Contacts of the strand formed by residues 354 - 368 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU* 3.6 34.1 - - + -
216A PHE 3.4 29.2 - - - -
217A ASN* 4.0 6.3 - - + -
227A ARG 4.4 2.2 - - - -
228A TYR 4.5 0.2 - - - -
229A LEU* 3.9 16.8 - - + -
238A ALA* 4.6 1.6 - - + -
311A LYS* 3.5 2.0 - - - -
312A CYS* 2.7 43.6 + - - +
314A PHE* 4.0 31.9 - + + -
324A LEU* 3.0 37.4 + - + +
325A CYS 4.7 0.7 - - - -
326A LEU* 4.1 19.3 - - + -
331A ILE* 3.7 31.9 - - + -
351A GLY 3.9 16.5 + - - -
352A ALA 3.6 13.9 - - - -
353A SER* 1.4 75.8 + - - +
355A THR* 1.3 61.9 + - - +
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Residues in contact with THR 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ALA 3.6 1.6 - - - +
215A LEU* 3.3 9.0 - - - -
216A PHE* 2.9 69.4 + - + -
309A LEU* 3.5 38.4 - - + +
310A HIS 3.3 4.0 - - - -
311A LYS* 3.9 15.8 - - - +
354A TRP* 1.3 72.6 - - - +
356A ILE* 1.3 62.0 + - - +
9H G 5.6 1.2 + - - -
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 3.9 19.3 - - + -
213A VAL* 3.9 27.6 - - + -
214A ALA 3.7 1.6 - - - -
215A LEU* 3.8 22.4 - - + -
248A ILE* 4.1 14.1 - - + -
276A LEU* 5.7 0.2 - - + -
290A ILE* 3.9 22.7 - - + -
306A VAL* 3.9 2.9 - - + -
307A SER 3.6 19.5 - - - +
308A GLN* 3.8 0.7 - - - -
309A LEU* 2.7 33.3 + - - -
310A HIS 3.0 12.0 + - - +
312A CYS* 3.6 23.3 - - - -
314A PHE* 4.5 0.9 - - + -
354A TRP 3.6 0.6 + - - -
355A THR* 1.3 72.3 - - - +
357A ILE* 1.3 59.3 + - - +
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Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ALA* 3.4 23.6 - - + -
81A VAL* 3.8 18.4 - - + +
82A ALA* 5.8 0.4 - - - -
94A CYS 3.7 10.8 - - - +
95A PRO* 3.6 24.0 - - + -
207A ILE* 5.7 0.4 - - - -
213A VAL* 3.2 7.3 - - - -
214A ALA* 2.9 42.1 + - + +
216A PHE* 4.2 11.2 - - + -
308A GLN* 3.4 13.7 - - - +
309A LEU* 3.5 26.2 - - + -
356A ILE* 1.3 78.3 - - - +
358A SER* 1.3 71.8 + - - +
359A THR* 3.8 0.4 - - + +
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Residues in contact with SER 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ALA* 3.4 5.0 - - - -
80A LYS* 2.7 50.7 + - - +
206A CYS 4.8 3.0 + - - -
207A ILE* 4.0 13.7 - - - +
211A THR* 4.5 5.9 + - - -
212A LYS 3.5 11.7 + - - -
213A VAL* 4.2 2.9 - - - +
308A GLN* 2.7 35.5 + - - +
357A ILE* 1.3 75.9 - - - +
359A THR* 1.3 55.2 + - - +
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Residues in contact with THR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A HIS 3.2 13.0 - - - +
79A ALA* 4.0 4.7 - - + +
80A LYS* 3.8 16.0 + - - +
95A PRO* 4.8 1.6 - - + -
212A LYS* 3.0 39.4 + - - +
213A VAL 3.9 1.6 - - - -
214A ALA* 3.6 39.0 - - + +
243A TRP* 3.8 19.3 - - + -
245A ALA* 3.8 10.8 - - + +
357A ILE 3.8 0.7 - - - +
358A SER* 1.3 76.1 - - - +
360A ASP* 1.3 65.5 + - - +
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Residues in contact with ASP 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 3.9 3.3 - - - +
78A HIS* 2.9 46.4 + - - +
80A LYS* 3.6 32.5 + - + +
185A LYS* 3.4 33.8 + - + +
212A LYS* 5.9 5.4 - - - +
359A THR* 1.3 75.1 - - - +
361A LYS* 1.3 75.0 + - - +
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Residues in contact with LYS 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.8 23.5 - - + +
76A ILE 3.5 7.0 - - - +
77A LEU* 4.5 23.1 - - + -
185A LYS* 3.4 24.9 + - - -
