Contacts of the helix formed by residues 253 - 267 (chain C) in PDB entry 6Q2N
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 ASN 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C ARG* 4.5 11.4 + - - +
249C SER 4.0 9.4 - - - +
250C CYS* 2.9 21.7 + - - +
251C LYS 3.2 0.2 - - - -
252C THR* 1.3 79.4 - - - +
254C TYR* 1.3 72.8 + - - +
255C ILE* 3.8 7.8 + - - +
256C CYS* 3.6 21.9 + - + +
257C ARG* 3.3 19.2 + - - -
295C THR* 4.1 5.7 - - - -
296C VAL* 3.7 28.0 - - + +
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Residues in contact with TYR 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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253C ASN* 1.3 74.6 + - - +
255C ILE* 1.3 83.0 + - + +
257C ARG* 3.1 40.7 + - - +
258C SER* 3.0 24.9 + - - -
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Residues in contact with ILE 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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197C ARG* 3.7 33.0 - - - +
253C ASN* 3.8 6.3 + - - +
254C TYR* 1.3 92.1 - - + +
256C CYS* 1.3 61.7 + - - +
258C SER* 3.2 10.4 - - - -
259C ARG* 3.0 61.0 + - - +
295C THR* 3.8 4.3 - - + -
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Residues in contact with CYS 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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250C CYS* 2.0 50.0 - - - -
253C ASN* 3.6 22.6 - - + +
255C ILE* 1.3 78.1 - - - +
257C ARG* 1.3 56.1 + - - +
259C ARG* 3.1 5.3 + - - +
260C LEU* 2.9 28.8 + - - +
292C LEU* 4.7 1.1 - - - +
295C THR* 3.3 35.4 - - - +
296C VAL* 3.6 2.7 - - - -
297C MET* 3.6 18.8 - - - -
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Residues in contact with ARG 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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250C CYS* 3.9 8.2 - - - +
251C LYS* 3.8 29.0 + - + +
252C THR 5.3 0.4 - - - -
253C ASN 3.3 31.7 + - - +
254C TYR* 3.1 43.9 + - - +
256C CYS* 1.3 76.5 - - - +
258C SER* 1.3 60.6 + - - +
260C LEU* 4.3 8.3 - - + -
261C ALA* 2.9 32.8 + - + +
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Residues in contact with SER 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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254C TYR* 3.0 18.2 + - - -
255C ILE* 3.2 15.5 - - - -
257C ARG* 1.3 76.8 - - - +
259C ARG* 1.3 70.7 + - - +
261C ALA* 3.9 3.5 - - - +
262C ASP* 3.0 36.4 + - - +
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Residues in contact with ARG 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ARG* 4.4 17.7 + - - +
200C PHE* 5.4 9.9 + - - +
201C ASP* 5.4 8.9 + - - +
255C ILE* 3.0 41.9 + - - +
256C CYS* 3.1 4.9 + - - +
258C SER* 1.3 83.1 + - - +
260C LEU* 1.3 57.6 + - - +
262C ASP* 3.4 12.4 + - - +
263C PHE* 3.0 23.2 + - - +
287C LEU 5.4 1.3 - - - -
288C ALA 4.4 2.4 - - - +
290C SER 4.7 0.6 + - - -
291C GLY* 2.3 56.2 + - - +
292C LEU* 3.5 34.8 - - + +
293C ILE 3.8 10.5 + - - -
295C THR* 4.4 6.7 - - + +
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Residues in contact with LEU 260 (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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247C GLN* 4.7 15.0 - - + +
250C CYS* 3.8 23.3 - - + -
251C LYS* 5.6 6.3 - - + -
256C CYS 2.9 15.3 + - - +
257C ARG* 4.0 7.9 - - + +
258C SER 3.2 0.2 - - - -
259C ARG* 1.3 77.1 - - - +
261C ALA* 1.3 61.1 + - - +
263C PHE* 3.2 4.3 + - + +
