Contacts of the helix formed by residues 301 - 326 (chain B) in PDB entry 6E7P
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 PHE 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.0 42.0 - - + -
78B VAL* 4.2 20.4 - - + -
79B GLN* 3.9 27.1 - - - +
297B PHE 4.0 13.7 + - - +
298B ARG* 3.1 15.6 + - + +
300B LEU* 1.3 78.6 - - - +
302B ASP* 1.3 61.2 + - - +
303B VAL 3.1 2.0 - - - -
304B VAL* 3.0 36.6 + - + +
305B VAL* 3.5 4.8 + - + +
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLN* 3.9 18.6 + - - +
298B ARG 4.0 4.8 + - - -
299B LEU* 2.9 29.1 - - - +
301B PHE* 1.3 76.0 - - - +
303B VAL* 1.3 60.5 + - - +
304B VAL 3.1 0.2 - - - -
305B VAL* 3.0 14.4 + - - +
306B ILE* 2.7 40.6 + - + +
369B THR* 4.6 14.5 - - - +
372B LYS* 4.8 12.7 + - + +
373B ILE* 3.6 27.2 - - - +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU 4.6 1.6 - - - +
300B LEU* 3.3 50.0 - - + +
302B ASP* 1.3 89.3 + - - +
304B VAL* 1.3 63.5 + - + +
306B ILE* 3.3 22.5 + - + +
307B LEU* 2.8 34.6 + - + +
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.5 16.6 - - + -
300B LEU 4.2 12.8 - - - +
301B PHE* 3.0 27.3 + - + +
303B VAL* 1.3 79.4 - - + +
305B VAL* 1.3 59.4 + - - +
307B LEU* 3.6 11.8 - - + +
308B THR* 2.8 46.6 + - + +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 3.7 21.5 - - + +
76B VAL* 4.7 7.0 - - + -
79B GLN* 3.9 25.4 - - + +
301B PHE* 3.9 12.1 - - + +
302B ASP* 3.0 14.1 + - - +
304B VAL* 1.3 74.0 - - - +
306B ILE* 1.3 62.7 + - - +
308B THR* 4.0 5.6 - - - -
309B CYS* 3.4 29.5 + - - +
365B THR* 4.0 19.5 - - + -
366B ILE* 4.9 1.6 - - - +
369B THR* 3.8 27.6 - - + +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASP* 2.7 25.4 + - + +
303B VAL* 3.4 26.2 - - + +
304B VAL 3.2 0.2 - - - -
305B VAL* 1.3 74.1 - - - +
307B LEU* 1.3 53.7 + - + +
310B SER* 2.6 33.7 + - - -
366B ILE* 3.5 24.7 - - + +
369B THR* 4.4 13.5 - - - +
370B ILE* 5.8 6.7 - - + +
373B ILE* 4.5 21.8 - - + -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B VAL* 2.8 23.0 + - + +
304B VAL* 3.1 15.0 + - + +
306B ILE* 1.3 79.2 - - + +
308B THR* 1.3 58.6 + - + +
310B SER* 2.6 21.9 + - - +
311B LEU* 2.7 40.6 + - + +
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Residues in contact with THR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.5 16.7 - - + +
71B VAL* 4.6 22.7 - - + -
72B LYS* 4.8 9.8 - - - +
75B VAL* 4.5 9.7 - - + +
76B VAL* 5.9 0.3 - - - +
304B VAL* 2.8 38.4 + - + +
305B VAL* 3.9 6.6 + - - -
307B LEU* 1.3 75.9 - - + +
309B CYS* 1.3 65.0 + - - +
311B LEU* 4.1 7.7 - - + +
312B SER* 3.0 30.1 + - - -
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Residues in contact with CYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 4.5 9.4 - - - +
76B VAL* 4.0 17.7 - - - -
305B VAL* 3.4 18.9 + - - +
308B THR* 1.3 87.6 + - - +
310B SER* 1.3 58.4 + - - +
