Contacts of the helix formed by residues 243 - 259 (chain C) in PDB entry 5KKR
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 GLN 243 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C GLU* 4.8 0.2 - - - -
241C SER* 3.0 16.3 + - - +
242C VAL* 1.3 84.0 - - + +
244C SER* 1.3 60.8 + - - +
245C ASP 3.2 1.3 - - - -
246C ILE* 3.3 30.6 + - + +
346C PRO* 2.8 29.8 - - + +
347C ALA 5.0 0.3 - - - +
349C ARG* 2.8 34.4 + - - +
350C ALA 4.1 10.4 - - - +
351C ASP* 3.4 31.4 + - + +
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Residues in contact with SER 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C MET* 4.8 0.2 - - - -
231C SER* 2.5 26.5 + - - -
233C GLU* 3.5 17.9 + - - -
234C ARG* 3.3 16.1 + - - -
240C TYR* 3.8 16.6 - - - -
241C SER* 3.2 17.8 + - - -
242C VAL 3.1 0.6 - - - -
243C GLN* 1.3 78.0 - - - +
245C ASP* 1.3 65.3 + - - +
246C ILE 3.2 0.4 - - - -
247C TRP* 3.5 13.3 + - - +
248C SER* 3.5 13.7 + - - -
349C ARG* 3.7 0.9 - - - +
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Residues in contact with ASP 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 3.9 14.4 - - + +
187C MET* 3.4 18.7 - - - +
188C HIS* 3.2 29.7 + - - +
189C ARG* 3.2 31.6 + - - -
190C ASP* 3.8 1.4 + - - -
191C VAL* 3.8 18.0 + - + +
234C ARG* 5.1 1.2 + - - -
242C VAL* 3.4 13.4 + - - +
243C GLN 3.2 0.4 - - - -
244C SER* 1.3 77.3 + - - +
246C ILE* 1.3 58.6 + - - +
247C TRP 3.3 0.2 - - - -
248C SER* 3.3 10.7 + - - -
249C MET* 2.9 26.7 + - - +
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Residues in contact with ILE 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 5.1 3.1 - - + -
242C VAL 3.8 5.4 - - - +
243C GLN* 3.3 25.6 - - + +
244C SER 3.2 0.6 - - - -
245C ASP* 1.3 75.5 - - - +
247C TRP* 1.3 59.6 + - - +
249C MET* 3.1 10.7 + - + +
250C GLY 2.9 24.9 + - - -
341C CYS* 3.7 28.0 - - + +
349C ARG* 4.6 1.3 - - - -
350C ALA 3.2 27.1 - - - +
351C ASP* 3.7 22.9 - - - -
352C LEU* 3.8 16.6 - - + +
355C LEU* 3.6 25.6 - - + -
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Residues in contact with TRP 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C TYR 3.9 4.9 - - - -
230C MET 3.0 26.4 + - - -
231C SER* 3.5 12.8 - - - -
232C PRO* 3.5 24.7 - - + -
243C GLN 3.5 2.4 + - - -
244C SER 3.5 6.9 + - - +
246C ILE* 1.3 79.5 - - - +
248C SER* 1.3 58.9 + - - +
250C GLY 3.3 0.9 + - - +
251C LEU* 2.9 43.4 + - + +
263C ILE* 5.6 1.3 - - + -
317C ILE* 3.6 24.4 - - + +
322C PRO* 4.5 9.0 - - + -
323C PRO* 4.9 8.7 - - + -
341C CYS 3.8 12.7 + - - -
342C LEU* 3.2 56.0 - - + +
343C ILE 3.9 15.3 - - - -
344C LYS* 4.0 10.8 - - + -
349C ARG* 3.4 20.2 - - - +
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Residues in contact with SER 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ASP* 5.6 0.7 - - - -
191C VAL* 3.4 34.7 + - - +
229C TYR* 2.8 28.4 + - - +
231C SER 4.9 1.0 + - - -
244C SER 3.5 11.3 + - - -
245C ASP* 3.3 12.3 + - - -
246C ILE 3.2 0.4 - - - -
247C TRP* 1.3 78.5 - - - +
249C MET* 1.3 52.9 + - - +
251C LEU* 4.1 3.3 - - - +
252C SER* 2.5 38.4 + - - -
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Residues in contact with MET 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C SER* 4.4 11.0 - - - +
173C VAL* 3.7 42.2 - - + -
174C ILE* 4.6 6.3 - - + -
177C LEU* 5.7 2.5 - - + -
191C VAL* 4.2 9.6 - - + +
245C ASP 2.9 13.7 + - - +
246C ILE* 3.4 11.9 - - + +
248C SER* 1.3 76.9 - - - +
250C GLY* 1.3 58.2 + - - +
252C SER* 3.3 5.5 + - - -
253C LEU* 3.0 43.3 + - + +
337C PHE* 4.2 15.5 - - + -
341C CYS* 3.8 20.0 - - - -
355C LEU* 3.7 29.8 - - + -
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Residues in contact with GLY 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ILE 2.9 13.8 + - - -
247C TRP 3.8 1.6 - - - -
249C MET* 1.3 75.4 - - - +
251C LEU* 1.3 63.7 + - - +
253C LEU* 3.3 11.7 + - - +
254C VAL* 3.3 27.0 + - - +
