Contacts of the helix formed by residues 360 - 372 (chain B) in PDB entry 5X61
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 SER 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278B GLY 4.1 9.2 + - - -
280B GLY* 4.7 5.9 + - - -
359B GLU* 1.3 81.4 - - - +
361B ALA* 1.3 64.9 + - - +
363B ALA* 3.0 3.1 + - - +
364B VAL* 3.0 30.7 + - - +
385B GLN 3.1 12.3 + - - -
386B SER 3.6 15.0 + - - -
387B GLY* 4.0 0.5 - - - -
393B TRP* 3.6 17.6 - - - -
449B PHE* 6.0 0.5 - - - -
490B PHE* 4.9 3.8 - - - -
560B PHE* 4.4 1.2 - - - -
600B HIS* 3.0 29.7 + - - -
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Residues in contact with ALA 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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277B PHE 4.5 0.4 - - - -
278B GLY* 4.0 5.1 - - - -
279B GLY 4.2 0.2 - - - +
280B GLY* 3.5 30.1 - - - +
281B PHE* 3.5 31.8 - - + +
309B TYR* 4.5 2.0 - - - +
359B GLU 3.2 0.2 + - - -
360B SER* 1.3 82.2 + - - +
362B GLY* 1.3 56.8 + - - +
364B VAL* 3.3 8.5 - - - +
365B SER* 2.9 30.6 + - - -
393B TRP* 3.6 9.8 - - + -
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Residues in contact with GLY 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.4 19.2 - - - +
277B PHE 3.4 19.1 - - - -
278B GLY* 3.3 3.6 - - - -
358B GLY* 3.8 6.9 - - - -
359B GLU 2.9 8.7 + - - -
361B ALA* 1.3 80.1 - - - +
363B ALA* 1.3 55.9 + - - +
365B SER* 3.3 3.5 - - - -
366B VAL* 3.2 31.2 + - - +
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLY* 3.4 14.8 - - - +
359B GLU 3.4 4.0 - - - +
360B SER 3.0 10.8 + - - +
362B GLY* 1.3 74.0 - - - +
364B VAL* 1.3 56.8 + - - +
365B SER 3.1 4.7 - - - -
366B VAL* 3.3 10.7 - - - +
367B SER* 3.1 26.2 + - - -
384B LEU* 3.7 4.8 - - - +
385B GLN 3.3 33.7 - - - +
387B GLY* 3.7 16.6 - - - +
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Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 3.3 28.7 - - + -
360B SER 3.0 12.8 + - - +
361B ALA* 3.3 16.6 - - - +
363B ALA* 1.3 74.4 - - - +
365B SER* 1.3 58.2 + - - +
367B SER* 2.7 22.0 + - - +
368B LEU* 3.1 26.1 + - + +
387B GLY* 4.0 1.1 - - - -
388B SER 3.3 37.5 - - - +
389B PRO* 4.5 1.3 - - + -
393B TRP* 3.7 20.2 - - + -
394B ALA* 4.4 13.0 - - + -
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Residues in contact with SER 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.8 6.0 - - - +
281B PHE* 3.6 13.3 - - - -
309B TYR* 4.7 0.3 + - - -
330B LEU* 4.0 6.4 - - - +
333B GLN* 3.1 38.8 + - - -
361B ALA 2.9 19.8 + - - -
362B GLY 3.3 10.8 - - - -
363B ALA 3.1 0.2 - - - -
364B VAL* 1.3 74.6 - - - +
366B VAL* 1.3 64.3 + - - +
367B SER 3.1 1.3 - - - -
368B LEU* 3.1 16.0 + - - +
369B HIS* 3.1 20.7 + - - -
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.8 18.4 - - + -
356B LEU* 3.8 26.5 - - + +
357B PHE 4.0 2.2 - - - -
358B GLY* 3.9 15.9 - - - +
362B GLY 3.2 14.3 + - - +
363B ALA* 3.3 13.0 - - - +
365B SER* 1.3 74.2 - - - +
367B SER* 1.3 62.6 + - - +
369B HIS* 3.5 11.3 + - - +
370B LEU* 3.3 24.9 + - - +
379B PHE* 4.5 0.2 - - - -
382B ALA* 4.4 6.1 - - + +
383B ILE 3.8 11.2 - - - +
384B LEU* 3.5 25.4 - - + -
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Residues in contact with SER 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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363B ALA 3.1 13.6 + - - -
