Contacts of the helix formed by residues 397 - 413 (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 397 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B VAL* 1.3 77.9 - - - +
398B ARG* 1.3 57.7 + - - +
399B GLU* 3.7 8.3 + - - +
400B GLU* 3.1 25.8 + - - +
401B ALA* 2.9 27.9 + - - +
455B VAL* 6.1 0.2 - - - -
804B SO4 3.2 27.8 - - - -
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Residues in contact with ARG 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLY 3.4 22.4 + - - -
321A THR* 4.5 2.8 - - - +
322A PRO* 3.2 34.1 - - - +
318B PHE* 3.2 33.6 - - + -
320B GLY* 5.7 1.6 - - - -
397B SER* 1.3 68.7 - - - +
399B GLU* 1.3 67.9 + - - +
401B ALA* 3.4 2.3 + - - +
402B THR* 3.0 31.4 + - + +
454B VAL* 3.6 15.0 - - - -
455B VAL* 3.2 28.5 + - + +
456B ASP 4.2 11.4 + - - -
804B SO4 2.9 30.3 + - - +
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Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B SER* 3.3 7.2 + - - +
398B ARG* 1.3 77.2 - - - +
400B GLU* 1.3 60.9 + - - +
402B THR* 2.7 22.8 + - - -
403B LEU* 3.0 23.2 + - + +
804B SO4 2.9 32.1 + - - -
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Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B VAL* 4.6 4.7 - - + -
397B SER* 3.1 21.9 + - - +
399B GLU* 1.3 78.2 - - - +
401B ALA* 1.3 55.0 + - - +
403B LEU* 2.9 14.4 + - - +
404B ARG* 2.6 78.8 + - - +
407B ARG* 3.3 21.2 + - - -
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PHE 6.0 0.4 - - - +
318B PHE* 3.1 38.0 + - + +
396B VAL* 3.9 9.8 - - + +
397B SER 2.9 22.6 + - - +
398B ARG 3.8 0.4 - - - +
400B GLU* 1.3 72.9 - - - +
402B THR* 1.3 55.9 + - - +
404B ARG* 3.7 10.4 - - - +
405B ALA* 3.1 18.2 + - - +
450B PRO 6.0 0.2 - - - -
451B PHE* 4.6 5.9 - - + -
454B VAL* 3.8 20.2 - - + -
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Residues in contact with THR 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PHE* 3.5 17.9 - - + -
319B LEU* 3.3 39.4 - - - +
320B GLY* 5.0 0.2 - - - -
398B ARG* 3.0 17.6 + - + +
399B GLU* 2.7 24.3 + - - -
401B ALA* 1.3 74.1 - - - +
403B LEU* 1.3 63.6 + - - +
405B ALA* 3.2 3.7 + - - +
406B LEU* 2.9 36.9 + - - +
421B LEU* 5.9 1.1 - - - -
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Residues in contact with LEU 403 (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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399B GLU* 3.0 25.9 + - + +
400B GLU* 2.9 17.6 + - - +
402B THR* 1.3 75.8 + - - +
404B ARG* 1.3 59.4 + - - +
406B LEU* 3.4 15.2 + - + +
407B ARG* 2.9 51.9 + - - +
418B PRO* 6.3 1.6 - - + -
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Residues in contact with ARG 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B VAL* 3.5 29.3 - - - +
400B GLU* 2.6 58.7 + - - +
401B ALA* 3.7 8.7 - - - +
403B LEU* 1.3 71.8 - - - +
405B ALA* 1.3 56.7 + - - +
407B ARG* 3.5 19.6 + - - +
408B LEU* 3.1 26.9 + - - +
444B LEU* 4.0 25.8 - - - +
448B GLU* 5.2 8.9 + - - +
449B PHE 3.2 16.5 + - - +
450B PRO* 2.7 45.6 + - - +
451B PHE* 3.6 11.9 - - + -
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 3.7 27.2 - - + +
318B PHE 3.4 24.0 - - - +
319B LEU* 3.9 15.5 - - + -
401B ALA 3.1 4.4 + - - +
402B THR 3.4 9.0 - - - +
