Contacts of the helix formed by residues 353 - 370 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B HIS* 3.4 60.2 + - + +
278B GLN* 3.7 3.6 - - - +
279B LEU 3.5 16.6 + - - +
280B THR* 3.3 19.0 + - - +
327B ASP* 2.8 33.4 + - - +
352B ALA* 1.3 83.7 - - - +
354B PRO* 1.3 68.5 - - + +
355B CYS 2.9 0.9 + - - -
356B ASP 3.0 12.2 + - - -
357B VAL* 3.6 2.7 + - - +
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Residues in contact with PRO 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLU* 4.6 0.4 - - - +
352B ALA* 3.2 14.8 - - + +
353B GLN* 1.3 93.7 - - + +
355B CYS* 1.3 60.0 + - - +
357B VAL* 3.1 21.9 + - + +
358B TRP 3.1 5.5 + - - -
457B PRO* 3.8 33.7 - - + +
460B ARG* 2.9 35.7 + - + +
461B ILE 5.9 0.7 - - - +
462B THR* 6.5 0.9 - - + -
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Residues in contact with CYS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B THR* 4.4 5.8 - - + -
282B THR* 4.6 15.7 - - - -
335B VAL* 4.1 23.3 - - - -
336B ALA* 4.7 6.3 - - - -
342B PRO* 3.7 29.3 - - + +
344B GLU* 3.9 13.3 + - - +
345B VAL* 4.4 0.9 - - - -
351B TRP* 4.5 9.9 - - + -
352B ALA 2.9 15.5 + - - +
354B PRO* 1.3 77.7 - - - +
356B ASP* 1.3 64.0 + - - +
357B VAL 3.3 0.3 + - - -
358B TRP* 3.4 4.2 + - - +
359B SER* 3.2 24.3 + - - -
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Residues in contact with ASP 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.7 3.7 - - + +
275B HIS* 2.8 34.8 + - + +
280B THR* 3.3 7.3 - - - +
281B HIS* 2.8 25.3 + - - +
282B THR* 2.8 29.6 + - - -
284B LEU* 3.6 23.3 - - + +
353B GLN 3.0 3.0 + - - +
355B CYS* 1.3 77.6 - - - +
357B VAL* 1.3 57.6 + - - +
359B SER* 3.2 6.3 + - - -
360B ILE* 2.9 33.8 + - + +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B HIS* 4.4 4.5 - - + +
353B GLN* 4.0 12.8 - - + +
354B PRO* 3.1 12.9 + - + +
356B ASP* 1.3 74.3 - - - +
358B TRP* 1.3 64.8 + - - +
360B ILE* 3.3 8.6 + - - +
361B GLY 3.0 18.5 + - - -
452B MET* 3.7 34.3 - - + +
460B ARG* 4.1 6.3 - - + -
461B ILE* 3.4 28.0 - - + +
462B THR* 4.7 1.8 - - - -
463B LEU* 3.8 35.2 - - + +
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Residues in contact with TRP 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B TYR 3.5 20.4 - - - -
341B ARG 3.4 10.3 + - - -
342B PRO* 3.6 18.4 - - + -
343B PRO* 3.5 35.4 - - + -
354B PRO 3.1 5.7 + - - -
355B CYS 3.6 8.1 - - - +
357B VAL* 1.3 75.0 - - - +
359B SER* 1.3 62.1 + - - +
361B GLY* 3.1 4.2 + - - -
362B CYS* 3.1 34.2 + - - -
374B PHE* 3.7 23.9 - + - -
386B MET* 3.8 14.4 - - + -
390B LEU* 3.5 22.0 - - + -
452B MET 3.6 10.6 + - - -
453B LEU* 3.4 43.2 - - + +
454B GLU 3.7 14.1 - - - -
455B PHE* 4.4 2.7 - + - -
460B ARG* 3.9 11.6 - - - +
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Residues in contact with SER 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR 5.2 1.4 + - - -
284B LEU* 3.8 33.4 + - - -
336B ALA* 4.8 6.4 - - - +
340B TYR* 2.7 32.1 + - - +
355B CYS* 3.2 12.7 + - - -
356B ASP* 3.2 11.7 + - - -
358B TRP* 1.3 78.9 - - - +
360B ILE* 1.3 63.2 + - - +
362B CYS* 3.1 4.6 + - - +
363B ILE* 3.0 28.8 + - - +
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Residues in contact with ILE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B LEU* 4.4 31.0 - - + +
268B CYS* 4.6 6.5 - - - -
271B LEU* 4.2 8.1 - - + -
284B LEU* 4.0 20.0 - - + -
356B ASP 2.9 21.6 + - - +
357B VAL* 3.6 4.9 - - - +
359B SER* 1.3 71.4 - - - +
361B GLY* 1.3 67.6 + - - +
363B ILE* 3.1 9.2 + - + +
364B LEU* 2.9 33.6 + - + +
452B MET* 4.0 23.8 - - + -
463B LEU* 3.9 35.2 - - + -
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Residues in contact with GLY 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B VAL 3.0 14.6 + - - -
358B TRP 3.1 4.4 + - - -
360B ILE* 1.3 77.4 - - - +
362B CYS* 1.3 60.7 + - - +
364B LEU* 3.4 2.5 + - - +
365B PHE* 3.2 18.2 + - - +
449B MET* 3.8 15.4 - - - +
452B MET* 4.0 23.7 - - - -
453B LEU* 4.1 12.6 - - - -
