Contacts of the helix formed by residues 421 - 436 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A ASN* 4.3 6.0 + - - -
419A VAL 3.4 0.4 + - - -
420A PRO* 1.3 88.1 - - + +
422A SER* 1.3 62.7 + - - +
423A TYR 3.4 1.8 - - - -
424A SER* 2.8 30.3 + - - +
425A VAL* 3.3 16.2 + - + +
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Residues in contact with SER 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LEU* 3.7 12.5 - - - +
412A ILE* 3.7 21.3 - - - -
415A ILE* 3.6 8.7 - - - +
416A ASN* 3.3 19.0 + - - -
419A VAL* 2.5 38.7 + - - +
420A PRO 3.3 0.6 - - - -
421A HIS* 1.3 74.8 - - - +
423A TYR* 1.3 61.0 + - - +
425A VAL* 3.3 6.7 + - - +
426A LEU* 2.8 29.6 + - - +
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Residues in contact with TYR 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ILE* 3.7 27.3 - - + +
413A PRO* 3.5 30.3 - - + +
416A ASN* 3.2 50.0 + - + +
421A HIS* 3.4 0.8 - - - -
422A SER* 1.3 76.9 - - - +
424A SER* 1.3 56.0 + - - +
426A LEU* 3.1 7.4 + - + +
427A GLU* 2.7 44.5 + - - +
448A PRO* 3.7 29.8 - - + +
449A SER 4.3 1.8 - - - +
450A ARG* 3.6 47.7 - - + +
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Residues in contact with SER 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A HIS* 2.8 36.1 + - - +
423A TYR* 1.3 78.1 - - - +
425A VAL* 1.3 63.0 + - - +
427A GLU* 3.7 12.7 - - - +
428A ARG* 3.1 34.9 + - - +
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Residues in contact with VAL 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A VAL* 4.0 28.0 - - + +
372A LEU* 3.8 23.8 - - + +
380A PHE* 4.2 4.0 - - + -
420A PRO 5.5 1.3 - - - +
421A HIS* 3.3 16.1 + - + +
422A SER* 3.3 8.2 + - - +
423A TYR 3.2 0.6 - - - -
424A SER* 1.3 87.0 + - - +
426A LEU* 1.3 57.3 + - - +
428A ARG* 3.4 28.3 + - - +
429A PHE* 2.9 27.4 + - + +
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Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ILE* 4.1 20.9 - - + -
372A LEU* 3.9 11.9 - - + -
405A TYR* 5.9 0.2 - - + -
408A ILE* 3.7 22.7 - - + -
409A TYR* 3.3 33.0 - - + -
412A ILE* 4.3 13.5 - - + -
422A SER 2.8 17.7 + - - +
423A TYR* 3.1 8.9 + - + +
425A VAL* 1.3 77.6 - - - +
427A GLU* 1.3 57.0 + - - +
429A PHE* 3.1 9.6 + - + +
430A VAL* 2.7 37.6 + - + +
447A CYS* 3.4 21.8 - - - -
448A PRO* 5.2 1.6 - - + +
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Residues in contact with GLU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A TYR* 2.7 28.3 + - - +
424A SER* 3.7 13.4 - - - +
426A LEU* 1.3 69.8 - - - +
428A ARG* 1.3 68.0 + - + +
430A VAL* 4.2 7.0 - - - +
431A GLU* 3.1 25.5 + - - +
447A CYS* 4.4 13.9 - - - -
448A PRO 4.6 2.8 - - - +
449A SER* 4.1 23.9 - - - +
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Residues in contact with ARG 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A GLU* 2.5 41.1 + - - -
380A PHE* 3.9 19.6 - - + -
424A SER* 3.1 25.8 + - - +
425A VAL* 3.6 26.6 - - - +
427A GLU* 1.3 78.7 - - + +
429A PHE* 1.3 58.7 + - - +
431A GLU* 3.5 3.9 + - - +
432A GLU* 3.0 36.4 + - + +
