Contacts of the helix formed by residues 401 - 418 (chain B) in PDB entry 5IXC
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 401 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B LEU 3.8 1.1 + - - -
398B GLU* 2.6 48.4 + - - +
400B PHE* 1.3 73.5 - - - +
402B PRO* 1.4 69.0 - - - +
403B GLU* 3.1 11.9 + - - +
404B ARG* 2.9 31.4 + - - +
405B LEU* 3.0 10.3 + - - +
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Residues in contact with PRO 402 (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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400B PHE 4.0 2.6 - - - +
401B SER* 1.4 85.6 - - - +
403B GLU* 1.3 57.5 + - - +
405B LEU* 3.8 16.6 - - + +
406B ALA* 2.9 29.3 + - - +
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Residues in contact with GLU 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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398B GLU* 5.0 6.9 - - - +
401B SER* 3.1 11.2 + - - +
402B PRO* 1.3 82.8 - - - +
404B ARG* 1.3 65.9 + - + +
406B ALA* 3.6 5.2 - - - +
407B SER* 3.3 19.8 + - - -
410B ARG* 4.8 1.9 + - - -
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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
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394B LYS* 4.0 27.4 - - - +
398B GLU* 3.4 34.1 + - - +
399B VAL* 3.3 36.8 - - - +
401B SER* 2.9 9.4 + - - +
403B GLU* 1.3 84.0 + - + +
405B LEU* 1.3 61.1 + - - +
406B ALA 3.2 0.2 - - - -
407B SER* 2.6 24.9 + - - +
408B TYR* 2.8 32.1 + - + +
434B SER* 3.7 22.4 + - - -
438B GLY* 4.5 15.9 + - - -
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Residues in contact with LEU 405 (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 VAL 3.9 7.0 - - - +
400B PHE* 3.9 30.3 - - + +
401B SER 3.0 18.6 + - - +
402B PRO* 3.9 13.2 - - + -
404B ARG* 1.3 74.8 - - - +
406B ALA* 1.3 63.7 + - - +
408B TYR* 3.2 15.4 + - + +
409B ARG* 3.0 24.7 + - - +
584B ALA* 3.1 35.4 - - + +
585B LEU* 3.7 27.4 - - + +
587B GLN* 5.4 12.7 + - + +
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Residues in contact with ALA 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PRO 2.9 21.0 + - - +
403B GLU* 3.6 7.4 - - - +
404B ARG 3.2 0.2 - - - -
405B LEU* 1.3 76.4 - - - +
407B SER* 1.3 57.3 + - - +
409B ARG* 3.3 6.4 + - - +
410B ARG* 2.8 44.4 + - - +
587B GLN* 6.2 1.1 - - - +
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Residues in contact with SER 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B GLU 3.3 7.7 + - - -
404B ARG* 2.6 31.8 + - - +
406B ALA* 1.3 79.2 - - - +
408B TYR* 1.3 67.2 + - - +
410B ARG* 3.5 26.1 + - - +
411B GLU* 3.2 24.6 + - - +
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Residues in contact with TYR 408 (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 VAL* 3.4 27.9 + - - +
404B ARG* 2.8 35.7 + - + +
405B LEU* 3.2 20.8 + - + +
407B SER* 1.3 77.2 - - - +
409B ARG* 1.3 54.4 + - - +
411B GLU* 2.9 6.5 + - - +
412B LEU* 2.7 37.2 + - + +
427B LEU* 4.3 20.9 - - + -
430B LEU* 3.5 50.6 + - + +
431B VAL* 4.2 14.4 - - + -
434B SER* 3.0 32.4 + - - -
585B LEU* 5.4 0.4 - - + -
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Residues in contact with ARG 409 (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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405B LEU 3.0 15.4 + - - +
406B ALA* 3.8 5.4 - - - +
408B TYR* 1.3 76.8 - - - +
410B ARG* 1.3 56.9 + - - +
412B LEU* 3.0 10.2 + - - +
413B GLU* 2.7 55.0 + - - +
587B GLN* 3.9 28.1 + - - +
588B ALA* 5.6 1.4 - - - +
589B PHE* 3.0 59.6 + - + +
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Residues in contact with ARG 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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403B GLU 4.8 1.6 + - - -