364B VAL* 2.7 28.0 + - - -
366B VAL* 1.3 77.8 - - - +
368B LEU* 1.3 59.9 + - - +
370B LEU* 3.3 12.9 + - - +
371B LEU* 3.3 25.3 + - - +
384B LEU* 3.5 18.2 - - - -
388B SER* 4.6 0.2 - - - -
389B PRO* 3.2 37.3 - - - +
567B PHE* 4.2 2.6 - - - -
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Residues in contact with LEU 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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330B LEU* 3.8 29.6 - - + -
364B VAL* 3.1 24.7 + - + +
365B SER* 3.1 7.2 + - - +
367B SER* 1.3 80.0 + - - +
369B HIS* 1.3 54.0 + - - +
371B LEU* 3.2 6.2 + - + +
372B SER* 2.7 36.8 + - - -
389B PRO* 3.9 22.4 - - + -
394B ALA* 6.2 0.2 - - + -
395B LEU* 4.3 9.4 - - + -
453B PRO* 4.0 19.3 - - + -
459B PHE* 4.0 12.7 - - + -
460B LEU* 3.9 27.1 - - + +
464B PRO* 4.1 11.9 - - + -
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Residues in contact with HIS 369 (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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276B ILE* 4.0 8.1 - - + +
330B LEU 4.1 3.1 - - - -
333B GLN* 3.1 39.0 + - + +
334B ASN 4.1 6.1 - - - -
337B LEU* 4.1 11.4 - - + +
356B LEU* 3.9 17.0 - - + -
365B SER 3.1 23.3 + - - -
366B VAL 3.7 5.8 - - - +
367B SER 3.3 0.2 - - - -
368B LEU* 1.3 74.0 - - - +
370B LEU* 1.3 64.6 + - - +
371B LEU 3.1 1.0 + - - -
372B SER* 3.6 10.1 + - - +
375B SER* 2.8 37.2 + - - -
376B ARG* 4.1 2.3 + - - -
379B PHE* 3.5 28.2 - - + -
459B PHE* 3.4 24.4 - + - -
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Residues in contact with LEU 370 (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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366B VAL 3.3 16.1 + - - +
367B SER* 3.3 10.8 - - - +
369B HIS* 1.3 77.8 - - - +
371B LEU* 1.3 62.9 + - + +
376B ARG* 3.9 3.6 + - - -
379B PHE* 3.6 25.8 - - + -
382B ALA* 3.9 20.9 - - + -
384B LEU* 4.4 2.7 - - + -
473B PHE* 3.6 1.7 - - - -
474B LYS* 3.0 34.5 + - + +
476B THR* 3.7 20.6 - - + -
478B ILE* 4.1 6.7 - - + -
567B PHE* 3.8 29.8 - - + -
571B TYR* 3.3 22.2 - - + +
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Residues in contact with LEU 371 (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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210A ARG* 5.6 2.6 + - - -
367B SER 3.3 14.2 + - - +
368B LEU* 3.2 11.9 + - + +
369B HIS 3.1 0.4 - - - -
370B LEU* 1.3 82.6 - - + +
372B SER* 1.3 63.1 + - - +
373B ALA 3.7 1.0 + - - -
376B ARG* 3.3 18.8 + - - +
389B PRO* 4.6 6.5 - - + -
460B LEU* 4.4 11.6 - - + +
462B GLU 5.9 0.4 - - - +
464B PRO* 3.7 43.3 - - + +
467B SER* 3.7 24.7 + - - +
468B LEU* 4.0 16.2 - - + -
472B ARG 4.2 3.3 - - - +
473B PHE* 3.8 20.2 - - + -
567B PHE* 4.2 10.8 - - + -
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU 2.7 21.8 + - - -
369B HIS 3.6 2.7 + - - +
371B LEU* 1.3 75.1 - - - +
373B ALA* 1.3 64.7 + - - +
374B LEU 3.3 10.4 + - - -
375B SER* 3.7 10.0 + - - -
376B ARG* 3.3 25.5 + - - +
459B PHE* 2.9 56.0 + - - -
460B LEU* 4.5 1.8 - - - +
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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
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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