Contacts of the helix formed by residues 342 - 362 (chain B) in PDB entry 3A8X
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 PRO 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338B GLN* 6.1 2.7 - - - +
340B LYS 4.0 4.9 - - - +
341B LEU* 1.3 89.6 - - + +
343B GLU* 1.3 66.6 + - - +
344B GLU* 3.1 10.8 - - - +
345B HIS* 2.9 49.7 + - + +
346B ALA* 3.0 10.4 + - - +
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Residues in contact with GLU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU 3.6 2.0 + - - -
342B PRO* 1.3 71.3 - - - +
344B GLU* 1.3 60.7 + - - +
346B ALA* 3.2 3.0 + - - +
347B ARG* 2.7 63.5 + - - +
438B MET* 4.4 15.7 - - - -
476B LEU* 6.0 2.9 - - + +
477B SER* 2.7 35.7 + - - -
479B LYS* 4.2 9.7 - - - +
480B ALA* 3.8 5.8 - - - +
512B PHE* 3.4 24.6 - - + -
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B PRO* 4.0 8.7 - - + +
343B GLU* 1.3 86.2 + - - +
345B HIS* 1.3 68.5 + - + +
347B ARG* 3.4 28.1 + - - +
348B PHE* 3.1 22.2 + - - +
529B PRO* 5.5 0.9 - - - -
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Residues in contact with HIS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B HIS* 5.4 2.2 + - - -
338B GLN* 6.2 2.0 - - - -
341B LEU* 4.1 17.8 - - + +
342B PRO* 2.9 39.3 + - + +
344B GLU* 1.3 82.2 - - + +
346B ALA* 1.3 62.8 + - - +
348B PHE* 3.2 4.0 + - - +
349B TYR* 3.2 38.0 + - + -
529B PRO* 3.5 52.2 + - + +
530B PHE* 4.8 7.5 - - + +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 4.4 4.2 - - + +
342B PRO 3.0 8.8 + - - +
343B GLU 3.7 4.7 - - - +
345B HIS* 1.3 74.4 - - - +
347B ARG* 1.3 63.1 + - - +
349B TYR* 4.3 0.7 - - - +
350B SER* 3.0 29.8 + - - -
434B MET* 4.9 1.8 - - + +
437B MET* 4.0 29.9 - - + +
438B MET* 3.4 37.7 - - + -
512B PHE* 4.5 2.4 - - - -
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Residues in contact with ARG 347 (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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343B GLU* 2.7 53.6 + - - +
344B GLU* 3.5 32.9 + - - +
345B HIS 3.2 0.2 - - - -
346B ALA* 1.3 71.2 - - - +
348B PHE* 1.3 66.8 + - - +
350B SER* 3.1 2.6 + - - -
351B ALA* 3.0 24.8 + - - +
479B LYS* 5.0 4.2 - - - +
512B PHE* 2.5 68.2 + - + +
513B PHE* 4.0 4.8 - - + +
515B ASN* 5.0 11.7 - - - +
516B VAL* 3.8 29.4 - - + +
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Residues in contact with PHE 348 (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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344B GLU 3.1 10.4 + - - +
345B HIS 3.2 8.7 + - - +
347B ARG* 1.3 78.6 - - - +
349B TYR* 1.3 75.0 + + - +
351B ALA* 3.1 8.4 + - - +
352B GLU* 3.1 56.0 + - - +
381B GLY 4.1 7.0 - - - -
516B VAL* 6.0 0.2 - - - -
521B MET* 4.0 17.7 - - + -
526B VAL* 3.6 36.6 - - + -
527B VAL 4.5 1.1 - - - -
528B PRO* 3.4 40.2 - - + -
529B PRO* 3.4 22.9 - - + -
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Residues in contact with TYR 349 (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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331B LEU* 4.5 11.0 - - + -
334B HIS* 4.0 10.8 + - - -
341B LEU* 3.9 15.7 - - + -
345B HIS* 3.2 29.7 + - + +
348B PHE* 1.3 92.2 - + - +
350B SER* 1.3 57.1 + - - +
352B GLU* 3.3 3.4 + - - +
353B ILE* 2.9 36.7 + - + +
377B LEU* 3.7 16.7 - - + +
381B GLY 3.7 22.3 + - - -
