Contacts of the helix formed by residues 421 - 436 (chain B) in PDB entry 3EIJ
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 HIS 421 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372B LEU 5.5 3.1 - - - +
374B SER 6.0 1.3 - - - -
416B ASN* 4.5 1.6 + - - -
419B VAL* 4.7 7.2 - - + -
420B PRO* 1.3 102.6 + - + +
422B SER* 1.3 63.2 + - - +
423B TYR 3.3 2.0 - - - -
424B SER* 3.0 25.3 + - - +
425B VAL* 3.0 24.0 + - + +
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Residues in contact with SER 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 3.9 11.1 - - - +
412B ILE* 3.6 16.6 - - - +
415B ILE* 3.3 26.7 - - - +
416B ASN* 3.2 14.3 + - - -
419B VAL* 2.9 28.4 + - - +
420B PRO 2.8 5.8 + - - -
421B HIS* 1.3 75.1 - - - +
423B TYR* 1.3 57.5 + - - +
425B VAL* 3.4 3.0 + - - +
426B LEU* 2.8 31.7 + - - +
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Residues in contact with TYR 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ILE* 3.8 27.1 - - + +
413B PRO* 3.6 30.1 - - + +
416B ASN* 3.4 47.7 + - + +
421B HIS 3.2 0.8 + - - -
422B SER* 1.3 78.3 - - - +
424B SER* 1.3 63.1 + - - +
426B LEU* 3.4 6.5 + - + +
427B GLU* 3.1 30.5 + - - +
448B PRO* 3.8 29.2 - - + +
449B SER 4.1 7.6 - - - +
450B ARG* 3.7 48.2 + - + +
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B HIS* 3.0 22.9 + - - +
423B TYR* 1.3 78.4 - - - +
425B VAL* 1.3 64.9 + - - +
427B GLU* 3.6 11.2 - - - +
428B ARG* 3.2 34.3 + - - +
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Residues in contact with VAL 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B VAL* 3.8 26.7 - - + +
372B LEU* 3.8 22.4 - - + +
380B PHE* 4.3 11.1 - - + -
421B HIS* 3.0 27.3 + - + +
422B SER* 3.8 2.9 - - - +
424B SER* 1.3 79.2 + - - +
426B LEU* 1.3 60.4 + - - +
428B ARG* 3.3 22.6 + - - +
429B PHE* 2.9 27.7 + - - +
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Residues in contact with LEU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ILE* 4.5 10.5 - - + -
372B LEU* 4.0 15.0 - - + -
408B ILE* 3.9 26.2 - - + -
409B TYR* 3.8 20.4 - - + -
412B ILE* 4.4 12.6 - - + -
422B SER 2.8 20.5 + - - +
423B TYR* 3.7 6.7 - - + +
425B VAL* 1.3 76.2 - - - +
427B GLU* 1.3 57.2 + - - +
429B PHE* 3.1 9.1 + - + +
430B VAL* 2.8 44.1 + - + +
447B CYS* 3.3 29.2 - - - -
448B PRO* 4.4 11.4 - - + +
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Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B TYR* 3.1 19.1 + - - +
424B SER* 3.6 11.7 - - - +
426B LEU* 1.3 76.6 - - - +
428B ARG* 1.3 63.7 + - + +
430B VAL* 4.1 1.8 - - - +
431B GLU* 3.0 29.8 + - - +
447B CYS* 3.9 20.4 - - - -
448B PRO 5.2 2.7 - - - +
449B SER* 4.4 26.0 - - - +
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Residues in contact with ARG 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B GLY* 6.0 3.6 - - - -
377B GLU* 3.5 24.4 + - - -
380B PHE* 3.9 20.4 - - + -
424B SER* 3.2 23.3 + - - +
425B VAL* 3.7 26.5 - - - +
427B GLU* 1.3 78.3 - - + +
429B PHE* 1.3 62.6 + - - +
431B GLU* 3.4 4.8 + - - +
432B GLU* 3.1 27.8 + - + +
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Residues in contact with PHE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ILE* 4.7 15.5 - - + -
371B VAL* 4.0 21.5 - - + -
