.3 82.5 + - + +
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Residues in contact with PRO 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS* 3.9 26.0 - - + +
51A TRP* 4.9 5.4 - - + +
107B ARG* 3.1 49.3 + - + +
242B ILE 5.3 2.9 - - - +
245B ASN* 1.3 101.5 + - + +
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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