Contacts of the helix formed by residues 249 - 266 (chain T) 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 ASP 249 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244T GLY* 2.8 25.9 + - - +
247T ARG* 4.2 10.8 - - + +
248T ASN* 1.3 70.4 - - - +
250T LYS* 1.3 65.2 + - - +
251T GLN 3.3 2.2 - - - -
252T LEU* 3.2 13.2 + - + +
253T CYS* 3.0 22.0 + - - +
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Residues in contact with LYS 250 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248T ASN 3.5 6.7 + - - +
249T ASP* 1.3 73.7 - - - +
251T GLN* 1.3 57.6 + - - +
253T CYS* 3.2 8.4 + - - +
254T LEU* 2.8 30.6 + - - +
288T ASP* 4.7 21.3 - - + +
292T VAL* 5.6 1.4 - - - +
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Residues in contact with GLN 251 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249T ASP 3.3 0.4 - - - -
250T LYS* 1.3 77.3 - - - +
252T LEU* 1.3 58.6 + - - +
254T LEU* 3.2 8.0 + - - +
255T THR* 3.0 29.0 + - - -
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Residues in contact with LEU 252 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240T ASN 5.2 5.6 - - - +
244T GLY* 4.5 9.2 - - - -
249T ASP* 3.2 21.3 + - + +
251T GLN* 1.3 76.0 - - - +
253T CYS* 1.3 61.2 + - - +
255T THR* 4.5 3.1 - - - +
256T ALA* 2.9 35.8 + - + +
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Residues in contact with CYS 253 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241T PHE* 5.2 9.1 - - - +
244T GLY* 4.9 1.4 - - - -
245T TYR* 5.0 15.0 - - + +
249T ASP 3.0 13.4 + - - +
250T LYS* 3.2 11.6 + - - +
252T LEU* 1.3 76.5 - - - +
254T LEU* 1.3 62.7 + - - +
256T ALA* 4.4 2.4 - - - +
257T SER* 3.0 29.8 + - - -
292T VAL* 4.5 17.7 - - + +
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Residues in contact with LEU 254 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250T LYS 2.8 16.5 + - - +
251T GLN* 3.2 8.5 + - - +
253T CYS* 1.3 77.5 - - - +
255T THR* 1.3 58.3 + - - +
257T SER* 4.2 1.8 - - - -
258T LYS* 3.1 28.1 + - - +
292T VAL* 5.1 11.2 - - + +
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Residues in contact with THR 255 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205T GLN* 4.5 3.2 - - - +
206T SER* 4.5 24.5 - - - -
209T PRO* 4.3 22.7 - - - +
212T THR* 5.9 0.3 - - - -
251T GLN 3.0 15.7 + - - -
252T LEU* 4.4 3.4 - - - -
254T LEU* 1.3 75.0 - - - +
256T ALA* 1.3 65.9 + - - +
258T LYS* 3.3 7.0 + - - +
259T PHE* 3.0 22.0 + - - +
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Residues in contact with ALA 256 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237T LEU* 4.4 11.8 - - + +
240T ASN* 4.6 8.1 - - + -
241T PHE* 4.0 32.8 - - + +
252T LEU* 2.9 19.7 + - + +
253T CYS 4.4 0.7 - - - +
255T THR* 1.3 75.5 - - - +
257T SER* 1.3 62.3 + - - +
259T PHE* 3.2 8.9 + - - +
260T VAL* 3.0 21.5 + - - +
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Residues in contact with SER 257 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241T PHE* 5.2 4.4 - - - +
253T CYS 3.0 21.7 + - - -
254T LEU* 4.2 2.2 - - - -
256T ALA* 1.3 76.8 - - - +
258T LYS* 1.3 63.1 + - - +
260T VAL* 3.0 9.8 + - - +
261T ALA* 2.9 24.1 + - - +
277T MET* 6.3 2.5 - - - -
292T VAL* 5.1 6.3 - - - -
296T PHE* 4.3 23.8 - - - +
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Residues in contact with LYS 258 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209T PRO* 5.5 5.4 - - + +
212T THR* 4.8 14.9 - - - -
254T LEU 3.1 20.4 + - - +
255T THR* 3.6 9.2 - - - +
257T SER* 1.3 75.8 - - - +
259T PHE* 1.3 62.2 + - - +
261T ALA* 3.4 8.6 + - - +
262T HIS* 3.3 21.5 + - - +
295T GLY 6.1 0.4 - - - -
