Contacts of the helix formed by residues 353 - 370 (chain A) in PDB entry 3RAW
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 GLN 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A HIS* 3.4 62.0 + - + +
278A GLN* 3.8 1.2 - - - +
279A LEU 3.2 17.0 + - - +
280A THR* 3.2 21.4 + - - +
327A ASP* 3.0 25.5 + - - -
352A ALA* 1.3 76.7 - - - +
354A PRO* 1.3 68.9 - - + +
355A CYS 2.9 0.2 - - - -
356A ASP* 2.9 13.9 + - - +
357A VAL* 3.7 1.6 + - - -
417B ASN* 2.9 25.0 + - - -
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Residues in contact with PRO 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU* 4.4 0.7 - - - +
352A ALA* 3.1 15.0 - - + +
353A GLN* 1.3 93.0 - - + +
355A CYS* 1.3 61.0 + - - +
357A VAL* 3.1 21.9 + - + +
358A TRP 3.1 5.9 + - - -
457A PRO* 3.7 35.7 - - + +
460A ARG* 2.9 33.7 + - + +
461A ILE 5.9 0.9 - - - +
419B SER* 6.6 0.2 - - - -
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Residues in contact with CYS 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 4.5 5.2 - - + -
282A THR* 4.6 15.5 - - - -
335A VAL* 4.3 23.1 - - - -
336A ALA* 4.6 7.0 - - - -
342A PRO* 3.6 28.9 - - + +
344A GLU* 3.9 10.4 + - - -
345A VAL* 4.5 0.9 - - - -
351A TRP* 4.4 12.6 - - + -
352A ALA 2.9 16.1 + - - +
353A GLN 2.9 0.4 + - - -
354A PRO* 1.3 79.0 - - - +
356A ASP* 1.3 61.9 + - - +
358A TRP* 3.5 4.5 + - - +
359A SER* 3.1 25.1 + - - -
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Residues in contact with ASP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.7 3.9 - - + +
275A HIS* 3.0 34.7 + - + +
280A THR* 3.3 8.3 - - - +
281A HIS* 2.8 33.7 + - - +
282A THR* 2.8 30.0 + - - -
284A LEU* 3.7 17.8 - - + +
353A GLN 2.9 3.0 + - - +
355A CYS* 1.3 74.8 - - - +
357A VAL* 1.3 60.1 + - - +
359A SER* 3.3 5.9 + - - -
360A ILE* 2.9 33.8 + - + +
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A HIS* 4.3 5.2 - - + +
353A GLN 4.2 9.9 - - - +
354A PRO* 3.1 12.6 + - + +
356A ASP* 1.3 74.5 - - - +
358A TRP* 1.3 64.1 + - - +
360A ILE* 3.2 9.6 + - - +
361A GLY 3.0 17.8 + - - -
452A MET* 3.7 33.4 - - + +
460A ARG* 4.0 7.4 - - + -
461A ILE* 3.4 30.3 - - + +
462A THR* 4.7 1.3 - - - -
463A LEU* 3.7 35.9 - - + +
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Residues in contact with TRP 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A TYR 3.6 19.5 - - - -
341A ARG 3.5 10.9 + - - -
342A PRO* 3.6 19.1 - - + -
343A PRO* 3.7 33.0 - - + -
354A PRO 3.1 5.5 + - - -
355A CYS 3.6 8.5 - - - +
357A VAL* 1.3 75.1 - - - +
359A SER* 1.3 62.0 + - - +
361A GLY* 3.1 3.8 + - - -
362A CYS* 3.1 34.3 + - - -
374A PHE* 3.7 23.5 - + - -
386A MET* 3.9 15.0 - - + -
390A LEU* 3.6 22.0 - - + -
452A MET 3.6 9.3 + - - -
453A LEU* 3.2 40.1 - - + +
454A GLU 3.7 10.5 - - - -
455A PHE* 4.4 3.1 - + - -
460A ARG* 3.7 19.5 - - - +
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Residues in contact with SER 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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282A THR 5.2 1.6 + - - -
284A LEU* 3.9 32.0 + - - -
336A ALA* 4.9 3.5 - - - +
340A TYR* 2.7 30.8 + - - +
355A CYS* 3.1 16.5 + - - -
356A ASP* 3.5 10.5 + - - -
357A VAL 3.3 0.2 - - - -
358A TRP* 1.3 77.7 - - - +
360A ILE* 1.3 57.8 + - - +
362A CYS* 3.2 4.9 + - - +
363A ILE* 2.9 35.1 + - - +
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Residues in contact with ILE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ALA 5.4 0.7 - - - +
267A LEU* 4.3 34.3 - - + +
268A CYS* 4.7 3.8 - - - +
271A LEU* 4.1 8.7 - - + -
284A LEU* 3.9 19.7 - - + -
356A ASP 2.9 20.6 + - - +
357A VAL* 3.2 5.6 + - - +
359A SER* 1.3 73.2 - - - +
361A GLY* 1.3 61.6 - - - +
363A ILE* 3.0 9.1 + - + +
364A LEU* 2.8 38.5 + - + +
452A MET* 3.8 24.2 - - + -
463A LEU* 3.9 33.7 - - + -
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Residues in contact with GLY 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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357A VAL 3.0 11.1 + - - -
358A TRP 3.1 4.0 + - - -
360A ILE* 1.3 75.7 - - - +
362A CYS* 1.3 61.7 + - - +
364A LEU* 3.3 4.0 + - - +
365A PHE* 3.1 22.7 + - - +
449A MET* 3.9 11.2 - - - +
452A MET* 3.8 26.6 - - - -
453A LEU* 4.2 14.8 - - - +
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Residues in contact with CYS 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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339A HIS 3.8 9.4 - - - +
