Contacts of the helix formed by residues 243 - 262 (chain U) in PDB entry 6FF7
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 THR 243 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242U VAL* 1.3 75.6 - - - +
244U MET* 1.3 64.6 + - - +
245U ASP* 3.1 11.5 + - - -
246U LYS* 3.1 23.4 + - - +
247U VAL* 3.7 3.8 + - - +
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Residues in contact with MET 244 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242U VAL 3.5 3.9 + - - -
243U THR* 1.3 72.4 - - - +
245U ASP* 1.3 56.1 + - - +
246U LYS 3.2 0.2 - - - -
247U VAL* 3.2 10.8 + - + +
248U HIS* 2.9 32.2 + - + +
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Residues in contact with ASP 245 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140U LEU* 4.3 23.2 - - + +
141U HIS* 4.6 16.7 - - + +
144U THR* 5.5 1.2 - - - -
243U THR* 3.1 9.3 - - - -
244U MET* 1.3 79.1 - - - +
246U LYS* 1.3 56.4 + - - +
248U HIS* 4.0 5.3 - - - +
249U TYR* 3.1 28.2 + - - +
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Residues in contact with LYS 246 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140U LEU* 5.2 3.3 - - - +
232U VAL* 5.2 15.5 - - + +
235U SER* 6.3 1.6 - - - -
236U VAL* 5.6 11.2 - - + +
242U VAL* 5.8 3.4 - - + -
243U THR* 3.1 17.7 + - - +
245U ASP* 1.3 76.8 - - - +
247U VAL* 1.3 64.8 + - - +
249U TYR* 3.4 6.0 + - - +
250U CYS* 3.1 23.6 + - - +
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Residues in contact with VAL 247 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242U VAL* 6.5 1.1 - - + -
243U THR 3.7 3.5 + - - +
244U MET* 3.2 16.5 + - - +
246U LYS* 1.3 78.9 - - - +
248U HIS* 1.3 56.9 + - - +
250U CYS* 3.2 7.8 + - - +
251U GLU* 2.9 27.8 + - - +
294U ASP* 4.8 18.4 - - + +
298U PHE* 5.7 2.3 - - - +
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Residues in contact with HIS 248 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144U THR* 4.9 8.1 - - - -
244U MET 2.9 16.6 + - - +
245U ASP* 4.2 5.4 - - - +
247U VAL* 1.3 73.3 - - - +
249U TYR* 1.3 66.5 + - - +
251U GLU* 3.6 7.4 - - - +
252U ARG* 3.0 26.2 + - - +
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Residues in contact with TYR 249 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140U LEU* 4.7 16.8 - - + +
143U GLN 6.1 0.2 - - - -
144U THR* 4.5 14.1 - - - +
147U LEU* 5.6 2.0 - - - +
232U VAL* 5.7 9.0 - - + -
245U ASP 3.1 20.0 + - - +
246U LYS* 3.7 7.4 - - - +
247U VAL 3.3 0.2 - - - -
248U HIS* 1.3 76.3 - - - +
250U CYS* 1.3 58.6 + - - +
252U ARG* 3.9 2.8 - - - +
253U PHE* 3.0 29.3 + - - +
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Residues in contact with CYS 250 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229U PHE* 6.5 0.2 - - - -
232U VAL* 6.3 2.0 - - + +
233U LEU* 5.5 14.6 - - + +
246U LYS 3.1 11.1 + - - +
247U VAL* 3.2 10.1 + - - +
249U TYR* 1.3 79.9 - - - +
251U GLU* 1.3 62.2 + - - +
253U PHE* 3.3 7.9 + - - +
254U ILE* 3.2 22.3 + - - +
288U LEU* 6.0 6.1 - - + -
298U PHE* 5.6 8.1 - - + -
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Residues in contact with GLU 251 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247U VAL 2.9 16.1 + - - +
248U HIS* 3.6 9.6 - - - +
249U TYR 3.2 0.2 - - - -
250U CYS* 1.3 76.7 - - - +
252U ARG* 1.3 62.2 + - - +
254U ILE* 3.2 7.7 + - - +
255U GLU* 3.0 21.0 + - - +
297U LEU* 5.7 7.0 - - + -
298U PHE* 5.3 18.1 - - + +
301U LEU* 5.0 6.0 - - + +
449U CYS* 5.7 8.6 - - + +
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Residues in contact with ARG 252 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144U THR* 4.7 9.6 - - - +
147U LEU* 4.4 21.3 - - + +
148U LEU* 5.1 7.0 - - + +
151U ASP* 5.8 1.2 - - - +
248U HIS 3.0 17.0 + - - +
249U TYR* 4.0 4.7 - - - +
251U GLU* 1.3 77.5 - - - +
253U PHE* 1.3 63.1 + - - +
255U GLU* 3.4 10.3 + - - +
256U LEU* 3.0 21.3 + - - +
449U CYS* 5.7 4.7 - - + +
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Residues in contact with PHE 253 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147U LEU* 5.2 5.6 - - + +