296T PHE* 5.5 3.3 - - - +
299T GLU* 5.0 8.3 - - + +
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Residues in contact with PHE 259 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205T GLN* 5.2 14.4 - - + -
212T THR* 5.0 11.6 - - - -
216T ALA* 5.1 1.5 - - - +
237T LEU* 5.6 8.5 - - + -
255T THR 3.0 12.7 + - - +
256T ALA* 3.4 11.7 - - - +
257T SER 3.1 0.2 - - - -
258T LYS* 1.3 71.8 - - - +
260T VAL* 1.3 68.2 + - - +
262T HIS* 3.1 4.9 + - - +
263T LEU* 2.9 24.4 + - - +
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Residues in contact with VAL 260 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237T LEU* 6.0 4.4 - - + +
256T ALA 3.0 13.5 + - - +
257T SER* 3.0 12.1 + - - +
259T PHE* 1.3 75.6 - - - +
261T ALA* 1.3 64.1 + - - +
263T LEU* 3.2 7.2 + - - +
264T ILE* 3.0 22.7 + - - +
269T ALA* 5.3 2.9 - - - +
273T LEU* 6.2 4.3 - - + -
274T CYS* 6.3 3.4 - - - +
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Residues in contact with ALA 261 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257T SER 2.9 12.0 + - - +
258T LYS* 3.5 7.9 - - - +
259T PHE 3.2 0.2 - - - -
260T VAL* 1.3 75.5 - - - +
262T HIS* 1.3 58.8 + - - +
264T ILE* 3.2 7.6 + - - +
265T ASN* 2.9 25.0 + - - +
274T CYS* 6.2 1.6 - - - -
296T PHE* 4.0 7.2 - - + +
299T GLU* 3.5 32.5 - - + -
300T CYS* 3.6 26.7 - - + +
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Residues in contact with HIS 262 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212T THR* 4.5 8.7 - - - +
213T HIS* 4.5 10.5 - - + +
216T ALA* 3.5 24.0 - - + +
258T LYS 3.3 8.6 + - - +
259T PHE* 3.1 7.3 + - - +
261T ALA* 1.3 75.5 - - - +
263T LEU* 1.3 61.1 + - - +
264T ILE 3.2 1.3 - - - -
265T ASN* 3.6 10.3 - - + +
266T GLN* 3.0 27.9 + - - +
299T GLU* 5.5 1.5 - - + +
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Residues in contact with LEU 263 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216T ALA* 4.1 8.1 - - + +
219T VAL* 6.2 3.6 - - + -
234T LEU* 6.6 0.4 - - + -
259T PHE 2.9 16.4 + - - +
260T VAL* 3.8 7.4 - - - +
262T HIS* 1.3 75.3 - - - +
264T ILE* 1.3 59.6 + - - +
266T GLN* 3.4 4.9 + - - -
267T ASN 3.2 2.9 + - - -
268T VAL* 2.9 42.9 + - + +
269T ALA* 3.3 13.9 + - + -
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Residues in contact with ILE 264 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260T VAL 3.0 12.9 + - - +
261T ALA* 3.3 12.6 - - - +
263T LEU* 1.3 72.8 - - - +
265T ASN* 1.3 64.6 + - - +
266T GLN 3.0 1.3 - - - -
267T ASN* 3.0 14.4 + - - +
269T ALA* 3.7 22.1 - - + +
270T HIS 5.4 0.4 - - - -
271T GLU* 5.1 14.4 - - + -
274T CYS* 5.6 6.3 - - + -
300T CYS* 4.8 8.5 - - + -
303T LYS* 5.0 8.2 - - + +
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Residues in contact with ASN 265 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261T ALA 2.9 14.5 + - - +
262T HIS* 3.4 15.7 + - + +
264T ILE* 1.3 74.8 - - - +
266T GLN* 1.3 58.2 + - - +
267T ASN* 3.3 1.3 + - - +
299T GLU 5.1 7.6 - - - +
300T CYS* 5.9 0.2 - - - -
303T LYS* 4.5 16.2 - - + +
352T ILE* 3.2 41.4 - - + +
353T ILE* 5.3 5.2 - - - +
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Residues in contact with GLN 266 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216T ALA* 4.3 10.3 - - + +
217T ALA* 5.3 2.0 - - - +
220T ALA* 3.8 29.8 - - + +
262T HIS 3.0 16.2 + - - +
263T LEU* 3.8 6.1 - - - +
264T ILE 3.0 0.4 - - - -
265T ASN* 1.3 76.8 - - + +
267T ASN* 1.3 70.1 + - - +
268T VAL* 3.1 4.3 + - + +
360T VAL* 6.0 1.0 - - - +
365T GLN* 4.9 5.7 - - - +
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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