Contacts of the helix formed by residues 313 - 332 (chain C) in PDB entry 5ZR1
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 ASN 313 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C SER* 4.4 10.0 + - - +
271C ASN* 3.3 27.5 + - + +
306C MET* 2.5 42.9 + - + +
309C ASN 2.4 26.6 + - - -
310C THR* 3.0 22.6 - - - +
311C ASN 3.8 1.8 + - - -
312C HIS* 1.3 73.4 - - - +
314C LEU* 1.3 63.2 + - + +
315C GLN 3.4 0.7 - - - -
316C LEU* 3.0 5.2 + - - +
317C LEU* 2.6 37.0 + - - +
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 5.9 0.2 - - + -
76C ILE* 5.8 7.6 - - + -
79C ILE* 4.7 17.9 - - + -
270C SER* 3.7 32.5 + - - +
276C TYR* 3.8 19.1 - - + -
277C GLY* 3.7 32.1 - - - +
280C ILE* 3.8 22.0 - - + +
306C MET* 6.1 0.7 - - - -
312C HIS* 4.7 0.2 - - - +
313C ASN* 1.3 81.5 - - + +
315C GLN* 1.3 62.2 + - - +
317C LEU* 3.9 7.8 - - + +
318C THR* 2.7 32.7 + - - -
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Residues in contact with GLN 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ALA 4.8 0.5 - - - +
471B GLN* 3.5 54.2 + - + +
474B ASN* 3.3 39.2 - - - +
312C HIS* 4.8 7.3 - - + +
313C ASN 3.4 0.8 - - - +
314C LEU* 1.3 78.2 - - - +
316C LEU* 1.3 64.3 + - - +
318C THR* 3.6 5.0 + - - -
319C LYS* 3.0 33.5 + - - +
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LYS 3.8 18.4 - - - +
306C MET* 4.5 5.6 - - + -
309C ASN* 4.3 17.5 - - + +
312C HIS 3.6 15.3 + - - +
313C ASN* 3.0 9.2 + - - +
315C GLN* 1.3 81.6 + - - +
317C LEU* 1.3 64.2 + - - +
319C LYS* 3.8 23.8 - - + +
320C MET* 3.4 37.3 + - + +
479C ILE* 4.8 0.4 - - + -
480C PHE* 3.6 38.4 - - + -
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Residues in contact with LEU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C GLY* 4.7 4.0 - - - +
280C ILE* 3.7 33.9 - - + -
281C PHE* 4.3 12.3 - - + +
302C ILE* 3.6 30.3 - - + -
306C MET* 3.9 24.0 - - - -
313C ASN 2.6 19.9 + - - +
314C LEU* 3.9 12.1 - - + +
316C LEU* 1.3 74.1 - - - +
318C THR* 1.3 61.1 + - - +
320C MET* 3.5 7.1 + - + +
321C LEU* 3.3 45.0 + - + +
425C ILE* 4.2 9.6 - - + -
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Residues in contact with THR 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PHE* 4.1 14.6 - - + -
69C HIS* 3.8 17.5 - - + +
72C VAL* 4.2 12.7 - - + +
280C ILE* 3.9 16.6 - - - +
314C LEU 2.7 22.4 + - - -
315C GLN* 3.9 6.7 - - - -
316C LEU 3.4 0.2 - - - -
317C LEU* 1.3 74.8 - - - +
319C LYS* 1.3 60.9 + - - +
321C LEU* 3.4 4.6 + - - +
322C ASP* 3.0 50.4 + - - +
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Residues in contact with LYS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B PHE* 4.1 22.1 - - + -
470B ALA 4.8 3.0 + - - -
474B ASN* 3.6 34.1 - - + +
475B PHE 2.9 29.0 + - - +
476B VAL* 5.6 0.9 - - - +
477B PHE* 5.4 2.6 - - - -
315C GLN* 3.0 27.4 + - - +
316C LEU* 3.9 18.2 - - + +
317C LEU 3.3 0.2 - - - -
318C THR* 1.3 77.2 - - - +
320C MET* 1.3 56.3 + - - +
322C ASP* 4.1 5.1 - - - +
323C TYR* 3.2 27.5 + - - +
479C ILE* 3.8 35.1 + - + +