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Residues in contact with PHE 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ILE* 4.1 19.5 - - + -
371A VAL* 3.8 14.4 - - + -
372A LEU* 5.9 0.7 - - + -
380A PHE* 3.5 45.1 - + + -
383A ILE* 3.3 32.8 - - + -
384A LEU* 4.0 15.3 - - + -
387A LEU* 3.8 16.8 - - + -
405A TYR* 4.0 9.2 - + - -
425A VAL* 2.9 18.6 + - + +
426A LEU* 3.1 13.9 + - + +
428A ARG* 1.3 75.6 - - - +
430A VAL* 1.3 66.3 + - - +
432A GLU* 3.3 2.8 + - - +
433A CYS* 3.0 45.5 + - - -
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Residues in contact with VAL 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A TYR* 4.2 9.9 - - + -
409A TYR* 2.7 42.6 - - + +
426A LEU* 2.7 32.2 + - + +
427A GLU* 4.2 3.1 - - - +
429A PHE* 1.3 73.1 - - - +
431A GLU* 1.3 58.8 + - - +
433A CYS* 3.3 5.6 + - - -
434A PHE* 2.9 24.8 + - - +
439A ILE* 3.5 9.1 - - + +
444A ARG* 3.8 37.7 - - + +
447A CYS* 4.0 8.5 - - + -
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A GLU 3.1 20.1 + - - +
428A ARG* 3.7 5.2 - - - +
429A PHE 3.2 0.2 - - - -
430A VAL* 1.3 76.2 - - - +
432A GLU* 1.3 55.7 + - + +
434A PHE* 3.2 8.0 + - - +
435A GLN* 2.7 65.1 + - - +
444A ARG* 2.9 40.9 + - - -
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Residues in contact with GLU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A PHE* 3.6 20.8 - - + -
384A LEU* 3.3 28.6 - - + +
428A ARG* 3.0 27.1 + - + +
429A PHE 3.5 4.0 - - - +
431A GLU* 1.3 75.4 - - - +
433A CYS* 1.3 58.4 + - - +
435A GLN* 3.5 6.3 + - - +
436A ALA* 3.0 30.5 + - - +
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Residues in contact with CYS 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A LEU* 3.2 31.0 - - - -
387A LEU* 4.8 0.9 - - - -
405A TYR* 3.2 25.6 - - - +
429A PHE* 3.0 31.2 + - - +
430A VAL* 3.6 6.3 - - - +
432A GLU* 1.3 75.8 - - - +
434A PHE* 1.3 62.3 + - - +
436A ALA* 3.4 2.2 + - - -
437A GLY 3.1 3.8 + - - -
438A ILE* 2.9 47.5 + - + +
439A ILE* 3.9 10.5 - - + -
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Residues in contact with PHE 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A VAL 2.9 16.6 + - - +
431A GLU* 3.7 10.5 - - - +
433A CYS* 1.3 75.3 - - - +
435A GLN* 1.3 68.3 + - - +
437A GLY* 2.8 20.1 + - - -
439A ILE* 3.2 27.3 - - + +
440A SER 4.0 6.7 - - - -
441A LYS* 3.7 36.6 - - + -
444A ARG* 3.7 48.9 - - + -
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Residues in contact with GLN 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLU* 2.7 54.7 + - - +
432A GLU* 3.9 7.2 - - - +
434A PHE* 1.3 82.3 - - - +
436A ALA* 1.3 59.1 + - - +
437A GLY 3.2 0.6 + - - -
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Residues in contact with ALA 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A LEU* 6.1 0.2 - - + -
388A LYS* 4.0 38.8 - - + +
392A LYS* 4.2 11.3 + - - -
432A GLU 3.0 18.7 + - - +
433A CYS* 3.9 5.6 - - - +
434A PHE 3.1 0.2 - - - -
435A GLN* 1.3 77.1 - - - +
437A GLY* 1.3 60.7 + - - +
438A ILE* 3.5 6.7 + - + +
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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