383B ILE* 3.3 24.1 - - + +
437B MET* 3.3 35.4 - - + -
529B PRO* 4.1 8.3 - - + +
530B PHE* 3.7 30.8 + - - +
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Residues in contact with SER 350 (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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346B ALA 3.0 22.8 + - - -
347B ARG* 3.1 3.1 + - - -
349B TYR* 1.3 77.7 - - - +
351B ALA* 1.3 51.8 - - - +
353B ILE* 3.8 4.2 - - - +
354B SER* 2.7 37.9 + - - -
430B LEU* 4.0 11.4 - - - +
434B MET* 3.6 35.4 - - - +
437B MET* 5.3 2.4 - - - -
513B PHE* 3.1 24.7 - - - -
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Residues in contact with ALA 351 (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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347B ARG 3.0 14.2 + - - +
348B PHE 3.1 9.2 + - - +
350B SER* 1.3 75.1 + - - +
352B GLU* 1.3 64.8 + - - +
355B LEU* 3.1 28.8 + - - +
513B PHE* 4.3 3.6 - - + -
516B VAL* 4.4 6.5 - - + -
518B TRP* 3.5 29.8 - - + -
521B MET* 3.9 23.6 - - + -
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Residues in contact with GLU 352 (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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305B PHE* 3.4 42.6 - - + +
348B PHE* 3.1 30.0 + - + +
349B TYR 3.3 3.3 + - - +
351B ALA* 1.3 76.6 - - - +
353B ILE* 1.3 62.3 + - - +
355B LEU* 3.4 1.8 + - - -
356B ALA* 3.2 17.7 + - - +
382B HIS* 2.5 38.2 + - - +
383B ILE* 2.9 44.9 + - + +
521B MET* 3.8 16.6 - - - +
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Residues in contact with ILE 353 (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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331B LEU* 4.6 0.9 - - + -
349B TYR* 2.9 37.0 + - + +
350B SER* 3.8 8.1 - - - +
352B GLU* 1.3 73.8 - - - +
354B SER* 1.3 61.6 + - - +
356B ALA* 3.0 4.5 + - - +
357B LEU* 2.9 40.8 + - + +
370B LEU* 3.8 22.9 - - + -
375B VAL* 4.2 20.6 - - + -
383B ILE* 3.8 23.6 - - + -
385B LEU* 4.1 7.2 - - + -
430B LEU* 4.2 9.6 - - + -
433B LEU* 4.1 26.0 - - + -
437B MET* 5.6 0.2 - - - -
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Residues in contact with SER 354 (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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350B SER 2.7 25.2 + - - -
351B ALA 3.6 6.1 - - - -
353B ILE* 1.3 76.6 - - - +
355B LEU* 1.3 55.9 + - - +
357B LEU* 3.3 1.0 + - - -
358B ASN* 2.9 33.1 + - - +
427B TRP* 3.7 20.7 - - - -
430B LEU* 3.6 18.2 - - - +
504B PHE* 4.2 9.0 - - - -
507B ILE* 4.3 9.4 - - - +
513B PHE* 4.6 4.0 - - - -
518B TRP* 4.3 13.5 - - - -
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Residues in contact with LEU 355 (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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303B HIS* 3.6 9.1 + - + +
305B PHE* 4.0 13.9 - - + -
351B ALA 3.1 17.6 + - - +
352B GLU 3.6 6.7 - - - +
353B ILE 3.3 0.2 - - - -
354B SER* 1.3 79.2 - - - +
356B ALA* 1.3 56.4 + - - +
358B ASN* 4.1 2.0 + - - +
359B TYR* 3.1 27.2 + - - +
504B PHE* 4.2 22.4 - - + -
518B TRP* 4.0 21.1 - - + +
521B MET* 3.7 26.9 - - + -
522B GLU* 3.8 46.2 - - + +
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Residues in contact with ALA 356 (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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303B HIS* 3.9 9.6 - - - -
