Contacts of the helix formed by residues 250 - 261 (chain C) in PDB entry 6CAJ
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 GLY 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C ILE* 5.1 5.2 - - - +
219C ASP* 5.3 4.5 - - - -
222C ILE* 4.3 9.7 - - - +
249C THR* 1.3 79.9 + - - +
251C THR* 1.3 61.8 + - - +
252C HIS 3.3 2.0 - - - -
253C THR* 3.4 15.7 - - - -
254C LEU* 3.4 16.5 + - - +
314C ASP* 2.9 7.6 + - - +
388F ILE* 6.4 0.4 - - - -
389F PRO* 3.5 22.5 + - - +
392F SER* 6.0 1.6 - - - -
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Residues in contact with THR 251 (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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168C ILE* 3.7 21.4 - - - +
234C ILE* 3.3 28.0 - - + +
247C ALA* 3.7 18.4 - - + -
248C VAL 3.3 18.6 + - - +
249C THR 3.4 1.6 - - - -
250C GLY* 1.3 75.4 - - - +
252C HIS* 1.3 62.9 + - - +
253C THR 3.2 0.7 - - - -
254C LEU* 3.4 9.6 + - - +
255C ALA* 2.9 27.5 + - - +
314C ASP* 2.9 14.4 + - - +
316C VAL* 3.8 13.5 - - + +
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Residues in contact with HIS 252 (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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251C THR* 1.3 79.0 - - - +
253C THR* 1.3 58.2 + - - +
255C ALA* 3.3 3.6 + - - +
256C LEU* 2.9 51.9 + - + +
314C ASP* 2.9 15.3 + - + +
315C TYR* 3.0 28.3 + + - +
316C VAL* 3.8 7.5 - - + -
317C PRO* 3.5 30.7 - - + +
320C LEU* 3.6 17.3 - - + +
392F SER* 3.1 28.0 - - - +
429F ALA* 5.7 0.2 - - - +
430F HIS* 4.2 16.1 + + - -
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Residues in contact with THR 253 (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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222C ILE* 4.8 3.8 - - + -
250C GLY* 3.4 16.6 + - - -
251C THR 3.2 0.4 - - - -
252C HIS* 1.3 78.7 - - - +
254C LEU* 1.3 56.1 + - - +
256C LEU* 3.3 4.0 + - - +
257C ALA* 2.9 29.6 + - + +
388F ILE* 4.8 10.0 + - + +
392F SER* 3.9 17.2 - - - -
422F GLN* 3.3 42.2 - - + +
425F LEU* 5.7 0.2 - - - +
426F VAL* 3.7 26.8 - - + +
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Residues in contact with LEU 254 (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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166C MET* 3.7 32.1 - - + +
167C THR 4.7 7.4 - - - +
168C ILE* 4.3 18.2 - - + -
222C ILE* 3.8 24.2 - - + +
226C MET* 4.0 11.9 - - - -
232C VAL* 3.7 32.1 - - + -
234C ILE* 3.8 17.7 - - + -
250C GLY 3.4 5.1 + - - +
251C THR* 3.4 15.2 + - - +
252C HIS 3.3 0.4 - - - -
253C THR* 1.3 78.2 - - - +
255C ALA* 1.3 57.0 + - - +
257C ALA 3.8 0.5 - - - -
258C ALA* 2.9 30.9 + - - +
265C LEU* 5.3 0.4 - - + -
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Residues in contact with ALA 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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234C ILE* 6.3 0.2 - - + -
251C THR 2.9 16.9 + - - +
252C HIS 3.6 5.8 - - - +
253C THR 3.3 0.2 - - - -
254C LEU* 1.3 74.7 - - - +
256C LEU* 1.3 58.9 + - - +
258C ALA* 3.8 1.3 - - - +
259C LYS* 2.9 30.1 + - - +
265C LEU* 3.9 25.3 - - + +
316C VAL* 4.2 11.7 - - + -
320C LEU* 3.8 31.1 - - + +
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Residues in contact with LEU 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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252C HIS* 2.9 47.3 + - + +
253C THR 3.3 4.0 + - - +
255C ALA* 1.3 74.8 - - - +
257C ALA* 1.3 59.2 + - - +
259C LYS* 3.3 5.7 + - + +
260C HIS* 2.9 28.4 + - - +
320C LEU* 3.8 23.6 - - + -
425F LEU* 4.1 10.6 - - + +
426F VAL* 3.9 28.3 - - + -
429F ALA* 3.7 32.8 - - + -
430F HIS* 5.1 0.7 - - - +
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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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222C ILE* 4.6 4.5 - - + -
223C PHE* 3.8 24.2 - - + -
226C MET* 3.8 21.5 - - + -
253C THR* 2.9 16.6 + - + +
254C LEU* 3.9 5.6 - - - +
256C LEU* 1.3 75.9 - - - +
258C ALA* 1.3 58.8 + - - +
260C HIS* 3.4 0.5 + - - +
261C HIS* 2.9 35.2 + - - +
425F LEU* 3.9 13.4 - - + +
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Residues in contact with ALA 258 (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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226C MET* 3.7 12.3 - - + +
232C VAL* 3.8 7.2 - - + -
254C LEU 2.9 18.8 + - - +
255C ALA 3.8 0.9 - - - +
257C ALA* 1.3 75.0 - - - +
259C LYS* 1.3 54.9 + - - +
261C HIS 4.4 0.2 - - - +
262C SER* 2.8 27.5 + - - -
263C THR* 2.8 35.8 + - - +
265C LEU* 3.7 23.8 - - + -
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Residues in contact with LYS 259 (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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255C ALA 2.9 17.8 + - - +
256C LEU* 3.3 5.6 + - + +
258C ALA* 1.3 74.1 - - - +
260C HIS* 1.3 65.3 + - - +
262C SER* 3.6 13.2 + - - +
263C THR 5.4 0.2 - - - -
265C LEU* 5.0 2.0 - - + +
319C GLU* 4.2 18.1 + - - +
320C LEU* 3.7 28.0 - - + +
495E GLU* 4.2 22.0 + - - +
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Residues in contact with HIS 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PHE* 3.8 24.1 - + + -
256C LEU 2.9 17.0 + - - +
257C ALA 3.5 5.2 - - - +
258C ALA 3.3 0.2 - - - -
259C LYS* 1.3 79.3 - - - +
261C HIS* 1.3 59.4 + + - +
262C SER 3.3 0.7 + - - -
260D HIS 3.8 6.9 - - - +
262D SER* 2.3 55.8 + - - -
425F LEU* 3.6 36.1 - - + +
493F PRO* 5.0 8.5 - - + +
495F GLU* 4.9 10.4 + - - +
496F LEU* 4.9 8.8 - - + +
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Residues in contact with HIS 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PHE* 3.3 34.3 + + - -
226C MET* 3.5 32.0 - - + +
227C SER* 4.0 29.2 + - - -
257C ALA 2.9 25.4 + - - +
258C ALA* 4.5 1.3 - - - +
260C HIS* 1.3 77.8 - + - +
262C SER* 1.3 68.8 + - - +
263C THR* 3.3 15.5 + - + +
261D HIS* 3.5 24.1 + - - +
262D SER* 3.4 31.1 + - - -
263D THR* 5.7 1.0 - - - +
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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