312B SER* 3.5 2.6 + - - -
313B PHE* 2.8 27.9 + - - +
362B ASP* 3.4 32.1 - - + +
365B THR* 3.7 30.1 - - + -
366B ILE* 5.1 8.7 - - + -
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Residues in contact with SER 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ILE* 2.6 18.4 + - - -
307B LEU* 2.6 23.6 + - - +
309B CYS* 1.3 78.3 - - - +
311B LEU* 1.3 63.8 + - - +
313B PHE* 3.0 11.0 + - - +
314B LEU* 2.8 28.1 + - - +
366B ILE* 4.0 15.6 - - - +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.3 16.7 - - + +
307B LEU* 2.7 43.1 + - + +
308B THR* 4.1 6.7 - - + +
310B SER* 1.3 76.2 + - - +
312B SER* 1.3 57.0 + - - +
314B LEU* 3.6 13.0 + - + +
315B LEU* 3.2 23.2 + - - +
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.2 15.2 - - - +
69B GLN* 3.7 5.4 + - - +
72B LYS* 3.4 32.6 + - - -
308B THR 3.0 18.8 + - - -
309B CYS 3.8 1.8 - - - -
311B LEU* 1.3 73.8 - - - +
313B PHE* 1.3 59.6 + - - +
314B LEU 3.2 1.1 - - - -
315B LEU* 3.7 6.3 - - - +
316B CYS* 3.1 42.4 + - - +
362B ASP* 3.7 2.2 + - - +
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B CYS 2.8 21.4 + - - +
310B SER* 3.0 11.8 + - - +
312B SER* 1.3 72.4 - - - +
314B LEU* 1.3 62.4 + - - +
316B CYS* 5.4 1.6 - - - -
317B ALA* 3.5 27.7 + - + +
359B VAL* 3.6 36.3 - - + +
362B ASP* 4.2 22.7 - - + +
363B VAL* 4.1 16.6 - - + -
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B SER 2.8 13.6 + - - +
311B LEU* 3.7 15.0 - - + +
312B SER 3.2 0.2 - - - -
313B PHE* 1.3 81.4 - - - +
315B LEU* 1.3 69.6 + - + +
317B ALA* 4.4 1.7 - - - +
318B ARG* 3.6 24.1 + - + +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS* 3.5 59.7 - - + +
68B LEU* 5.5 7.6 - - + -
311B LEU 3.2 15.2 + - - +
312B SER* 3.4 6.7 + - - +
314B LEU* 1.3 84.2 - - + +
316B CYS* 1.3 76.7 + - - +
318B ARG* 3.3 26.8 + - + +
319B SER* 3.8 4.5 + - - -
355B TYR* 6.1 2.2 - - + -
801B HZ7 4.2 15.7 - - - +
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Residues in contact with CYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS 5.8 0.9 - - - -
69B GLN* 4.4 13.7 - - - -
312B SER* 3.1 33.4 + - - +
313B PHE* 5.4 0.2 - - - -
315B LEU* 1.3 89.8 - - - +
317B ALA* 1.3 61.5 + - - +
319B SER* 3.2 17.2 + - - -
320B LEU* 3.3 14.1 + - - +
355B TYR* 3.9 33.5 - - + +
358B LEU* 4.7 9.6 - - + -
359B VAL* 4.6 13.9 - - + -
362B ASP* 5.6 0.7 - - - -
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PHE* 3.5 27.1 + - + +
314B LEU* 4.4 2.2 - - - +
315B LEU 3.3 0.8 - - - -
316B CYS* 1.3 76.1 - - - +
318B ARG* 1.3 55.5 + - - +
319B SER 3.2 0.2 - - - -
320B LEU* 3.1 21.8 + - + +
321B LEU* 2.7 41.3 + - + +
359B VAL* 4.8 6.4 - - + +
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 3.6 17.1 + - + +
315B LEU* 3.3 22.3 + - - +
316B CYS 3.2 0.4 - - - -
317B ALA* 1.3 79.0 - - - +
319B SER* 1.3 55.6 + - - +
321B LEU* 3.2 19.0 + - + +