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Residues in contact with CYS 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B HIS 3.9 8.3 - - - +
340B TYR* 3.7 21.5 - - + -
358B TRP* 3.1 45.1 + - - -
359B SER 3.1 6.9 + - - +
361B GLY* 1.3 75.1 - - - +
363B ILE* 1.3 59.1 + - - +
365B PHE* 3.4 8.1 + - - +
366B GLU* 3.0 27.4 + - - +
373B LEU* 4.6 14.6 + - + +
374B PHE* 3.8 24.9 - - - -
453B LEU* 4.0 4.0 - - - -
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Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.2 11.0 - - + -
284B LEU* 3.8 15.3 - - + -
285B LYS* 3.6 31.4 - - - +
286B PRO* 4.0 18.2 - - + -
289B ILE* 4.0 9.4 - - + -
340B TYR* 4.1 6.1 - - + -
359B SER 3.0 20.0 + - - +
360B ILE* 3.5 11.2 - - + +
362B CYS* 1.3 74.7 - - - +
364B LEU* 1.3 60.2 + - - +
366B GLU* 3.0 8.2 + - - +
367B TYR* 2.8 66.7 + - + +
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 4.2 8.1 - - + +
264B ALA* 3.7 41.3 - - + +
267B LEU* 4.4 15.3 - - + -
360B ILE* 2.9 22.9 + - + +
361B GLY* 3.4 2.4 + - - +
363B ILE* 1.3 76.5 - - - +
365B PHE* 1.3 63.2 + - - +
367B TYR* 3.3 14.9 + - + +
368B TYR* 3.0 24.8 + - - +
445B LEU* 4.6 11.2 - - + -
448B LEU* 4.7 6.1 - - + -
449B MET* 3.2 23.4 - - + +
452B MET* 3.9 29.2 - - + -
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Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B GLY 3.2 10.0 + - - +
362B CYS 3.5 8.5 - - - +
363B ILE 3.1 0.4 - - - -
364B LEU* 1.3 79.4 - - - +
366B GLU* 1.3 59.5 - - - +
368B TYR* 3.1 5.0 + + - +
369B ARG* 2.9 42.3 + - + +
371B PHE* 3.6 38.1 - + - -
373B LEU* 3.5 52.9 - - + -
431B LEU* 4.1 13.7 - - + -
434B TYR* 3.7 40.6 - + + -
446B PHE* 5.0 3.8 - + - -
449B MET* 3.5 18.1 - - + +
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Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B PHE* 4.8 12.1 - - - -
247B LEU* 3.9 19.5 - - + +
252B PHE* 6.1 0.7 - - - -
286B PRO* 3.7 15.5 - - + +
340B TYR* 2.4 41.5 + - - -
362B CYS 3.0 11.3 + - - +
363B ILE* 3.0 9.7 + - - +
365B PHE* 1.3 75.9 - - - +
367B TYR* 1.3 57.0 + - + +
370B GLY* 2.8 31.4 + - - +
371B PHE* 3.5 24.2 - - - +
372B THR* 3.4 27.0 + - - -
373B LEU 4.9 0.2 + - - -
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Residues in contact with TYR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B THR* 2.7 45.3 + - + +
247B LEU* 5.2 3.6 - - + -
254B PRO* 3.4 2.9 - - - +
255B TYR* 2.9 54.8 + + + +
260B VAL* 3.9 15.0 - - + -
263B MET* 4.0 32.1 - - + -
267B LEU* 4.4 9.0 - - + -
286B PRO* 4.2 11.2 - - + +
289B ILE* 3.3 25.3 - - + +
363B ILE* 2.8 39.0 + - + +
364B LEU* 3.7 17.0 - - + +
366B GLU* 1.3 73.4 - - - +
368B TYR* 1.3 60.8 + - - +
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Residues in contact with TYR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B PRO* 3.1 16.4 - - - +
255B TYR 4.4 3.7 - - - +
257B LEU* 4.3 11.0 - - + -
260B VAL* 4.0 15.3 - - + -
364B LEU 3.0 17.7 + - - +
365B PHE* 3.1 6.9 + + - +
367B TYR* 1.3 79.6 - - - +
369B ARG* 1.3 72.6 + - + +
434B TYR 3.8 12.1 - - - -
435B MET* 3.9 0.5 - - - -
436B LEU* 2.9 39.1 + - + +
442B HIS* 2.7 39.2 + + - -
445B LEU* 3.3 27.8 - - + -
446B PHE* 3.5 34.5 - + - -
449B MET* 5.0 0.4 - - + -
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Residues in contact with ARG 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PHE 4.1 1.7 - - - +
254B PRO* 3.6 16.3 - - - +
365B PHE* 2.9 40.9 + - + +
368B TYR* 1.3 94.6 - - + +
370B GLY* 1.3 60.0 + - - +
371B PHE* 3.2 48.0 + - + +
433B SER 4.8 1.4 + - - -
434B TYR* 2.8 56.7 + - - +
435B MET 5.0 0.4 + - - -
436B LEU* 3.8 24.7 - - - +
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Residues in contact with GLY 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 3.8 18.8 - - - +
252B PHE* 3.3 47.1 - - - +
254B PRO* 3.7 3.4 - - - +
366B GLU* 2.8 25.5 + - - +
368B TYR 3.7 0.8 - - - -
369B ARG* 1.3 72.9 - - - +
371B PHE* 1.3 59.3 + - - +
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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