305B PHE* 3.8 27.4 - - + +
306B LEU* 4.2 7.8 - - + +
352B GLU 3.2 9.1 + - - +
353B ILE* 3.0 9.7 + - - +
355B LEU* 1.3 76.9 - - - +
357B LEU* 1.3 65.3 + - - +
359B TYR* 3.3 3.1 + - - +
360B LEU* 3.0 30.1 + - - +
385B LEU* 3.9 17.0 - - + -
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Residues in contact with LEU 357 (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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353B ILE* 2.9 32.4 + - + +
354B SER 3.7 3.4 - - - +
356B ALA* 1.3 77.0 - - - +
358B ASN* 1.3 51.9 + - - +
360B LEU* 3.2 7.1 + - - +
361B HIS* 2.7 46.2 + - + -
367B TYR* 3.8 31.9 - - + -
370B LEU* 4.2 11.7 - - + -
385B LEU* 4.0 6.5 - - + -
426B ASP* 3.8 40.2 - - + +
427B TRP* 3.8 28.3 - - + -
430B LEU* 4.2 3.6 - - + -
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Residues in contact with ASN 358 (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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354B SER 2.9 17.5 + - - +
355B LEU* 4.2 3.3 + - - +
357B LEU* 1.3 76.8 - - - +
359B TYR* 1.3 57.5 + - - +
361B HIS* 3.9 13.5 + - - +
362B GLU* 2.9 53.5 + - - +
427B TRP* 4.2 6.5 - - + -
504B PHE* 3.4 56.8 - - + +
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Residues in contact with TYR 359 (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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299B GLN 3.5 20.5 + - - -
300B ALA* 4.2 6.5 + - - -
302B ASN* 5.7 1.0 + - - +
303B HIS* 3.3 44.3 + + + +
306B LEU* 3.8 14.6 - - + -
355B LEU 3.1 20.2 + - - +
356B ALA 3.4 5.4 - - - +
358B ASN* 1.3 76.5 - - - +
360B LEU* 1.3 68.0 + - + +
361B HIS 3.3 0.3 + - - -
362B GLU* 3.5 22.6 + - - +
363B ARG* 2.5 63.4 + - - +
522B GLU* 5.7 3.1 - - - -
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Residues in contact with LEU 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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296B VAL* 4.1 23.6 - - + +
299B GLN* 5.4 4.0 - - + -
300B ALA* 5.1 3.8 - - + -
306B LEU* 3.3 41.1 - - + -
356B ALA 3.0 27.6 + - - +
357B LEU* 3.4 9.6 - - - +
359B TYR* 1.3 79.0 - - + +
361B HIS* 1.3 63.7 + - + +
363B ARG* 3.1 11.4 + - + +
364B GLY 3.5 0.2 + - - -
365B ILE* 3.0 55.2 + - + +
367B TYR* 4.9 17.9 - - + -
385B LEU* 4.6 6.3 - - + -
388B TYR* 5.2 2.0 - - + -
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Residues in contact with HIS 361 (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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357B LEU* 2.7 29.6 + - + +
358B ASN* 3.4 11.8 + - - +
359B TYR 3.2 0.4 - - - -
360B LEU* 1.3 69.0 - - + +
362B GLU* 1.3 58.6 + - - +
363B ARG 2.8 10.9 + - - -
364B GLY 3.0 12.0 + - - -
365B ILE 3.3 13.2 - - - -
423B PHE* 3.0 58.0 - + + +
426B ASP* 2.6 41.6 + - + +
427B TRP* 3.4 42.1 + + - -
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Residues in contact with GLU 362 (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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358B ASN* 2.9 41.3 + - - +
359B TYR* 3.6 15.8 - - - +
361B HIS* 1.3 73.3 - - - +
363B ARG* 1.3 79.8 + - - +
364B GLY 3.7 0.7 - - - -
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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