Contacts of the helix formed by residues 315 - 336 (chain R) in PDB entry 5KZ5
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 MET 315 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 6.4 0.2 - - - -
169O GLU* 3.1 14.0 + - - +
239R LYS 5.1 5.6 - - - +
241R PRO* 4.2 34.8 - - + -
311R ALA 3.3 26.6 + - - +
312R GLN* 3.8 14.1 - - + +
314R GLU* 1.4 74.4 - - - +
316R GLU* 1.4 80.7 + - - +
318R ASP* 4.3 6.1 - - - -
319R HIS* 3.0 51.0 + - + +
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Residues in contact with GLU 316 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143O ARG* 3.4 38.1 + - - +
169O GLU* 3.3 47.8 + - - +
170O GLY* 5.3 0.4 - - - -
314R GLU 3.1 2.6 + - - -
315R MET* 1.4 101.2 - - - +
317R TYR* 1.4 62.8 + - - +
319R HIS* 4.4 1.1 - - - +
320R LYS* 3.2 49.4 + - - +
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Residues in contact with TYR 317 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.8 38.3 - - + +
168O ALA* 3.5 23.3 + - + +
169O GLU 5.2 0.2 - - - -
170O GLY* 6.3 0.7 - - - -
314R GLU* 3.2 7.0 + - + +
316R GLU* 1.4 77.8 - - - +
318R ASP* 1.4 62.5 + - - +
320R LYS* 3.6 12.0 + - + +
321R ARG* 3.4 26.9 + - + +
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Residues in contact with ASP 318 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.5 28.5 - - + +
43A ARG 4.9 2.1 + - - -
44A THR 5.2 2.1 + - - +
46A ILE* 3.5 22.7 - - - +
314R GLU* 3.1 42.1 + - + +
315R MET* 4.1 3.4 - - - +
317R TYR* 1.4 80.3 - - - +
319R HIS* 1.4 61.9 + - - +
321R ARG* 3.3 4.9 + - - +
322R ILE* 3.2 47.9 + - - +
412R ARG* 4.7 4.1 + - - -
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Residues in contact with HIS 319 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212R LYS* 6.2 2.5 - - - -
239R LYS* 3.8 20.8 + - + +
240R ILE* 3.4 29.2 - - + +
315R MET* 3.0 33.7 + - + +
316R GLU* 4.4 1.8 - - - +
318R ASP* 1.4 76.3 - - - +
320R LYS* 1.4 56.7 + - + +
322R ILE* 3.4 19.9 + - + -
323R SER* 3.0 33.0 + - - -
351R PRO* 3.8 22.3 - - + +
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Residues in contact with LYS 320 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316R GLU* 3.2 47.0 + - - +
317R TYR* 3.7 13.9 - - + +
318R ASP 3.3 0.2 - - - -
319R HIS* 1.4 73.6 - - + +
321R ARG* 1.3 63.5 + - - +
323R SER* 3.0 20.3 + - - -
324R LYS* 3.4 11.4 + - - +
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Residues in contact with ARG 321 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.0 33.1 - - + +
317R TYR* 3.4 18.6 + - + +
318R ASP 3.3 9.5 + - - +
319R HIS 3.3 0.2 - - - -
320R LYS* 1.3 80.9 - - - +
322R ILE* 1.4 61.2 + - + +
324R LYS* 3.6 32.9 + - - +
325R LEU* 3.3 60.7 + - + +
416R GLU* 3.3 37.2 + - - +
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Residues in contact with ILE 322 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 5.2 2.0 - - + -
239R LYS* 4.9 7.2 - - + +
318R ASP* 3.2 44.2 + - - +
319R HIS* 3.7 14.8 - - + +
321R ARG* 1.4 75.1 - - + +
323R SER* 1.4 59.3 + - - +
325R LEU* 3.3 13.9 + - + +
326R SER* 2.9 31.1 + - - -
351R PRO* 3.7 27.4 - - + -
412R ARG* 3.4 49.1 - - - +
414R THR* 5.1 4.0 - - - +
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Residues in contact with SER 323 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319R HIS* 3.0 22.2 + - - -
320R LYS* 3.0 21.7 + - - -
322R ILE* 1.4 76.0 - - - +
324R LYS* 1.4 58.4 + - - +
326R SER* 3.2 16.6 + - - -
327R GLU* 3.3 18.4 + - - +
349R HIS* 4.3 8.5 + - - -
351R PRO* 5.2 3.4 - - - -
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Residues in contact with LYS 324 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320R LYS 3.4 8.8 + - - +
321R ARG* 3.6 26.6 - - - +
322R ILE 3.4 0.6 - - - -
323R SER* 1.4 79.4 + - - +
325R LEU* 1.3 63.2 + - - +
327R GLU* 3.3 26.9 - - - +
328R ARG* 3.4 16.5 + - + +
416R GLU* 3.5 23.2 + - - -
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Residues in contact with LEU 325 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321R ARG* 3.3 51.6 - - + +
322R ILE* 3.3 8.9 + - + +
324R LYS* 1.3 76.6 - - - +
326R SER* 1.3 63.9 + - - +
328R ARG* 3.4 7.9 + - - +
329R LEU* 3.2 21.7 + - - +
414R THR* 3.5 30.5 - - + +
415R THR* 4.1 16.6 - - - -
416R GLU* 3.6 42.0 - - - +
419R VAL* 3.7 12.5 - - + +
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Residues in contact with SER 326 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322R ILE* 2.9 19.1 + - - -
323R SER* 3.2 6.8 + - - -
325R LEU* 1.3 75.5 - - - +
