Contacts of the strand formed by residues 354 - 368 (chain C) in PDB entry 4J2X
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 TRP 354 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LEU* 3.8 34.8 - - + -
216C PHE* 3.5 26.0 - - - -
217C ASN* 3.7 14.8 - - + -
227C ARG 4.1 2.9 - - - -
228C TYR 4.8 0.2 - - - -
229C LEU* 4.1 16.2 - - + -
238C ALA* 4.6 2.2 - - + -
311C LYS* 4.3 2.0 - - - -
312C CYS* 2.8 45.0 + - - +
313C ALA* 5.0 0.4 - - - -
314C PHE* 3.9 24.2 - + + -
324C LEU* 3.2 34.3 + - + +
325C CYS 4.6 1.6 - - - -
326C LEU* 3.6 17.7 - - + -
331C ILE* 3.6 32.3 - - + -
351C GLY 4.0 19.0 + - - -
352C ALA 3.8 14.1 - - - -
353C SER* 1.3 75.2 + - - +
355C THR* 1.3 60.5 + - - +
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Residues in contact with THR 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ALA 3.6 1.9 - - - +
215C LEU* 3.4 7.1 - - - -
216C PHE* 2.8 71.9 + - + -
217C ASN* 5.7 0.2 - - - -
218C ARG* 5.8 2.1 + - - +
309C LEU* 3.8 35.2 - - + +
310C HIS 3.5 4.9 - - - +
311C LYS* 3.6 19.6 - - + +
353C SER 4.4 0.2 + - - -
354C TRP* 1.3 70.4 - - - +
356C ILE* 1.4 60.1 + - - +
8F G 5.3 3.5 + - - -
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Residues in contact with ILE 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ILE* 3.9 15.3 - - + -
213C VAL* 3.8 37.9 - - + -
214C ALA 3.6 3.4 - - - +
215C LEU* 3.7 17.7 - - + -
248C ILE* 4.1 18.2 - - + -
268C ILE* 6.1 0.2 - - + -
290C ILE* 4.3 13.0 - - + -
306C VAL* 3.8 22.2 - - + -
307C SER 3.9 9.9 - - - +
308C GLN* 5.1 0.2 - - - -
309C LEU* 2.8 34.8 + - - -
310C HIS* 3.1 16.7 + - + +
312C CYS* 4.0 6.5 - - - -
314C PHE* 4.8 1.1 - - + -
354C TRP 3.7 1.0 + - - -
355C THR* 1.4 71.7 - - - +
357C ILE* 1.3 59.6 + - - +
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Residues in contact with ILE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA* 3.6 28.0 - - + -
81C VAL* 3.7 20.4 - - + +
82C ALA* 5.9 0.4 - - - -
94C CYS 4.2 10.1 - - - +
95C PRO* 3.7 22.2 - - + -
207C ILE* 5.6 0.2 - - - -
213C VAL* 3.4 4.3 - - - -
214C ALA* 2.9 40.1 + - + +
216C PHE* 4.0 14.4 - - + -
308C GLN* 3.5 15.0 - - - +
309C LEU* 3.6 26.2 - - + -
356C ILE* 1.3 77.4 - - - +
358C SER* 1.3 65.4 + - - +
359C THR* 3.9 1.6 - - + +
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Residues in contact with SER 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA* 3.4 6.2 - - - +
80C LYS* 2.8 53.4 + - - +
206C CYS 4.6 2.1 + - - -
207C ILE* 3.7 16.5 - - - +
211C THR* 4.6 5.0 + - - -
212C LYS 3.5 11.7 + - - -
213C VAL* 4.3 3.4 - - - +
308C GLN* 2.9 32.9 + - - +
357C ILE* 1.3 72.1 - - - +
359C THR* 1.3 54.5 + - - +
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Residues in contact with THR 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C HIS 3.3 12.6 - - - +
79C ALA* 3.9 5.8 - - + +
80C LYS* 3.7 13.9 + - - -
95C PRO* 4.8 3.1 - - + -
212C LYS* 3.1 46.2 + - - +
213C VAL 4.2 0.4 - - - -
214C ALA* 3.7 23.1 - - + +
243C TRP* 3.5 30.3 - - + -
245C ALA* 3.7 5.5 - - - +
357C ILE 3.9 3.1 - - - +
358C SER* 1.3 77.7 - - - +
360C ASP* 1.3 64.6 + - - +
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Residues in contact with ASP 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE 3.9 0.3 - - - +
77C LEU* 3.8 1.6 - - - +
78C HIS* 2.9 44.4 + - - +
80C LYS* 3.9 27.8 - - + +
185C LYS* 3.7 27.1 - - + +
186C ARG 5.3 1.6 - - - +
212C LYS* 4.1 12.7 + - - +
243C TRP* 5.5 0.2 - - - -
359C THR* 1.3 75.8 - - - +
361C LYS* 1.4 77.0 + - - +
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Residues in contact with LYS 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.7 26.1 - - + +
76C ILE 3.3 4.3 - - - -
77C LEU* 3.5 25.4 - - + -
78C HIS* 4.7 0.7 - - - -
185C LYS* 3.4 23.4 - - - +