338C VAL* 4.5 6.5 - - - +
341C CYS* 4.0 19.7 - - - +
342C LEU* 3.9 9.4 - - - +
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C SER 3.4 26.0 - - - +
229C TYR* 3.7 22.7 - - + -
230C MET 5.0 1.1 - - - +
247C TRP* 2.9 34.5 + - + +
248C SER* 4.1 3.8 - - - +
250C GLY* 1.3 75.7 - - - +
252C SER* 1.3 62.9 + - - +
254C VAL* 3.8 1.2 + - - -
255C GLU* 3.6 4.9 + - - +
261C TYR* 4.0 6.7 - - + +
262C PRO* 3.6 32.6 - - + +
263C ILE* 4.3 12.3 - - + -
317C ILE* 5.5 1.3 - - + -
323C PRO* 3.8 31.2 - - + -
342C LEU* 3.4 12.1 - - + +
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Residues in contact with SER 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C VAL* 4.0 7.5 + - - +
192C LYS* 4.4 1.3 - - - -
193C PRO* 3.7 32.0 - - - +
196C ILE* 6.1 3.8 - - - -
229C TYR* 3.8 12.9 - - - -
248C SER 2.5 24.2 + - - -
249C MET* 3.4 7.1 - - - -
250C GLY 3.1 0.2 - - - -
251C LEU* 1.3 76.2 - - - +
253C LEU* 1.3 57.6 + - - +
255C GLU* 2.8 25.6 + - - +
256C MET* 2.9 19.9 + - - +
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LEU* 4.0 29.7 - - + +
169C VAL* 5.5 7.2 - - + -
170C SER* 3.8 21.5 - - - +
249C MET* 3.0 33.6 + - + +
250C GLY* 3.3 7.2 + - - +
252C SER* 1.3 76.1 - - - +
254C VAL* 1.3 61.8 + - - +
256C MET* 3.3 10.5 + - + +
257C ALA* 3.1 25.1 + - - +
334C PHE* 4.5 8.1 - - + -
337C PHE* 3.6 35.2 - - + -
338C VAL* 4.2 13.9 - - + -
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Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C GLY 3.3 16.2 - - - +
251C LEU* 3.9 2.5 - - - +
252C SER 3.1 0.6 - - - -
253C LEU* 1.3 76.3 - - - +
255C GLU* 1.3 60.4 + - - +
257C ALA* 3.3 1.2 + - - +
258C VAL* 3.2 33.2 + - + +
262C PRO* 3.7 28.7 - - + -
323C PRO* 4.7 4.5 - - + -
324C LYS 4.4 12.6 - - - +
325C LEU* 4.0 29.6 - - + +
338C VAL* 4.4 11.4 - - + -
342C LEU* 4.0 20.2 - - + -
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Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LEU* 3.5 17.3 - - + +
193C PRO* 3.7 8.2 - - - +
227C ARG* 3.1 30.2 + - - -
229C TYR* 2.5 31.5 + - - -
251C LEU 3.6 3.9 + - - +
252C SER 2.8 12.6 + - - +
254C VAL* 1.3 73.0 - - - +
256C MET* 1.3 61.1 + - - +
259C GLY* 2.9 28.6 + - - -
260C ARG* 3.4 28.0 - - - +
261C TYR* 3.7 16.1 + - - +
262C PRO* 3.8 9.8 - - + +
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Residues in contact with MET 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LEU* 3.7 42.2 - - + +
155C LEU* 3.4 28.2 - - + +
160C ARG* 4.0 0.2 - - - -
161C ILE* 2.9 53.4 + - + +
166C LEU* 3.7 22.9 - - + -
193C PRO* 3.7 25.8 - - - -
252C SER* 2.9 25.3 + - - +
253C LEU* 3.6 12.3 - - + +
254C VAL 3.3 0.2 - - - -
255C GLU* 1.3 77.3 - - - +
257C ALA* 1.3 59.1 + - - +
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ARG* 3.5 19.1 - - - +
161C ILE 4.0 10.4 - - - +
166C LEU* 3.8 10.1 - - + -
253C LEU 3.1 16.0 + - - +
254C VAL 3.7 4.3 - - - +
255C GLU 3.2 0.4 - - - -
256C MET* 1.3 80.6 - - - +
258C VAL* 1.3 59.9 + - - +
325C LEU* 4.2 12.1 - - + -
330C PHE* 3.5 36.7 - - + -
334C PHE* 4.3 2.5 - - + -
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Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C ARG* 4.2 16.2 + - - +
254C VAL* 3.2 24.9 - - + +
257C ALA* 1.3 82.7 - - + +
259C GLY* 1.3 60.9 + - - +
260C ARG* 3.3 31.4 - - + +
262C PRO* 5.7 1.8 - - + -
274C MET* 3.6 23.2 - - + +
325C LEU* 4.8 2.2 - - + -
326C PRO* 4.1 32.3 - - + -
330C PHE* 4.7 2.7 - - + -
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Residues in contact with GLY 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C LEU* 4.1 7.2 - - - -
159C GLY 3.3 27.4 + - - +
160C ARG* 4.2 0.6 - - - +
255C GLU* 2.9 14.5 + - - -
256C MET 4.3 0.8 - - - -
257C ALA 3.6 1.8 - - - -
258C VAL* 1.3 78.7 - - - +
260C ARG* 1.3 61.1 + - - +
274C MET* 5.2 1.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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