406B ALA* 2.8 25.1 + - - +
407B SER* 3.5 33.2 + - - +
409B ARG* 1.3 78.2 - - + +
411B GLU* 1.3 55.7 + - - +
413B GLU* 3.4 35.1 - - - +
414B LEU* 3.6 10.7 + - - +
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Residues in contact with GLU 411 (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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407B SER 3.2 15.5 + - - +
408B TYR* 2.9 9.9 + - - +
410B ARG* 1.3 77.1 - - - +
412B LEU* 1.3 60.3 + - - +
413B GLU 3.3 0.9 - - - -
414B LEU* 3.4 14.3 + - + +
415B ARG* 2.9 36.4 + - + +
430B LEU* 3.8 16.6 - - + +
440B VAL* 5.8 1.4 - - - +
519B ARG* 2.7 44.2 + - - -
522B PHE* 4.1 6.6 - - - -
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Residues in contact with LEU 412 (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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408B TYR* 2.7 21.3 + - + +
409B ARG* 3.5 8.5 - - - +
411B GLU* 1.3 73.7 - - + +
413B GLU* 1.3 51.9 + - - +
415B ARG* 3.2 14.1 + - + +
416B ALA* 2.4 39.7 + - + +
422B THR* 5.1 11.7 - - + +
423B THR 5.3 4.7 - - - +
426B ASP* 4.3 21.3 - - + +
427B LEU* 4.7 22.7 - - + +
430B LEU* 3.6 25.1 - - + -
522B PHE* 5.3 0.4 - - + -
589B PHE* 4.1 24.9 - - + -
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Residues in contact with GLU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ARG* 2.7 39.9 + - - +
410B ARG* 3.4 34.2 - - - +
412B LEU* 1.3 70.1 - - - +
414B LEU* 1.3 63.4 + - + +
416B ALA* 3.6 7.8 - - - +
417B GLU* 2.7 36.4 + - - +
589B PHE* 4.6 4.6 - - + -
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Residues in contact with LEU 414 (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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410B ARG 3.6 13.0 + - - +
411B GLU* 3.4 17.9 + - + +
412B LEU 3.3 0.2 - - - -
413B GLU* 1.3 83.2 - - + +
415B ARG* 1.3 61.9 + - + +
417B GLU* 4.0 3.9 - - + +
418B GLN* 3.0 25.4 + - + +
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Residues in contact with ARG 415 (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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411B GLU* 2.9 24.0 + - + +
412B LEU* 3.4 13.7 - - + +
414B LEU* 1.3 76.3 - - + +
416B ALA* 1.3 52.8 + - - +
418B GLN* 2.6 41.9 - - - +
420B HIS* 3.4 62.9 + - + +
421B PRO 4.4 1.6 + - - -
426B ASP* 2.3 36.2 + - - +
518B PRO* 4.3 15.0 - - - +
522B PHE* 3.9 42.8 - - - +
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Residues in contact with ALA 416 (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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412B LEU 2.4 29.8 + - - +
413B GLU* 3.2 7.8 + - - +
415B ARG* 1.3 72.1 - - - +
417B GLU* 1.3 59.3 + - - +
418B GLN 2.7 13.4 - - - +
420B HIS* 4.2 13.4 - - - +
422B THR* 3.8 23.3 - - + -
589B PHE* 5.3 4.7 - - + -
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Residues in contact with GLU 417 (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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413B GLU 2.7 18.8 + - - +
414B LEU* 4.0 4.9 - - - +
416B ALA* 1.3 68.9 - - - +
418B GLN* 1.3 68.1 + - - +
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Residues in contact with GLN 418 (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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414B LEU* 3.0 15.5 + - + +
415B ARG* 2.6 25.8 - - - +
416B ALA 2.7 15.2 - - - +
417B GLU* 1.3 82.6 - - - +
419B GLY* 1.3 70.1 + - - +
420B HIS* 3.0 21.6 + - - -
513B ARG* 5.2 4.4 - - - +
515B ILE* 4.7 5.9 - - - +
516B PRO* 4.1 28.1 - - - +
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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
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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