Contacts of the helix formed by residues 287 - 310 (chain B) in PDB entry 5IXC
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 CYS 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ASN 3.7 2.0 + - - -
286B LEU* 1.3 78.1 - - - +
288B ALA* 1.3 66.4 + - - +
289B GLU* 3.3 19.3 - - - +
290B GLU* 3.1 31.0 + - - +
291B GLN* 3.2 11.3 + - - +
486B TYR* 4.0 17.9 - - - -
487B GLU* 3.6 36.7 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU 3.9 0.2 + - - -
287B CYS* 1.3 73.3 - - - +
289B GLU* 1.3 65.2 + - - +
291B GLN* 3.2 9.1 + - - +
292B ALA* 2.9 29.8 + - - +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B CYS* 3.3 17.6 - - - +
288B ALA* 1.3 82.0 + - + +
290B GLU* 1.3 57.0 + - - +
292B ALA* 3.5 7.5 + - - +
293B PHE* 2.9 28.8 + - - +
296B ARG* 4.7 1.2 + - - -
449B ARG* 5.7 4.1 + - - +
486B TYR* 3.4 47.0 - - + +
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Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.8 22.8 - - + +
287B CYS* 3.1 23.6 + - - +
289B GLU* 1.3 78.7 - - - +
291B GLN* 1.3 57.3 + - - +
293B PHE* 3.3 3.0 + - + +
294B LEU* 2.9 30.5 + - + +
356B TYR* 2.6 32.3 + - + +
459B LEU* 3.7 20.1 - - + +
486B TYR* 4.0 14.5 - - + -
487B GLU* 4.9 4.0 - - - +
661B ARG* 4.3 4.7 + - - -
664B ARG* 2.9 33.5 + - - -
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 4.0 35.3 + - + +
287B CYS 3.2 15.7 + - - +
288B ALA* 3.2 11.4 + - - +
290B GLU* 1.3 74.5 - - - +
292B ALA* 1.3 64.3 + - - +
294B LEU* 3.3 26.0 + - - +
295B SER* 3.4 14.4 + - - -
663B GLY* 5.3 2.0 + - - -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ALA 2.9 16.1 + - - +
289B GLU* 3.6 7.2 - - - +
291B GLN* 1.3 74.0 - - - +
293B PHE* 1.3 64.9 + - - +
295B SER* 3.0 18.4 + - - -
296B ARG* 3.2 31.7 + - - +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLU 2.9 18.0 + - - +
290B GLU 3.5 7.0 - - - +
292B ALA* 1.3 75.7 - - - +
294B LEU* 1.3 60.9 + - + +
296B ARG* 3.1 14.0 + - - +
297B ARG* 2.7 61.6 + - + -
355B THR* 3.8 15.3 - - + -
452B LEU* 3.7 37.2 - - + -
455B GLY* 4.3 7.2 - - - -
457B ASN 3.5 19.3 - - - -
459B LEU* 3.4 44.2 - - + -
486B TYR* 3.6 17.5 - + + +
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 4.4 12.3 - - + -
290B GLU* 2.9 17.6 + - + +
291B GLN* 3.4 26.9 - - - +
292B ALA 3.2 0.4 - - - -
293B PHE* 1.3 84.9 - - + +
295B SER* 1.3 55.9 + - - +
297B ARG* 4.5 1.1 - - - +
298B LYS* 3.0 60.1 + - + +
317B GLU* 4.6 0.4 - - - -
322B VAL* 5.5 3.1 - - + -
355B THR* 3.4 34.1 - - + -
356B TYR* 3.5 26.9 - - + +
663B GLY 5.6 1.1 - - - +
664B ARG 5.6 3.6 - - - +
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLN 3.4 7.6 + - - -
292B ALA* 3.0 12.2 + - - -
294B LEU* 1.3 76.3 - - - +
296B ARG* 1.3 68.6 + - - +
297B ARG 3.3 0.3 + - - -
298B LYS* 3.3 10.1 + - - +
299B GLN* 3.5 15.3 + - - +
317B GLU* 2.6 30.6 + - - +
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLU 4.7 0.4 + - - -
292B ALA* 3.2 36.5 + - - +
293B PHE* 3.1 18.6 + - - +
295B SER* 1.3 78.9 - - - +
297B ARG* 1.3 62.6 + - - +
299B GLN* 3.1 35.6 + - - +
300B VAL* 3.6 8.5 - - - +
452B LEU 3.1 22.6 + - - -
453B GLU* 3.0 27.2 + - - +
454B ARG* 4.4 5.8 - - - +
455B GLY* 4.0 15.4 - - - +
486B TYR* 3.1 22.4 + - - -
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B PHE* 2.7 43.5 + - + +
294B LEU* 4.2 3.8 - - - +
296B ARG* 1.3 73.9 - - - +
298B LYS* 1.3 64.8 + - - +
299B GLN 3.2 0.7 + - - -
300B VAL* 3.2 14.6 + - - +
301B VAL* 3.0 26.7 + - + +
351B LEU* 3.2 21.4 + - - +
352B ASP* 3.5 18.4 + - - +
354B VAL 2.9 25.6 + - - -
355B THR* 4.1 17.5 - - + +
377B SER* 5.3 1.2 + - - -
378B GLN* 5.0 1.2 - - - +
455B GLY* 2.8 35.4 + - - -
456B GLN* 3.1 24.7 + - - +
457B ASN 3.2 18.8 + - - +
458B PRO* 3.7 9.1 - - - +
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU* 3.0 53.0 + - + +
295B SER 3.8 4.9 - - - +
296B ARG 3.3 0.6 - - - -
297B ARG* 1.3 77.6 - - - +
299B GLN* 1.3 56.9 + - - +
301B VAL* 4.2 6.7 - - - -
302B ALA* 2.9 27.4 + - - +
317B GLU* 3.7 43.3 - - + +
320B VAL* 3.5 37.2 - - + +
322B VAL* 4.2 19.8 - - + +