403B LEU 3.2 0.4 - - - -
404B ARG* 1.3 77.1 - - - +
406B LEU* 1.3 61.2 + - - +
408B LEU* 3.1 6.9 + - - +
409B ALA* 2.9 26.2 + - - +
428B LEU* 4.9 3.4 - - + +
451B PHE* 4.1 3.8 - - + -
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 4.1 19.5 - - + -
402B THR* 2.9 24.9 + - - +
403B LEU* 4.0 15.7 - - + +
405B ALA* 1.3 75.7 - - - +
407B ARG* 1.3 57.4 - - - +
409B ALA* 3.3 3.3 + - + -
410B GLU* 2.8 25.4 + - - +
416B HIS* 3.3 48.0 - - + +
417B GLU 4.4 7.0 - - - +
418B PRO* 3.8 29.8 - - + -
421B LEU* 5.1 4.5 - - + -
424B ALA* 4.5 13.2 - - + -
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Residues in contact with ARG 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B GLU* 3.3 25.1 + - - -
403B LEU* 2.9 42.5 + - + +
404B ARG* 3.5 25.7 - - - +
406B LEU* 1.3 74.4 - - + +
408B LEU* 1.3 60.6 + - - +
410B GLU* 3.7 14.7 - - - +
411B ALA* 2.9 31.4 + - - +
444B LEU* 5.8 2.0 - - - +
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 6.0 0.7 - - + -
313B SER* 3.7 30.3 - - - +
317B LEU* 3.9 13.0 - - + -
404B ARG 3.1 14.5 + - - +
405B ALA 3.1 7.4 + - - +
407B ARG* 1.3 72.7 - - - +
409B ALA* 1.3 65.4 + - - +
411B ALA* 4.0 3.1 - - - +
412B VAL* 3.1 25.7 + - + +
428B LEU* 4.6 11.2 - - + -
436B LEU* 3.3 37.7 - - + +
439B ASN* 4.1 10.8 - - + -
440B GLU* 4.0 21.3 - - - +
451B PHE* 3.7 14.8 - - + -
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Residues in contact with ALA 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ALA 2.9 13.6 + - - +
406B LEU* 3.4 13.0 - - + +
407B ARG 3.3 0.2 - - - -
408B LEU* 1.3 77.6 - - - +
410B GLU* 1.3 58.2 + - - +
412B VAL* 3.5 0.9 - - - +
413B GLY 3.1 4.9 + - - -
414B CYS* 2.7 38.0 + - + +
415B PRO 3.8 21.1 - - - +
416B HIS* 4.2 2.2 - - + -
424B ALA* 4.6 5.6 - - + -
428B LEU* 4.0 24.2 - - + +
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Residues in contact with GLU 410 (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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406B LEU 2.8 17.5 + - - +
407B ARG* 3.7 16.0 - - - +
409B ALA* 1.3 77.2 - - - +
411B ALA* 1.3 62.7 + - - +
413B GLY* 3.3 12.0 + - - -
414B CYS 4.1 1.1 - - - -
416B HIS* 3.1 49.1 + - + +
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ARG 2.9 18.4 + - - +
408B LEU 4.0 2.9 - - - +
410B GLU* 1.3 77.8 - - - +
412B VAL* 1.3 60.5 + - - +
413B GLY* 3.2 1.1 + - - -
439B ASN* 4.2 34.1 - - + +
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 3.1 21.7 + - + +
409B ALA 3.5 9.0 - - - +
411B ALA* 1.3 76.7 - - - +
413B GLY* 1.3 55.2 + - - +
414B CYS* 4.0 11.2 - - - -
428B LEU* 3.9 22.0 - - + -
431B LYS* 3.1 25.9 + - + +
435B VAL* 3.7 43.1 - - + +
436B LEU* 4.1 13.2 - - + -
439B ASN* 4.9 9.2 - - + +
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Residues in contact with GLY 413 (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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409B ALA 3.1 1.8 + - - -
410B GLU 3.3 8.9 + - - -
411B ALA 3.2 4.6 - - - -
412B VAL* 1.3 80.0 - - - +
414B CYS* 1.3 62.7 + - - +
415B PRO* 4.6 1.6 - - - +
427B CYS* 4.7 0.9 - - - -
431B LYS* 3.8 11.1 + - - -
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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