212A LYS* 5.6 16.1 - - - +
360A ASP* 1.3 83.8 + - - +
362A ALA* 1.4 69.8 + - - +
363A GLU* 3.8 24.7 + - + +
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Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A VAL 3.7 1.2 - - - +
75A LEU* 3.3 8.5 - - - +
76A ILE* 2.8 39.8 + - + +
183A LEU 3.6 24.0 - - - +
184A SER* 4.1 11.4 - - - -
185A LYS* 4.2 17.0 - - + +
361A LYS* 1.4 72.0 - - - +
363A GLU* 1.3 61.1 + - - +
364A TYR* 3.8 14.1 - - + +
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Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A THR* 4.1 15.0 - - + +
74A VAL 3.6 3.4 - - - -
75A LEU* 3.5 21.8 - - + -
185A LYS* 5.6 0.6 - - - +
361A LYS* 3.8 24.6 + - + -
362A ALA* 1.3 74.0 - - - +
364A TYR* 1.4 74.0 + - - +
365A THR* 4.3 7.8 + - - +
382A VAL* 3.7 17.8 - - - +
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Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLN 3.8 1.0 - - - +
73A THR* 3.1 3.8 - - - -
74A VAL 2.8 43.3 + - - +
76A ILE* 4.2 4.5 - - + -
182A PHE* 3.6 37.2 - + + -
183A LEU* 2.5 45.1 + - - +
184A SER 4.8 0.9 + - - -
185A LYS* 5.5 3.7 - - - +
362A ALA* 3.8 19.1 - - + +
363A GLU* 1.4 83.1 - - - +
365A THR* 1.3 62.1 + - - +
366A PHE* 4.3 2.9 - - - -
380A VAL* 3.8 36.1 - - + -
382A VAL* 3.9 15.3 - - + -
403A ASN* 4.4 10.2 + - - -
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Residues in contact with THR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASP* 3.5 26.0 - - + +
72A GLN 3.5 3.4 - - - +
73A THR* 3.0 28.8 + - - +
363A GLU* 4.5 8.7 + - - +
364A TYR* 1.3 74.9 + - - +
366A PHE* 1.3 62.6 + - - +
380A VAL* 3.6 7.9 - - - +
462A TYR* 3.4 25.9 - - - +
463A SER* 3.6 29.7 + - - +
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Residues in contact with PHE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASP* 3.8 3.9 - - - -
72A GLN* 3.0 79.8 + - + +
74A VAL* 4.3 8.1 - - + -
106A TRP* 4.1 9.4 - + - -
173A TYR* 5.3 1.3 - - - -
179A ILE* 3.7 23.6 - - + -
182A PHE* 3.7 20.6 - + - -
364A TYR 4.3 4.3 - - - -
365A THR* 1.3 76.7 - - - +
367A TYR* 1.3 64.2 + - - +
368A GLU* 5.5 3.8 - - + -
377A VAL* 3.7 31.0 - - + -
380A VAL* 4.3 9.6 - - + -
460A VAL* 4.1 3.1 - - + -
461A ILE 3.4 8.1 - - - -
462A TYR* 3.6 23.6 - - + -
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Residues in contact with TYR 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 5.7 0.7 - - - -
64A ASN 5.5 0.9 - - - -
65A TYR* 3.3 46.3 + + + -
68A GLU* 5.1 6.7 + - + +
70A GLY* 3.1 30.7 - - - -
71A ASP* 3.8 12.3 - - - +
72A GLN* 4.6 8.1 - - - +
108A LYS* 3.6 32.2 + - + -
366A PHE* 1.3 79.1 - - - +
368A GLU* 1.3 67.1 + - - +
369A GLY* 2.9 31.7 + - - -
460A VAL* 3.3 6.9 - - - -
461A ILE* 2.8 42.3 + - + +
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLN* 4.3 14.4 + - - +
109A LYS* 2.8 42.7 + - - +
112A GLN* 3.6 6.2 - - - +
173A TYR* 4.7 5.4 + - - -
366A PHE* 5.6 2.5 - - + -
367A TYR* 1.3 81.2 + - - +
369A GLY* 1.3 63.2 + - - +
370A MET 3.2 3.1 - - - -
371A GLY* 3.1 26.7 + - - +
372A PRO* 3.3 23.9 - - + +
373A VAL* 4.8 11.1 + - + +
377A VAL* 5.4 10.5 - - + +
460A VAL* 4.8 7.2 - - + +
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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
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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