Contacts of the helix formed by residues 431 - 444 (chain C) in PDB entry 4E2I
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 GLY 431 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393C TRP* 5.2 3.1 - - - -
397C LEU* 3.9 11.7 - - - +
430C SER* 1.3 79.3 - - - +
432C LYS* 1.3 61.3 + - - +
433C THR 3.6 1.3 - - - -
434C THR* 3.4 19.8 - - - -
435C LEU* 2.9 25.8 + - - +
547C PHE* 3.3 17.9 - - - -
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Residues in contact with LYS 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B LYS* 4.6 4.9 - - - +
540B ARG* 5.9 1.3 - - - +
424C PHE* 3.9 16.9 - - + +
426C GLY 3.2 28.3 - - - +
427C PRO 2.9 21.6 + - - -
428C ILE* 4.8 0.4 - - - +
429C ASP* 3.6 16.0 - - - +
430C SER* 3.0 22.4 + - - +
431C GLY* 1.3 72.9 - - - +
433C THR* 1.3 67.5 + - - +
434C THR 2.9 5.7 + - - -
435C LEU* 3.0 1.4 + - - -
436C ALA* 2.7 38.8 + - - +
474C ASP* 4.7 3.6 - - - -
527C THR* 4.9 7.6 - - + -
528C MET 3.9 3.8 - - - +
529C ASN* 3.3 21.1 - - - +
547C PHE* 3.4 26.8 - - + -
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Residues in contact with THR 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LYS* 5.5 5.4 + - - -
502B ASP* 4.1 24.6 + - + +
504B SER* 3.5 28.0 - - - +
505B VAL* 5.1 3.8 - - + -
540B ARG* 4.6 4.7 + - - -
432C LYS* 1.3 86.2 + - - +
434C THR* 1.3 57.3 + - - +
435C LEU 3.5 0.2 - - - -
436C ALA* 4.6 0.2 - - - -
437C ALA* 3.1 24.8 - - - +
473C GLU* 3.1 34.6 + - - +
474C ASP* 4.4 6.8 + - - -
527C THR* 5.5 1.1 - - - +
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Residues in contact with THR 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B SER* 5.4 1.3 - - - -
393C TRP* 3.9 15.2 - - + -
394C LEU* 4.8 2.0 - - + -
397C LEU* 5.3 1.1 - - + -
431C GLY* 3.4 21.0 - - - -
432C LYS 2.9 0.8 - - - -
433C THR* 1.3 80.8 - - - +
435C LEU* 1.3 59.7 + - - +
437C ALA 4.1 0.2 - - - -
438C ALA* 3.5 7.6 + - - +
569C ILE* 3.2 50.8 - - + +
570C GLN* 3.5 25.0 - - + +
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Residues in contact with LEU 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 5.5 5.4 - - + -
397C LEU* 4.4 6.5 - - + -
398C LEU* 4.1 3.6 - - + -
401C MET* 3.8 34.1 - - + -
404C VAL* 6.4 1.6 - - + -
405C VAL* 5.5 1.3 - - + -
424C PHE* 3.5 28.3 - - + -
431C GLY 2.9 15.6 + - - +
432C LYS 3.9 1.1 - - - +
434C THR* 1.3 75.4 - - - +
436C ALA* 1.3 63.4 + - - +
437C ALA 2.9 6.3 + - - -
438C ALA* 3.1 2.4 + - + -
439C LEU* 2.9 49.8 + - + +
545C ILE* 5.6 1.3 - - + -
547C PHE* 3.6 15.9 - - + -
569C ILE 5.4 0.2 - - - -
575C LEU* 4.3 20.4 - - + -
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Residues in contact with ALA 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424C PHE* 3.8 14.5 - - + -
432C LYS 2.7 20.1 + - - +
433C THR* 4.6 0.4 - - - -
435C LEU* 1.3 74.8 - - - +
437C ALA* 1.3 59.7 + - - +
439C LEU* 4.3 6.4 - - - +
440C LEU* 3.7 13.9 + - - +
471C VAL* 3.7 23.4 - - + +
473C GLU* 3.8 12.3 - - - +
525C ILE* 4.6 6.0 - - + +
527C THR* 3.7 27.6 - - + -
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Residues in contact with ALA 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B SER* 3.0 30.3 - - - +
505B VAL* 3.8 13.7 - - + +
433C THR 3.1 21.7 + - - +
434C THR 4.1 3.4 - - - +
435C LEU 2.9 1.0 - - - -
436C ALA* 1.3 80.0 - - - +