229U PHE* 4.7 19.3 - - + -
249U TYR 3.0 19.0 + - - +
250U CYS* 3.5 9.2 - - - +
251U GLU 3.1 0.4 - - - -
252U ARG* 1.3 77.6 - - - +
254U ILE* 1.3 56.4 + - - +
256U LEU* 3.1 9.5 + - - +
257U MET* 2.9 25.5 + - - +
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Residues in contact with ILE 254 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250U CYS 3.2 10.4 + - - +
251U GLU* 3.7 7.6 - - - +
253U PHE* 1.3 75.7 - - - +
255U GLU* 1.3 60.7 + - - +
257U MET* 3.2 9.1 + - - +
258U ILE* 2.9 31.0 + - - +
298U PHE* 5.4 2.5 - - - +
301U LEU* 4.1 27.9 - - + +
302U LEU* 5.1 3.8 - - + +
305U LEU* 5.1 7.0 - - + +
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Residues in contact with GLU 255 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151U ASP* 5.8 3.4 - - + -
251U GLU 3.0 12.9 + - - +
252U ARG* 3.4 14.4 - - - +
254U ILE* 1.3 78.7 - - - +
256U LEU* 1.3 59.9 + - - +
258U ILE* 3.4 6.6 + - - +
259U ASP* 3.2 23.0 + - - +
301U LEU* 5.2 3.0 - - + +
449U CYS* 4.9 15.9 - - + -
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Residues in contact with LEU 256 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147U LEU* 5.2 7.9 - - + +
151U ASP* 4.8 20.2 - - + +
252U ARG 3.0 13.3 + - - +
253U PHE* 3.1 11.9 + - - +
255U GLU* 1.3 75.0 - - - +
257U MET* 1.3 64.7 + - - +
259U ASP* 3.3 6.0 + - - +
260U LEU* 3.0 24.8 + - - +
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Residues in contact with MET 257 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253U PHE 2.9 12.2 + - - +
254U ILE* 3.2 13.2 + - - +
256U LEU* 1.3 77.1 - - - +
258U ILE* 1.3 56.9 + - - +
260U LEU* 3.4 5.5 + - - +
261U GLU* 2.9 32.4 + - - +
305U LEU* 5.2 9.6 - - + -
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Residues in contact with ILE 258 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254U ILE 2.9 15.7 + - - +
255U GLU* 3.6 8.1 - - - +
256U LEU 3.3 0.2 - - - -
257U MET* 1.3 76.3 - - - +
259U ASP* 1.3 57.6 + - - +
261U GLU* 3.1 6.5 + - - +
262U ALA* 2.8 33.7 + - + +
301U LEU 5.6 1.1 - - - +
304U MET* 5.3 9.4 - - + +
305U LEU* 5.0 19.9 - - + +
308U TYR* 5.0 2.9 - - + +
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Residues in contact with ASP 259 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151U ASP* 5.6 10.1 - - + +
154U PHE* 6.0 5.6 - - + -
155U ASN* 5.7 8.1 - - + +
255U GLU 3.2 14.6 + - - +
256U LEU* 3.3 5.6 + - - +
258U ILE* 1.3 78.1 - - - +
260U LEU* 1.3 62.5 + - - +
262U ALA* 3.3 12.9 + - - +
263U LEU* 3.4 18.0 + - - +
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Residues in contact with LEU 260 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154U PHE* 5.8 7.0 - - + +
256U LEU 3.0 17.2 + - - +
257U MET* 3.7 6.5 - - - +
259U ASP* 1.3 76.4 - - - +
261U GLU* 1.3 57.2 - - - +
263U LEU 3.2 9.5 - - - +
266U THR* 3.5 20.4 - - - +
267U ARG* 3.2 25.6 + - - -
270U PHE* 5.5 6.7 - - + -
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Residues in contact with GLU 261 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257U MET 2.9 18.9 + - - +
258U ILE* 3.6 4.3 - - - +
260U LEU* 1.3 77.1 - - - +
262U ALA* 1.3 59.0 + - - +
263U LEU 3.3 2.3 + - - -
267U ARG* 3.6 18.1 - - - +
271U ASN* 6.4 3.1 - - + +
305U LEU* 5.7 1.1 - - - +
308U TYR* 3.9 31.7 - - + +
309U THR* 5.1 2.5 - - - +
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Residues in contact with ALA 262 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258U ILE 2.8 18.0 + - - +
259U ASP* 3.3 6.0 + - - +
260U LEU 3.3 0.4 - - - -
261U GLU* 1.3 76.0 - - - +
263U LEU* 1.3 59.4 + - - +
264U LEU 4.3 0.5 + - - -
308U TYR* 5.2 7.0 - - + -
458U GLN 4.9 6.8 - - - +
459U PHE* 5.0 1.2 - - - -
460U LEU* 4.4 22.0 + - - +
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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
------------------------------------------------------------
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