355B THR* 5.2 7.6 - - + +
807B ARG* 4.7 9.3 - - - +
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Residues in contact with GLN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B SER 3.5 7.4 + - - +
296B ARG* 3.1 34.5 + - - +
298B LYS* 1.3 78.3 - - - +
300B VAL* 1.3 61.5 + - + +
302B ALA* 3.5 7.3 - - + +
303B LYS* 3.0 26.5 + - - +
454B ARG 5.9 0.2 + - - -
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG 3.6 15.7 - - - +
297B ARG* 3.6 22.0 - - - +
299B GLN* 1.3 75.7 - - + +
301B VAL* 1.3 61.1 + - - +
303B LYS* 3.6 10.4 - - + +
304B ALA* 2.8 27.2 + - - +
352B ASP* 4.1 20.6 - - + +
378B GLN* 5.2 6.1 - - - +
454B ARG 4.2 6.3 - - - +
455B GLY 3.2 24.7 - - - +
456B GLN* 5.1 1.3 - - - -
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG* 3.0 31.6 + - + +
298B LYS* 3.7 5.4 - - - +
300B VAL* 1.3 75.6 - - - +
302B ALA* 1.3 54.0 + - - +
304B ALA* 3.7 1.2 - - - +
305B LEU* 2.8 47.3 + - + +
320B VAL* 3.5 22.4 - - + -
321B PRO 4.3 5.6 - - - +
323B VAL* 5.6 0.2 - - + -
352B ASP 3.3 19.7 - - - +
353B CYS* 3.6 28.0 - - - +
354B VAL 4.2 0.2 - - - +
355B THR* 4.1 14.4 - - - +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B LYS 2.9 20.1 + - - +
299B GLN* 3.5 10.1 - - - +
300B VAL 3.3 0.2 - - - -
301B VAL* 1.3 73.5 - - - +
303B LYS* 1.3 66.2 + - - +
305B LEU* 3.4 1.8 + - - +
306B LYS* 3.1 24.4 + - - +
315B LEU* 4.1 41.3 + - + +
320B VAL* 4.1 9.6 - - + -
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B GLN 3.0 17.5 + - - +
300B VAL* 3.6 10.5 - - + +
302B ALA* 1.3 77.0 - - - +
304B ALA* 1.3 55.7 + - - +
306B LYS* 3.5 4.4 + - - +
307B GLN* 2.1 47.5 - - - +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B VAL 2.8 22.3 + - - +
301B VAL 3.3 3.6 + - - +
303B LYS* 1.3 75.4 - - - +
305B LEU* 1.3 57.3 + - - +
307B GLN* 3.5 5.7 + - - +
308B ALA* 3.1 28.8 + - - +
349B GLY 4.6 5.3 - - - +
352B ASP* 3.3 39.5 - - + +
353B CYS* 4.0 7.0 - - - -
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B VAL* 2.8 40.8 + - + +
302B ALA 3.8 3.8 - - - +
304B ALA* 1.3 69.9 - - - +
306B LYS* 1.3 59.7 + - - +
308B ALA* 4.3 1.6 - - + -
309B LEU* 2.7 57.9 + - + +
311B LEU* 4.4 4.5 - - + -
315B LEU* 3.9 20.4 - - + -
320B VAL* 4.5 1.3 - - + -
321B PRO* 3.6 33.9 - - + -
353B CYS* 3.9 19.7 - - + -
800B LEU* 4.2 25.4 - - + +
804B LEU* 4.9 2.7 - - + -
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Residues in contact with LYS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA 3.1 13.3 + - - +
303B LYS* 3.7 3.1 - - - +
305B LEU* 1.3 78.8 - - - +
307B GLN* 1.3 70.2 + - - +
310B GLN* 2.8 24.4 + - - +
311B LEU* 2.8 46.9 + - + +
312B ASP 4.5 2.4 + - - -
313B ARG* 3.8 20.5 - - - +
314B ASP* 2.7 33.4 + - - +
315B LEU* 6.2 1.6 - - + +
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Residues in contact with GLN 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B LYS* 2.1 46.8 + - - +
304B ALA* 3.5 6.0 + - - +
305B LEU 3.2 0.4 - - - -
306B LYS* 1.3 81.1 - - - +
308B ALA* 1.3 67.4 + - - +
310B GLN* 3.3 28.7 + - - +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B ALA 3.1 16.5 + - - +
305B LEU* 3.8 6.3 - - + +
307B GLN* 1.3 80.3 - - - +
309B LEU* 1.3 65.8 + - + +
310B GLN* 5.1 1.7 - - - +
348B LEU 5.3 3.4 - - - +
349B GLY 4.5 8.1 - - - +
350B LEU* 4.1 25.6 - - + -
353B CYS* 4.6 2.7 - - - -
797B LEU* 4.0 19.2 - - + +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 2.7 35.4 + - + +
308B ALA* 1.3 76.1 - - + +
310B GLN* 1.3 67.7 + - - +
311B LEU* 3.5 15.2 + - + -
797B LEU* 3.7 33.7 - - + +
800B LEU* 4.3 14.8 - - + -
801B ARG* 2.7 60.0 + - + +
804B LEU* 3.8 28.5 - - + -
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Residues in contact with GLN 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LYS 2.8 12.7 + - - +
307B GLN* 3.3 25.2 + - - +
308B ALA 5.1 1.1 - - - +
309B LEU* 1.3 81.4 - - - +
311B LEU* 1.3 61.0 + - - +
801B ARG* 4.6 2.4 + - - -
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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