212C LYS* 4.4 16.3 - - - +
280C VAL* 6.4 0.4 - - - +
360C ASP* 1.4 84.6 + - - +
362C ALA* 1.3 60.0 + - - +
363C GLU* 3.3 23.5 + - + +
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Residues in contact with ALA 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL 4.3 1.1 - - - -
75C LEU* 3.4 11.1 - - - +
76C ILE* 3.0 36.1 + - + +
78C HIS* 4.8 0.2 - - - -
183C LEU 3.7 23.3 - - - +
184C SER* 4.0 14.8 - - - -
185C LYS* 4.1 15.9 - - - +
361C LYS* 1.3 72.3 - - - +
363C GLU* 1.3 61.5 + - - +
364C TYR* 3.7 13.5 - - + +
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Residues in contact with GLU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR* 3.9 15.4 - - + +
74C VAL 3.3 4.7 - - - -
75C LEU* 3.6 15.1 - - + +
185C LYS* 4.9 2.7 + - - +
361C LYS* 3.3 32.8 + - + +
362C ALA* 1.3 75.2 - - - +
364C TYR* 1.3 76.9 + - - +
365C THR* 4.2 7.8 + - - +
382C VAL* 4.2 9.5 - - - +
465C SER* 5.4 3.1 + - - -
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Residues in contact with TYR 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLN 3.5 2.4 - - - +
73C THR* 3.2 1.9 - - - -
74C VAL* 2.9 43.1 + - + +
76C ILE* 4.7 1.8 - - + -
182C PHE* 3.7 40.8 - + + -
183C LEU* 2.6 38.2 + - - +
184C SER 4.7 1.4 + - - -
185C LYS* 4.6 8.8 + - - -
362C ALA* 3.7 20.5 - - + +
363C GLU* 1.3 79.8 - - - +
365C THR* 1.3 61.6 + - - +
366C PHE* 4.1 3.2 - - - -
380C VAL* 3.8 37.2 - - + -
382C VAL* 3.7 24.2 - - + -
402C GLN* 5.5 2.6 + - - -
403C ASN* 4.7 6.8 + - - -
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Residues in contact with THR 365 (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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71C ASP* 3.5 41.1 - - + +
72C GLN 3.4 2.9 - - - +
73C THR* 3.1 26.7 + - - +
363C GLU* 4.2 8.0 + - - +
364C TYR* 1.3 73.2 + - - +
366C PHE* 1.3 58.5 + - - +
380C VAL* 3.5 15.8 - - - +
462C TYR* 3.9 13.0 - - - +
463C SER* 3.8 25.9 + - - +
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Residues in contact with PHE 366 (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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71C ASP* 3.8 4.2 - - - -
72C GLN* 3.0 88.2 + - + +
74C VAL* 4.0 11.0 - - + -
106C TRP* 4.3 5.6 - + - -
173C TYR* 5.5 1.1 - - - -
179C ILE* 3.8 22.0 - - + -
182C PHE* 4.0 18.8 - + - -
364C TYR 4.1 4.5 - - - -
365C THR* 1.3 76.1 - - - +
367C TYR* 1.3 66.6 + - - +
368C GLU* 5.2 1.8 - - + -
377C VAL* 3.7 31.6 - - + -
380C VAL* 4.4 10.8 - - + -
460C VAL* 4.2 2.2 - - + -
461C ILE 3.3 8.7 - - - -
462C TYR* 3.8 23.1 - - + -
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Residues in contact with TYR 367 (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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64C ASN 5.3 1.4 + - - -
65C TYR* 3.5 39.4 - + + -
69C ARG 3.5 16.4 + - - -
70C GLY* 3.2 32.3 - - - -
71C ASP* 4.0 10.5 - - - +
72C GLN* 5.0 4.9 - - - +
108C LYS* 4.1 16.3 + - + -
366C PHE* 1.3 80.3 - - - +
368C GLU* 1.4 60.2 + - - +
369C GLY* 2.8 37.9 + - - -
460C VAL* 3.2 8.1 - - - +
461C ILE* 2.8 47.5 + - + +
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Residues in contact with GLU 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLN* 4.6 14.5 - - - +
109C LYS* 2.7 43.3 + - - +
112C GLN* 4.1 2.4 - - - +
173C TYR* 5.5 0.4 + - - -
366C PHE* 5.7 1.1 - - + -
367C TYR* 1.4 79.6 - - - +
369C GLY* 1.3 62.0 + - - +
370C MET 3.3 2.9 - - - -
371C GLY* 3.3 23.1 + - - +
372C PRO* 3.4 18.5 - - - +
373C VAL* 3.4 31.9 + - + +
377C VAL* 5.1 9.2 - - + +
460C VAL* 4.9 5.6 - - - +
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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
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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