372B LEU* 5.8 0.4 - - + -
380B PHE* 3.4 54.4 - + + -
383B ILE* 4.2 9.2 - - + -
384B LEU* 3.8 18.2 - - + -
387B LEU* 4.0 19.3 - - + -
405B TYR* 3.8 16.2 - + - -
425B VAL 2.9 18.1 + - - +
426B LEU* 3.5 11.7 - - + +
428B ARG* 1.3 74.0 - - - +
430B VAL* 1.3 67.2 + - - +
432B GLU* 3.2 3.6 + - - +
433B CYS* 3.0 49.2 + - - -
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Residues in contact with VAL 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 4.2 13.0 - - + -
409B TYR* 3.4 24.5 - - + +
426B LEU* 2.8 40.5 + - + +
427B GLU* 4.1 3.8 - - - +
429B PHE* 1.3 74.6 - - - +
431B GLU* 1.3 57.7 + - - +
433B CYS* 3.3 7.7 + - - +
434B PHE* 3.0 27.5 + - - +
439B ILE* 3.6 6.5 - - + +
444B ARG* 3.7 37.2 - - + +
447B CYS* 3.9 13.9 - - + -
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLU 3.0 20.2 + - - +
428B ARG* 3.8 5.8 - - - +
430B VAL* 1.3 78.3 - - + +
432B GLU* 1.3 57.2 + - + +
434B PHE* 3.6 2.4 + - - +
435B GLN* 2.8 54.6 + - - +
444B ARG* 3.2 39.8 + - - -
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Residues in contact with GLU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLU* 5.4 1.7 - - - +
380B PHE* 3.8 23.4 - - + -
384B LEU* 4.2 25.3 - - + +
428B ARG* 3.1 18.8 + - + +
429B PHE 3.2 7.8 + - - +
431B GLU* 1.3 73.3 - - + +
433B CYS* 1.3 61.2 + - - +
435B GLN* 3.3 9.1 + - - +
436B ALA* 2.9 29.3 + - - +
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Residues in contact with CYS 433 (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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384B LEU* 3.4 22.2 - - - -
387B LEU* 4.9 0.7 - - - -
405B TYR* 2.9 29.4 - - - +
429B PHE* 3.0 32.7 + - - -
430B VAL* 3.6 9.2 - - - +
432B GLU* 1.3 77.4 - - - +
434B PHE* 1.3 60.9 + - - +
436B ALA* 3.2 3.3 + - - -
437B GLY 3.1 15.9 + - - -
438B ILE* 3.1 32.5 + - + +
439B ILE* 4.0 11.2 - - + -
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Residues in contact with PHE 434 (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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430B VAL 3.0 12.4 + - - +
431B GLU* 3.8 3.1 - - - +
433B CYS* 1.3 75.2 - - - +
435B GLN* 1.3 77.8 + - - +
436B ALA 3.0 0.2 - - - -
437B GLY* 2.9 19.9 + - - -
439B ILE* 3.6 27.5 - - + +
440B SER 3.7 8.7 - - - -
441B LYS* 3.5 40.4 - - + -
444B ARG* 3.4 50.7 - - + -
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Residues in contact with GLN 435 (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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431B GLU* 2.8 48.3 + - - +
432B GLU* 3.7 13.2 - - - +
433B CYS 3.3 0.2 - - - -
434B PHE* 1.3 90.1 - - - +
436B ALA* 1.3 56.3 + - - +
437B GLY 3.3 1.1 + - - -
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Residues in contact with ALA 436 (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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384B LEU* 5.2 1.6 - - + -
388B LYS* 3.9 35.2 - - + -
392B LYS* 4.5 9.8 + - - +
432B GLU 2.9 16.6 + - - +
433B CYS* 3.6 7.4 - - - +
434B PHE 3.0 0.2 - - - -
435B GLN* 1.3 76.8 - - - +
437B GLY* 1.3 61.0 + - - +
438B ILE* 3.3 7.9 + - + +
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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