327R GLU* 1.4 60.2 + - - +
329R LEU* 3.3 12.2 + - - +
330R ILE* 3.3 29.0 + - - +
349R HIS* 3.0 30.2 - - - -
351R PRO* 3.8 27.2 - - - +
354R ILE* 5.8 3.5 - - - +
414R THR* 4.6 6.5 - - - +
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Residues in contact with GLU 327 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323R SER 3.3 17.9 + - - +
324R LYS* 3.3 18.1 - - - +
326R SER* 1.4 76.9 + - - +
328R ARG* 1.4 76.7 + - - +
330R ILE* 3.5 7.7 + - - +
331R GLN* 3.3 50.3 + - - +
346R PRO* 4.0 13.3 - - - +
347R LYS* 5.7 0.7 - - - -
349R HIS* 3.7 17.2 + - - +
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Residues in contact with ARG 328 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324R LYS* 3.4 19.6 + - + +
325R LEU* 3.5 11.0 - - - +
326R SER 3.3 0.6 - - - -
327R GLU* 1.4 88.3 + - - +
329R LEU* 1.4 59.6 + - - +
331R GLN* 3.3 12.9 + - - +
332R ASN* 3.1 39.9 + - - +
416R GLU* 3.1 28.5 + - - -
419R VAL* 3.5 13.0 - - + +
420R ASP* 3.3 49.1 + - - +
423R VAL* 4.0 12.3 - - - +
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Residues in contact with LEU 329 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325R LEU 3.2 10.5 + - - +
326R SER* 3.3 15.5 + - - +
328R ARG* 1.4 76.7 - - - +
330R ILE* 1.3 60.4 + - - +
332R ASN* 3.3 5.4 + - - +
333R ILE* 3.2 38.8 + - + +
354R ILE* 4.5 17.7 - - + -
408R PHE* 4.6 9.4 - - + -
410R ILE* 3.9 27.8 - - + -
414R THR* 6.1 2.0 - - + -
418R GLU* 4.7 4.9 - - + +
419R VAL* 3.7 28.2 - - + +
422R THR* 3.7 39.9 - - + +
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Residues in contact with ILE 330 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326R SER* 3.3 14.5 + - - +
327R GLU* 3.8 7.9 - - - +
328R ARG 3.4 0.2 - - - -
329R LEU* 1.3 71.4 - - + +
331R GLN* 1.4 63.9 + - - +
333R ILE* 3.6 8.0 + - - +
334R MET* 3.2 25.4 + - + +
342R MET* 3.5 48.0 - - + -
346R PRO* 4.1 14.1 - - + -
349R HIS* 3.4 37.7 - - + +
353R CYS 6.1 0.2 - - - +
354R ILE* 4.2 24.7 - - + -
356R LEU* 5.0 6.1 - - + +
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Residues in contact with GLN 331 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327R GLU* 3.3 43.2 + - - +
328R ARG* 3.3 13.7 + - - +
330R ILE* 1.4 79.6 - - + +
332R ASN* 1.4 64.9 + - - +
334R MET* 3.5 4.7 + - - +
335R LYS* 3.1 59.3 + - - +
346R PRO* 6.0 4.0 - - + -
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Residues in contact with ASN 332 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328R ARG* 3.1 39.2 + - - +
329R LEU* 3.3 7.6 + - - +
331R GLN* 1.4 77.4 - - - +
333R ILE* 1.3 62.6 + - + +
335R LYS* 4.2 4.0 - - - +
336R SER* 3.0 31.4 + - - -
419R VAL* 3.4 28.5 + - - +
422R THR* 5.3 2.0 - - + -
423R VAL* 3.4 40.8 - - + +
426R CYS* 5.0 1.1 - - - -
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Residues in contact with ILE 333 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329R LEU* 3.2 37.3 + - + +
330R ILE* 3.9 7.6 - - - +
332R ASN* 1.3 76.9 - - - +
334R MET* 1.4 65.8 + - - +
336R SER* 4.1 0.7 - - - -
337R LEU* 3.4 41.4 + - + +
340R VAL* 5.7 0.4 - - + -
354R ILE* 5.0 5.6 - - + -
356R LEU* 4.2 31.2 - - + -
358R PHE* 4.9 5.8 - - + -
408R PHE* 5.6 7.6 - - + -
422R THR* 3.9 24.7 - - + -
426R CYS* 3.9 13.0 - - - -
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Residues in contact with MET 334 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330R ILE* 3.2 18.4 + - + +
331R GLN* 3.7 6.5 - - - +
333R ILE* 1.4 81.0 - - - +
335R LYS* 1.3 64.6 + - + +
337R LEU 3.0 24.9 - - - +
340R VAL* 3.5 30.1 - - + +
341R VAL* 3.7 1.1 - - - -
342R MET* 3.3 36.1 - - + +
356R LEU* 3.7 16.8 - - + -
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Residues in contact with LYS 335 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331R GLN* 3.1 49.1 + - - +
332R ASN* 4.2 4.3 - - - +
334R MET* 1.3 84.0 - - + +
336R SER* 1.3 60.1 + - - +
337R LEU 3.5 1.9 - - - +
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Residues in contact with SER 336 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332R ASN 3.0 19.4 + - - -
333R ILE 3.5 1.1 + - - -
334R MET 3.3 0.4 - - - -
335R LYS* 1.3 78.6 - - - +
337R LEU* 1.3 62.3 + - - +
338R PRO* 4.0 5.4 - - - +
423R VAL* 4.3 12.1 + - - +
426R CYS* 3.5 27.7 - - - +
427R ILE* 4.2 19.6 - - - +
430R VAL* 4.4 9.7 - - - +
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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
------------------------------------------------------------
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