Contacts of the helix formed by residues 286 - 308 (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 THR 286 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284T ARG 3.2 6.6 + - - -
285T PRO* 1.3 74.5 - - - +
287T ASP* 1.3 67.7 + - - +
288T ASP* 3.2 5.4 - - - -
289T SER* 3.8 18.0 - - - -
290T VAL* 2.8 25.1 + - - +
332T VAL* 6.0 0.9 - - - -
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Residues in contact with ASP 287 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286T THR* 1.3 72.4 - - - +
288T ASP* 1.3 58.7 + - - +
290T VAL* 4.0 4.6 - - - +
291T GLU* 3.1 28.3 + - - +
331T ARG* 5.4 11.9 - - + -
332T VAL* 5.4 10.9 - - + +
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Residues in contact with ASP 288 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250T LYS* 4.7 20.6 - - + +
286T THR* 3.2 5.4 - - - -
287T ASP* 1.3 77.4 - - - +
289T SER* 1.3 64.5 + - - +
291T GLU* 3.3 7.5 + - - +
292T VAL* 3.0 23.9 + - - +
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Residues in contact with SER 289 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281T LEU* 3.3 35.0 - - - +
284T ARG 4.6 4.0 - - - -
286T THR* 3.1 23.0 + - - -
288T ASP* 1.3 78.6 - - - +
290T VAL* 1.3 58.3 + - - +
292T VAL* 3.6 4.6 + - - +
293T ALA* 3.1 27.5 + - - +
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Residues in contact with VAL 290 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281T LEU 4.7 1.1 + - - -
285T PRO* 5.2 9.6 - - + +
286T THR 2.8 18.4 + - - +
287T ASP* 4.0 4.3 - - - +
289T SER* 1.3 76.0 - - - +
291T GLU* 1.3 59.4 + - - +
293T ALA* 3.3 6.2 + - - +
294T ILE* 2.9 33.5 + - - +
332T VAL* 5.0 17.3 - - + +
335T MET* 5.7 5.6 - - + -
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Residues in contact with GLU 291 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287T ASP 3.1 17.5 + - - +
288T ASP* 3.3 8.5 + - - +
290T VAL* 1.3 77.2 - - - +
292T VAL* 1.3 61.2 + - - +
294T ILE* 4.2 3.3 - - - +
295T GLY* 3.2 19.6 + - - -
335T MET* 5.5 6.3 - - - +
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Residues in contact with VAL 292 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250T LYS 5.6 0.7 - - - +
253T CYS* 4.5 28.5 - - + +
254T LEU* 5.1 9.0 - - + +
257T SER* 5.1 5.2 - - - -
281T LEU* 5.6 3.6 - - + -
288T ASP 3.0 16.2 + - - +
289T SER* 3.8 6.5 - - - +
291T GLU* 1.3 73.0 - - - +
293T ALA* 1.3 65.7 + - - +
295T GLY* 3.9 0.7 - - - -
296T PHE* 3.0 26.5 + - - +
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Residues in contact with ALA 293 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278T LEU* 5.0 15.1 - - + +
281T LEU* 3.9 19.9 - - + +
282T LEU* 5.4 4.9 - - + +
289T SER 3.1 18.1 + - - +
290T VAL* 3.3 7.4 + - - +
292T VAL* 1.3 78.1 - - - +
294T ILE* 1.3 58.1 + - - +
296T PHE* 3.4 6.2 + - - +
297T LEU* 2.9 29.5 + - - +
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Residues in contact with ILE 294 (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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290T VAL 2.9 17.0 + - - +
291T GLU* 4.3 3.1 - - - +
293T ALA* 1.3 76.5 - - - +
295T GLY* 1.3 65.1 + - - +
297T LEU* 3.4 6.0 + - - +
298T LYS* 3.1 22.9 + - - +
335T MET* 4.3 28.5 - - + +
336T ILE* 5.9 0.2 - - - -
339T MET* 4.8 12.8 - - + +
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Residues in contact with GLY 295 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258T LYS* 6.1 0.4 - - - -
291T GLU 3.2 16.1 + - - -
292T VAL 4.0 1.3 - - - -
294T ILE* 1.3 77.8 - - - +
296T PHE* 1.3 59.3 + - - +
298T LYS* 3.5 16.9 - - - +
299T GLU* 3.6 10.2 + - - +
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Residues in contact with PHE 296 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257T SER* 4.3 25.6 - - - +
258T LYS* 5.5 2.5 - - - +
261T ALA* 4.0 8.6 - - + +
292T VAL 3.0 19.3 + - - +
293T ALA* 3.4 8.5 - - - +
295T GLY* 1.3 74.7 - - - +
297T LEU* 1.3 63.8 - - - +
298T LYS 3.2 0.2 - - - -
299T GLU* 3.2 14.7 + - - +
300T CYS* 3.2 13.3 + - - +
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Residues in contact with LEU 297 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278T LEU* 6.4 1.8 - - + -
293T ALA 2.9 17.6 + - - +
294T ILE* 3.4 6.9 + - - +
296T PHE* 1.3 74.0 - - - +
298T LYS* 1.3 58.7 + - - +
300T CYS* 5.2 1.3 - - - -
301T GLY* 2.7 36.6 + - - +
339T MET* 6.0 4.9 - - + -