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Residues in contact with MET 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C PHE* 4.4 1.4 - - - -
301C PHE* 4.4 8.1 - - - -
302C ILE* 3.6 54.5 - - + +
305C LYS* 3.9 11.9 - - + -
306C MET* 4.6 4.3 - - + +
316C LEU* 3.4 34.1 + - + +
317C LEU* 3.5 9.2 + - - +
318C THR 3.3 0.2 - - - -
319C LYS* 1.3 76.0 - - - +
321C LEU* 1.3 64.6 + - - +
324C SER* 3.2 24.9 + - - -
475C LEU* 3.9 9.3 - - + +
479C ILE* 4.4 14.1 - - + -
480C PHE* 3.7 34.1 - - + -
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PHE* 4.1 14.4 - - + -
280C ILE 4.7 1.3 - - - +
281C PHE* 4.4 17.9 - - + -
284C PHE* 3.7 60.9 - - + -
298C PHE* 4.1 19.5 - - + -
302C ILE* 4.6 8.1 - - + -
317C LEU* 3.3 41.7 + - + +
318C THR 4.0 2.9 - - - +
320C MET* 1.3 76.5 - - - +
322C ASP* 1.3 62.3 + - - +
324C SER* 3.2 14.5 + - - -
325C LEU* 3.2 14.9 + - - +
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Residues in contact with ASP 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PHE* 4.8 10.4 - - + -
65C HIS* 4.4 11.4 + - - +
68C PHE* 3.3 16.3 - - - -
69C HIS* 2.9 41.9 + - - -
318C THR* 3.0 27.2 + - - +
319C LYS* 4.1 5.5 - - - +
321C LEU* 1.3 77.1 - - - +
323C TYR* 1.3 54.2 + - - +
325C LEU* 3.0 7.9 + - - +
326C MET* 2.6 43.6 + - - +
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Residues in contact with TYR 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLN* 4.0 6.1 + - - -
307B GLU* 3.2 32.0 + - + -
312B PHE* 3.8 23.8 - + + -
476B VAL* 3.9 10.9 - - + +
478B HIS* 4.8 0.5 + - - -
319C LYS 3.2 17.5 + - - +
320C MET 4.5 0.4 - - - +
322C ASP* 1.3 79.7 - - - +
324C SER* 1.3 56.4 + - - +
326C MET* 3.8 11.9 - - + +
327C SER* 3.0 25.5 + - - -
474C LEU* 4.1 23.3 - - + +
475C LEU* 4.2 10.1 - - + -
478C SER* 2.9 36.2 + - - -
479C ILE* 3.7 25.8 - - + -
403F GLY 4.3 2.1 + - - -
405F MET* 4.1 17.3 - - - +
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Residues in contact with SER 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C PHE* 4.9 0.3 - - - -
298C PHE* 3.4 32.6 - - - -
320C MET 3.2 16.4 + - - -
321C LEU* 3.2 11.8 + - - -
323C TYR* 1.3 78.1 - - - +
325C LEU* 1.3 59.3 + - - +
327C SER* 3.7 7.0 - - - -
328C TYR 3.2 19.1 + - - -
468C LEU* 3.5 24.9 - - - +
475C LEU* 4.2 13.9 - - - +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TYR* 3.5 23.7 - - + -
64C LEU* 3.7 28.0 - - + +
65C HIS* 4.6 15.9 - - + +
68C PHE* 5.4 5.4 - - + -
284C PHE* 3.6 30.3 - - + -
287C THR* 5.2 1.1 - - - +
288C VAL* 4.8 1.8 - - + -
292C LEU* 5.4 4.0 - - + -
321C LEU 3.2 11.8 + - - +
322C ASP* 3.0 10.6 + - - +
324C SER* 1.3 79.7 + - - +
326C MET* 1.3 62.5 + - - +
327C SER 3.2 0.6 + - - -
328C TYR* 3.5 8.2 + - - +
329C PHE* 3.2 47.8 - - + -
468C LEU* 4.7 4.3 - - + -
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Residues in contact with MET 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PHE* 3.5 48.9 - - + +
307B GLU* 3.7 24.7 - - + -
310B GLN* 3.7 16.4 - - + -
312B PHE* 3.5 27.8 - - + -
61C TYR* 3.2 26.5 - - + +
65C HIS* 5.4 0.4 - - + -
322C ASP* 2.6 27.6 + - + +
323C TYR* 3.8 11.2 - - + +
325C LEU* 1.3 74.9 - - - +