322B ARG* 2.8 32.2 + - - +
801B HZ7 3.8 33.3 + - - -
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 4.6 14.0 - - - -
315B LEU 3.8 4.0 + - - -
316B CYS* 3.2 12.6 + - - -
317B ALA 3.2 0.2 - - - -
318B ARG* 1.3 77.1 - - - +
320B LEU* 1.3 60.7 + - - +
322B ARG* 3.5 10.1 - - - +
323B GLY* 2.8 26.7 + - - -
352B ASN* 4.9 2.3 + - - -
355B TYR* 4.6 16.5 - - - -
801B HZ7 3.6 32.4 + - - -
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B CYS 3.3 8.7 + - - +
317B ALA* 3.1 17.8 + - + +
319B SER* 1.3 78.5 - - - +
321B LEU* 1.3 61.1 + - + +
323B GLY* 4.0 1.3 - - - +
324B PHE* 3.2 26.0 + - - +
351B VAL* 3.8 33.2 - - + +
352B ASN 5.0 1.3 - - - +
355B TYR* 4.3 19.5 - - + +
356B ILE* 4.6 18.4 - - + +
359B VAL* 3.7 31.4 - - + -
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA* 2.7 24.3 + - + +
318B ARG* 3.4 22.0 - - + +
319B SER 3.2 0.2 - - - -
320B LEU* 1.3 74.0 - - + +
322B ARG* 1.3 60.8 + - - +
324B PHE* 4.6 2.5 - - - +
325B LEU* 3.2 28.6 + - + +
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Residues in contact with ARG 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 4.7 23.4 + - - +
47B TYR* 6.1 3.2 - - - +
48B PHE* 5.2 16.9 - - + +
318B ARG* 2.8 21.3 + - + +
319B SER* 3.1 11.2 + - - +
321B LEU* 1.3 78.5 - - - +
323B GLY* 1.3 64.2 + - - +
325B LEU* 3.4 5.8 + - + +
326B LEU* 3.1 42.5 + - + +
801B HZ7 2.9 65.4 + - - -
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Residues in contact with GLY 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 4.5 21.5 - - - -
319B SER 2.8 14.5 + - - -
320B LEU* 3.4 2.2 + - - -
322B ARG* 1.3 78.3 - - - +
324B PHE* 1.3 59.6 - - - +
326B LEU* 3.5 11.1 + - - +
327B GLN* 3.3 20.9 + - - +
350B PHE* 4.8 8.6 - - - +
351B VAL* 5.3 7.2 - - - -
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Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU 3.2 17.0 + - - +
321B LEU* 4.7 2.5 - - - +
323B GLY* 1.3 74.3 - - - +
325B LEU* 1.3 66.7 + - - +
327B GLN* 3.2 45.1 + - - +
328B ASN* 4.2 2.4 + - - +
351B VAL* 5.2 6.7 - - + +
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 5.7 1.8 - - - +
321B LEU* 3.2 21.6 + - + +
322B ARG* 3.6 5.6 - - + +
323B GLY 3.3 0.4 - - - -
324B PHE* 1.3 83.4 - - - +
326B LEU* 1.3 74.0 + - + +
327B GLN 3.3 2.3 + - - -
328B ASN* 3.7 8.4 + - - +
329B GLU* 3.0 23.1 - - - +
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 6.2 0.4 - - + -
44B ARG* 3.4 41.1 - - + +
45B LEU* 4.5 25.4 - - + +
48B PHE* 6.3 5.4 - - + -
322B ARG* 3.1 46.5 + - + +
323B GLY* 3.5 8.9 + - - +
324B PHE 3.3 0.6 - - - -
325B LEU* 1.3 92.0 - - + +
327B GLN* 1.3 60.7 + - - +
328B ASN 3.5 0.4 - - - -
329B GLU* 3.4 21.4 + - + +
330B PHE* 4.3 10.0 + - - +
350B PHE* 5.5 3.0 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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