264C PHE* 2.9 36.6 + - + +
292C LEU* 3.7 17.9 - - + +
297C MET* 4.2 19.5 - - + -
328C PHE* 4.4 23.6 - - + -
332C PHE* 4.4 15.0 - - + -
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Residues in contact with ALA 261 (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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257C ARG* 2.9 21.1 + - + +
258C SER* 4.0 3.8 - - - +
260C LEU* 1.3 73.5 - - - +
262C ASP* 1.3 57.5 + - - +
264C PHE* 3.5 12.4 + - - +
265C THR* 2.5 37.9 + - - +
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Residues in contact with ASP 262 (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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258C SER* 3.0 31.3 + - - +
259C ARG* 3.4 17.2 - - - +
261C ALA* 1.3 77.8 - - - +
263C PHE* 1.3 56.6 + - - +
265C THR* 3.0 6.5 + - - -
266C ASN* 2.6 49.4 + - - +
287C LEU 4.9 5.3 - - - +
288C ALA* 4.1 9.2 - - - -
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Residues in contact with PHE 263 (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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259C ARG 3.0 17.2 + - - +
260C LEU* 3.2 6.9 + - + +
262C ASP* 1.3 73.2 - - - +
264C PHE* 1.3 66.7 + - - +
265C THR 3.3 0.3 + - - -
266C ASN 3.4 6.9 + - - -
267C CYS* 3.7 28.0 + - + -
288C ALA* 3.5 20.8 - - + +
289C TYR* 3.5 34.8 - + + -
292C LEU* 3.6 19.7 - - + -
331C PHE* 3.7 29.0 - + - -
332C PHE* 3.7 34.3 - + + -
335C ASN* 5.1 1.6 - - - -
338C LEU* 3.6 25.1 - - + -
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Residues in contact with PHE 264 (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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247C GLN* 5.3 5.8 - - - -
260C LEU* 2.9 22.0 + - + +
261C ALA* 3.5 15.0 - - - +
263C PHE* 1.3 77.7 - - - +
265C THR* 1.3 60.3 + - - +
268C GLN* 3.4 27.0 + - - +
328C PHE* 3.6 35.7 - + - -
331C PHE* 4.0 26.2 - + - -
76E TYR* 4.7 2.9 - - - -
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Residues in contact with THR 265 (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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261C ALA* 2.5 22.0 + - - +
262C ASP* 3.0 12.3 + - - -
264C PHE* 1.3 80.7 - - - +
266C ASN* 1.3 72.4 + - - +
267C CYS 4.0 0.2 - - - -
268C GLN* 4.3 1.8 - - - +
76E TYR* 3.4 35.5 + - + -
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Residues in contact with ASN 266 (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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262C ASP* 2.6 39.0 + - - +
263C PHE 3.4 2.6 + - - +
265C THR* 1.3 88.7 - - - +
267C CYS* 1.3 60.3 + - - +
268C GLN* 3.1 9.4 + - - +
281C ASN* 4.8 10.0 - - - +
284C ASP* 3.0 52.4 + - + +
285C CYS* 3.8 5.7 - - - +
287C LEU 5.0 0.4 - - - -
288C ALA* 3.4 12.7 - - + +
337C CYS* 4.9 3.8 - - - -
76E TYR* 5.1 1.2 + - - -
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Residues in contact with CYS 267 (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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263C PHE* 3.7 28.7 + - + -
266C ASN* 1.3 77.6 - - - +
268C GLN* 1.3 59.9 + - - +
269C PRO* 3.3 0.9 - - - +
285C CYS* 2.0 66.0 - - - -
288C ALA* 4.3 0.4 - - - -
331C PHE* 4.9 2.0 - - - -
335C ASN* 2.3 45.5 + - - +
337C CYS* 3.4 7.8 - - - +
338C LEU* 4.0 11.0 - - + +
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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