438C ALA* 1.3 66.5 + - - +
440C LEU* 3.1 21.1 + - - +
441C GLU* 3.4 6.4 + - - +
570C GLN* 4.3 9.6 - - + +
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Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 5.8 0.7 - - + -
434C THR 3.5 12.5 + - - +
435C LEU* 3.1 5.5 + - + +
437C ALA* 1.3 78.1 - - - +
439C LEU* 1.3 56.6 + - - +
441C GLU* 3.1 3.4 + - - -
442C LEU* 2.9 24.4 + - - +
569C ILE 4.4 3.1 - - - +
570C GLN* 3.7 21.9 + - - -
571C SER 3.5 19.3 - - - +
572C GLY* 3.4 9.3 - - - +
575C LEU* 3.5 22.7 - - + -
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Residues in contact with LEU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C VAL* 4.5 15.0 - - + -
408C PHE* 4.4 26.5 - - + -
424C PHE* 3.6 20.0 - - + -
435C LEU* 2.9 37.3 + - + +
436C ALA 4.4 3.8 - - - +
438C ALA* 1.3 76.6 - - - +
440C LEU* 1.3 63.4 + - - +
442C LEU* 3.6 12.8 - - + +
443C CYS* 3.0 29.0 + - - +
469C LEU* 4.7 2.7 - - + +
525C ILE* 3.5 28.0 - - + -
575C LEU* 3.5 21.3 - - + -
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Residues in contact with LEU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B VAL* 4.7 12.1 - - + -
506B LYS* 5.0 9.9 - - + +
436C ALA 3.7 11.2 + - - +
437C ALA* 3.1 15.5 + - - +
439C LEU* 1.3 80.4 - - - +
441C GLU* 1.3 56.6 + - - +
444C GLY* 2.8 29.1 + - - -
445C GLY 3.4 31.3 + - - +
446C LYS* 3.4 9.0 - - - +
447C ALA* 3.8 29.6 - - + +
469C LEU* 3.5 25.1 - - + -
471C VAL* 3.5 13.4 - - + +
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Residues in contact with GLU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B LYS* 5.2 10.4 + - - -
364C ARG* 2.8 48.6 + - - +
368C LEU* 3.7 7.2 - - + +
371C ARG* 3.4 24.2 + - - +
437C ALA 3.4 5.1 + - - +
438C ALA* 3.1 9.2 + - - +
440C LEU* 1.3 78.5 - - + +
442C LEU* 1.3 61.1 + - - +
443C CYS 3.3 0.2 - - - -
570C GLN 5.0 1.0 - - - +
571C SER* 3.5 12.3 + - - -
572C GLY* 2.8 29.9 + - - +
573C ILE* 4.1 2.8 + - - +
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Residues in contact with LEU 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364C ARG* 3.5 7.3 - - - +
365C PHE* 4.0 13.4 - - + -
368C LEU* 3.5 26.2 - - + +
405C VAL* 3.7 24.5 - - + -
409C LEU* 4.3 11.0 - - + -
438C ALA 2.9 15.5 + - - +
439C LEU* 3.2 11.4 + - + +
441C GLU* 1.3 77.7 - - - +
443C CYS* 1.3 60.1 + - - +
572C GLY* 3.6 21.0 - - - +
575C LEU* 3.6 26.2 - - + -
576C LEU* 3.8 12.6 - - + +
579C LEU* 3.8 23.3 - - + -
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Residues in contact with CYS 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C MET 5.4 0.3 - - - +
361C LEU* 3.7 25.2 - - + +
364C ARG* 3.2 20.2 - - - +
408C PHE* 4.0 14.6 - - - -
409C LEU* 3.5 32.1 - - - -
439C LEU* 3.0 15.6 + - - +
442C LEU* 1.3 83.6 - - - +
444C GLY* 1.3 59.5 + - - +
468C PHE* 3.8 11.0 - - + +
469C LEU* 3.5 28.3 - - + -
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Residues in contact with GLY 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ARG* 4.2 17.5 - - - -
440C LEU 2.8 22.6 + - - -
441C GLU 4.1 0.4 + - - -
442C LEU 3.8 0.2 - - - -
443C CYS* 1.3 75.9 - - - +
445C GLY* 1.3 57.9 + - - -
468C PHE* 3.4 23.5 - - - +
469C LEU* 3.4 13.4 - - - +
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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