327C SER* 1.3 60.2 + - - +
329C PHE* 4.0 0.3 + - - -
330C PHE* 3.4 23.9 + - - +
405F MET* 4.0 5.3 - - + +
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Residues in contact with SER 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C TYR* 3.0 20.8 + - - -
324C SER* 3.7 9.4 - - - -
325C LEU 3.2 0.4 - - - -
326C MET* 1.3 76.3 - - - +
328C TYR* 1.3 63.7 + - - +
330C PHE* 3.6 1.6 + - - +
331C GLN* 3.2 38.3 + - - +
474C LEU* 3.4 25.3 - - - +
475C LEU* 5.4 3.8 - - - +
405F MET* 3.6 18.6 - - - +
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Residues in contact with TYR 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C LEU* 3.5 21.2 - - + +
324C SER 3.2 15.9 + - - +
325C LEU* 3.9 6.1 - - - +
326C MET 3.3 0.6 - - - -
327C SER* 1.3 77.4 - - - +
329C PHE* 1.3 79.3 + + + +
331C GLN* 3.2 9.3 + - - +
332C ASN* 3.1 53.8 + - + +
334C PHE 4.0 5.4 + - - -
335C SER* 3.2 30.1 + - - -
338C ILE* 5.3 3.1 - - + -
465C LEU 2.8 27.2 + - - -
466C PHE* 3.3 19.1 - - - -
467C THR 3.4 29.4 - - - -
468C LEU* 3.8 13.7 - - + -
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Residues in contact with PHE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.8 12.7 - - + -
57C ARG* 3.1 37.6 + - - +
60C LEU* 3.5 31.9 - - + -
61C TYR* 3.5 31.6 - + + -
64C LEU* 3.8 28.5 - - + -
292C LEU* 4.5 6.1 - - + -
325C LEU* 3.2 45.4 + - + +
326C MET 4.8 0.9 - - - +
328C TYR* 1.3 89.1 - + - +
330C PHE* 1.3 58.4 + - - +
331C GLN 3.5 0.2 - - - -
332C ASN 4.7 0.4 - - - -
335C SER* 3.6 26.7 - - - -
338C ILE* 4.3 6.1 - - + -
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Residues in contact with PHE 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B PRO* 4.4 2.2 - - + -
303B GLN* 3.7 42.2 - - + -
306B PHE* 4.2 4.9 - + + -
40C PRO 3.5 23.8 - - - -
41C PHE* 3.5 30.1 - + + -
42C VAL* 4.5 16.8 + - + +
44C LEU* 3.8 11.9 - - - +
57C ARG* 4.7 3.5 + - - -
326C MET 3.4 18.6 + - - +
327C SER 4.0 2.9 - - - +
328C TYR 3.1 0.8 - - - -
329C PHE* 1.3 79.6 - - - +
331C GLN* 1.3 56.6 + - - +
332C ASN 3.8 0.2 - - - -
405F MET* 3.6 31.2 - - + -
406F LEU* 3.5 36.7 - - + +
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Residues in contact with GLN 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.4 15.4 - - - +
327C SER* 3.2 31.9 + - - +
328C TYR* 3.2 9.4 + - - +
330C PHE* 1.3 77.9 - - - +
332C ASN* 1.3 82.0 + - - +
333C ALA 3.9 0.5 + - - -
469C ASP 5.8 1.6 + - - -
474C LEU* 5.1 2.4 - - - +
405F MET* 2.9 29.8 - - - +
406F LEU* 4.0 10.6 - - + +
407F GLN* 4.7 4.5 - - - +
409F THR* 4.4 17.6 + - - +
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Residues in contact with ASN 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.6 2.9 - - - +
57C ARG* 3.5 11.1 - - - -
328C TYR* 3.1 40.5 + - + +
331C GLN* 1.3 99.1 + - - +
333C ALA* 1.3 62.6 + - - +
334C PHE* 4.1 8.8 - - + +
335C SER* 2.9 35.7 + - - +
464C GLU 5.7 1.2 + - - -
465C LEU* 4.5 19.3 + - - +
412F LEU* 6.3 0.4 - - - +
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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