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Residues in contact with LYS 298 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294T ILE 3.1 13.9 + - - +
295T GLY* 3.5 13.2 - - - +
296T PHE 3.2 0.2 - - - -
297T LEU* 1.3 79.8 - - - +
299T GLU* 1.3 60.2 + - - +
301T GLY* 4.1 2.9 + - - -
302T LEU 5.1 1.2 + - - -
342T VAL* 6.0 3.8 - - - -
347T PHE* 5.3 1.7 - - - +
350T HIS* 3.1 30.6 - - + +
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Residues in contact with GLU 299 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258T LYS* 5.0 9.6 - - + +
261T ALA* 3.5 25.2 - - + +
262T HIS* 5.5 1.5 - - + +
265T ASN* 5.1 6.8 - - - +
295T GLY 3.6 8.7 + - - +
296T PHE* 3.2 6.7 + - - +
298T LYS* 1.3 81.3 - - - +
300T CYS* 1.3 57.9 + - - +
301T GLY 3.6 0.2 - - - -
302T LEU* 5.3 0.7 + - - +
350T HIS* 5.0 7.2 - - - +
351T PRO 4.9 8.0 - - - +
352T ILE* 5.6 2.3 - - - +
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Residues in contact with CYS 300 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261T ALA* 3.6 31.9 - - + +
264T ILE* 4.8 8.7 - - + -
265T ASN* 5.9 0.7 - - - -
274T CYS* 5.1 13.5 - - + -
296T PHE 3.2 10.1 + - - +
297T LEU* 4.7 1.6 - - - -
299T GLU* 1.3 77.1 - - - +
301T GLY* 1.3 59.0 + - - +
302T LEU 3.4 2.5 - - - -
303T LYS* 3.3 11.9 + - + +
304T LEU* 2.8 30.1 + - + +
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Residues in contact with GLY 301 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297T LEU* 2.7 28.8 + - - -
298T LYS 4.1 1.2 + - - -
299T GLU 3.6 1.6 - - - -
300T CYS* 1.3 73.2 - - - +
302T LEU* 1.3 55.9 + - - +
304T LEU* 3.2 8.7 + - - +
305T THR* 2.9 30.1 + - - -
312T ILE* 5.3 1.6 - - - +
347T PHE* 5.5 0.7 - - - -
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Residues in contact with LEU 302 (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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298T LYS 5.1 1.2 + - - -
299T GLU 5.3 0.8 + - - +
300T CYS 3.4 0.6 - - - -
301T GLY* 1.3 74.6 - - - +
303T LYS* 1.3 62.7 + - - +
305T THR* 3.2 16.6 + - - -
306T GLN* 3.3 12.6 + - - +
346T GLY 5.2 1.8 - - - +
347T PHE* 3.9 20.1 - - + +
350T HIS 3.8 21.9 + - - +
351T PRO* 5.3 1.1 - - + -
352T ILE* 5.0 11.4 - - + +
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Residues in contact with LYS 303 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264T ILE* 5.0 6.3 - - + +
265T ASN* 4.5 24.7 - - + +
300T CYS* 3.3 14.6 + - + +
302T LEU* 1.3 79.1 - - - +
304T LEU* 1.3 61.7 + - - +
306T GLN* 3.0 16.9 + - - +
307T VAL* 3.1 16.0 + - - +
352T ILE* 4.9 13.8 - - + +
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Residues in contact with LEU 304 (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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271T GLU* 5.6 10.1 - - + -
274T CYS* 6.2 4.5 - - + -
300T CYS* 2.8 18.6 + - + +
301T GLY* 3.4 13.0 - - - +
303T LYS* 1.3 73.0 - - - +
305T THR* 1.3 56.3 + - - +
307T VAL* 5.4 0.9 - - - +
308T SER* 2.8 44.6 + - - +
312T ILE* 4.2 17.7 - - + +
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Residues in contact with THR 305 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301T GLY 2.9 12.5 + - - -
302T LEU* 3.4 13.2 - - - -
304T LEU* 1.3 76.6 - - - +
306T GLN* 1.3 62.3 + - - +
309T PRO* 3.6 28.5 - - - +
312T ILE* 4.7 7.5 - - - +
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Residues in contact with GLN 306 (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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302T LEU 3.3 7.9 + - - +
303T LYS* 3.0 11.5 + - - +
305T THR* 1.3 83.2 - - - +
307T VAL* 1.3 60.0 + - - +
309T PRO* 5.1 0.7 - - - +
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Residues in contact with VAL 307 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271T GLU* 5.3 11.2 - - + -
303T LYS 3.1 13.3 + - - +
304T LEU* 5.3 0.4 - - - -
306T GLN* 1.3 76.8 - - + +
308T SER* 1.3 63.4 + - - +
309T PRO 4.1 0.7 - - - -
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Residues in contact with SER 308 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271T GLU* 5.3 11.0 - - - -
304T LEU* 2.8 24.2 + - - +
307T VAL* 1.3 77.2 - - - +
309T PRO* 1.3 66.0 - - - +
310T ARG 3.2 3.1 - - - -
311T GLY* 3.1 17.9 + - - +
312T ILE* 3.1 10.2 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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