340A TYR* 3.8 18.8 - - + -
358A TRP* 3.1 42.8 + - - -
359A SER 3.6 6.7 - - - +
360A ILE 3.2 0.2 - - - -
361A GLY* 1.3 76.3 - - - +
363A ILE* 1.3 62.6 + - - +
365A PHE* 3.5 3.6 + - - +
366A GLU* 3.1 24.4 + - - +
373A LEU* 4.4 17.1 + - + +
374A PHE* 3.7 26.5 - - - -
453A LEU* 3.9 4.4 - - - +
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Residues in contact with ILE 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 4.3 7.9 - - + -
284A LEU* 3.8 14.8 - - + -
285A LYS* 3.6 31.0 - - - +
286A PRO* 4.0 8.7 - - + -
289A ILE* 4.0 13.0 - - + -
340A TYR* 4.0 17.5 - - + -
359A SER 2.9 21.1 + - - +
360A ILE* 3.0 10.5 + - + +
362A CYS* 1.3 76.6 - - - +
364A LEU* 1.3 59.8 + - - +
366A GLU* 3.1 6.6 + - - +
367A TYR* 2.9 64.5 + - + +
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Residues in contact with LEU 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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260A VAL* 4.3 7.8 - - + +
264A ALA* 3.5 42.6 - - + +
267A LEU* 4.4 11.2 - - + -
360A ILE* 2.8 26.1 + - + +
361A GLY 3.3 2.0 + - - +
363A ILE* 1.3 68.7 - - - +
365A PHE* 1.3 67.3 + - - +
367A TYR* 3.3 21.7 + - + +
368A TYR* 2.9 25.1 + - - +
445A LEU* 4.4 16.6 - - + -
448A LEU* 4.8 8.3 - - + -
449A MET* 3.5 18.2 - - + -
452A MET* 4.1 24.5 - - + -
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Residues in contact with PHE 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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361A GLY 3.1 12.1 + - - +
362A CYS 3.6 8.3 - - - +
364A LEU* 1.3 78.4 - - - +
366A GLU* 1.3 58.4 + - - +
368A TYR* 3.1 5.0 + + - +
369A ARG* 2.9 45.1 + - + +
371A PHE* 3.6 41.5 - + - -
373A LEU* 3.6 48.2 - - + -
431A LEU* 4.1 14.8 - - + -
434A TYR* 3.7 35.9 - + + -
446A PHE* 5.0 4.7 - + - -
449A MET* 3.3 17.8 - - - +
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Residues in contact with GLU 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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244A PHE* 4.5 15.6 - - - -
247A LEU* 4.1 12.5 - - + +
252A PHE* 6.2 0.2 - - - -
286A PRO* 3.8 16.5 - - + +
340A TYR* 2.5 39.1 + - - -
362A CYS 3.1 11.7 + - - +
363A ILE* 3.1 6.8 + - - +
365A PHE* 1.3 80.8 - - - +
367A TYR* 1.3 56.3 + - + +
370A GLY* 2.7 34.3 + - - +
371A PHE* 3.4 26.8 - - - +
372A THR* 3.8 23.8 + - - +
373A LEU 4.8 0.2 + - - -
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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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243A THR* 2.8 46.4 + - + +
247A LEU* 5.3 3.6 - - + -
254A PRO* 3.5 3.1 - - - +
255A TYR* 2.9 55.4 + + + -
260A VAL* 4.1 14.6 - - + -
263A MET* 4.1 30.1 - - + -
267A LEU* 4.4 9.0 - - + -
286A PRO* 4.3 11.2 - - + +
289A ILE* 3.3 23.4 - - + +
363A ILE* 2.9 35.8 + - + +
364A LEU* 3.6 20.0 - - + +
366A GLU* 1.3 77.2 - - - +
368A TYR* 1.3 60.6 + - - +
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Residues in contact with TYR 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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254A PRO* 3.1 15.8 - - - +
255A TYR 4.5 4.3 - - - +
257A LEU* 3.8 14.6 - - + -
260A VAL* 4.0 14.6 - - + -
364A LEU 2.9 16.7 + - - +
365A PHE* 3.1 5.8 + + - +
367A TYR* 1.3 80.2 - - - +
369A ARG* 1.3 71.0 + - + +
434A TYR 3.9 13.0 - - - -
435A MET* 3.9 2.3 - - - -
436A LEU* 2.9 36.1 + - + +
437A GLN 3.7 0.2 + - - -
442A HIS* 2.6 40.2 + + - +
445A LEU* 3.4 28.0 - - + -
446A PHE* 3.4 31.7 - + - -
449A MET* 5.1 0.7 - - + -
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Residues in contact with ARG 369 (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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252A PHE 4.1 2.1 - - - +
254A PRO* 3.6 18.6 - - - +
365A PHE* 2.9 43.4 + - + +
368A TYR* 1.3 94.6 - - + +
370A GLY* 1.3 60.2 + - - +
371A PHE* 3.3 45.6 + - + +
433A SER 4.7 1.2 + - - -
434A TYR* 2.6 55.1 + - - +
435A MET 4.7 1.0 + - - -
436A LEU* 4.0 26.0 - - - +
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Residues in contact with GLY 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 4.0 15.9 - - - +
252A PHE* 3.5 46.6 - - - +
254A PRO* 3.8 6.4 - - - +
366A GLU* 2.7 24.7 + - - +
368A TYR 3.8 0.6 - - - -
369A ARG* 1.3 73.1 - - - +
371A PHE* 1.3 60.8 + - - +
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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