Contacts of the helix formed by residues 431 - 444 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393I TRP* 5.2 2.9 - - - -
397I LEU* 3.9 11.3 - - - +
430I SER* 1.3 80.5 - - - +
432I LYS* 1.3 61.8 + - - +
433I THR 3.6 1.3 - - - -
434I THR* 3.4 19.6 + - - -
435I LEU* 2.9 26.2 + - - +
547I PHE* 3.3 16.5 - - - -
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Residues in contact with LYS 432 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418H LYS* 4.9 4.8 - - - +
540H ARG* 6.3 0.2 - - - +
424I PHE* 3.9 17.1 - - + +
426I GLY 3.2 28.5 - - - +
427I PRO 2.9 21.6 + - - -
428I ILE* 4.8 0.2 - - - +
429I ASP* 3.5 16.4 - - - +
430I SER* 3.0 22.4 + - - +
431I GLY* 1.3 72.8 - - - +
433I THR* 1.3 67.4 + - - +
434I THR 2.9 5.2 + - - -
435I LEU* 3.0 1.7 + - - +
436I ALA* 2.7 39.0 + - - +
474I ASP* 4.7 3.1 - - - -
527I THR* 4.9 7.4 - - + -
528I MET 3.9 4.3 - - - +
529I ASN* 3.3 21.1 - - - +
547I PHE* 3.4 27.3 - - + -
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Residues in contact with THR 433 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418H LYS* 5.6 6.3 + - - +
499H ASP* 6.1 0.2 - - - -
502H ASP* 4.4 18.1 + - + +
504H SER* 3.4 30.4 - - - +
505H VAL* 5.1 1.6 - - + -
540H ARG* 4.9 3.8 + - - -
431I GLY 3.6 0.2 - - - -
432I LYS* 1.3 86.6 + - - +
434I THR* 1.3 58.7 + - - +
436I ALA* 4.6 0.2 - - - -
437I ALA* 3.1 24.8 - - - +
473I GLU* 3.1 34.3 + - - +
474I ASP* 4.4 9.4 + - - -
527I THR* 5.8 1.1 - - - -
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Residues in contact with THR 434 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504H SER* 5.6 0.7 - - - -
393I TRP* 3.9 13.8 - - + -
394I LEU* 4.8 2.0 - - + -
397I LEU* 5.3 1.1 - - + -
431I GLY* 3.4 21.3 - - - -
432I LYS 2.9 0.8 - - - -
433I THR* 1.3 80.8 - - - +
435I LEU* 1.3 60.6 + - - +
437I ALA 4.1 0.2 - - - -
438I ALA* 3.5 7.6 + - - +
569I ILE* 3.2 51.0 - - + +
570I GLN* 3.5 25.0 - - + +
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Residues in contact with LEU 435 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394I LEU* 5.5 4.7 - - + -
397I LEU* 4.4 6.5 - - + -
398I LEU* 4.1 3.8 - - + -
401I MET* 3.8 34.8 - - + -
404I VAL* 6.4 1.3 - - + -
405I VAL* 5.5 1.1 - - + -
424I PHE* 3.5 29.2 - - + -
431I GLY 2.9 16.0 + - - +
434I THR* 1.3 76.1 - - - +
436I ALA* 1.3 61.6 + - - +
437I ALA 2.9 5.2 + - - -
438I ALA* 3.1 1.9 + - + -
439I LEU* 2.9 51.7 + - + +
545I ILE* 5.6 1.6 - - + -
547I PHE* 3.6 15.5 - - + -
569I ILE 5.4 0.2 - - - -
575I LEU* 4.3 20.6 - - + -
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Residues in contact with ALA 436 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424I PHE* 3.8 14.0 - - + -
432I LYS 2.7 20.9 + - - +
433I THR* 4.6 0.4 - - - -
435I LEU* 1.3 73.8 - - - +
437I ALA* 1.3 58.1 + - - +
439I LEU* 4.2 6.6 - - - +
440I LEU* 3.7 14.4 + - - +
471I VAL* 3.7 22.7 - - + +
473I GLU* 3.8 12.6 - - - +
525I ILE* 4.6 6.8 - - + +
527I THR* 3.7 27.4 - - + -
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Residues in contact with ALA 437 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504H SER* 3.2 30.7 - - - +
505H VAL* 4.3 8.5 - - + +
433I THR 3.1 22.7 + - - +
434I THR 4.1 3.4 - - - +
435I LEU 2.9 0.6 - - - -
436I ALA* 1.3 78.9 - - - +
438I ALA* 1.3 66.5 + - - +
440I LEU* 3.1 22.7 + - - +
441I GLU* 3.4 5.9 + - - +
570I GLN* 4.3 11.2 - - + +
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Residues in contact with ALA 438 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394I LEU* 5.8 0.7 - - + -
434I THR 3.5 11.9 + - - +
435I LEU* 3.1 5.5 + - + +
437I ALA* 1.3 79.0 - - - +
439I LEU* 1.3 58.9 + - - +
441I GLU* 3.1 3.0 + - - -
442I LEU* 2.9 23.7 + - - +
569I ILE 4.4 4.0 - - - +
570I GLN* 3.7 21.5 + - - -
571I SER 3.5 19.1 - - - +
572I GLY* 3.4 9.3 - - - +
575I LEU* 3.5 22.4 - - + -
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Residues in contact with LEU 439 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405I VAL* 4.5 14.8 - - + -
408I PHE* 4.4 27.6 - - + -
424I PHE* 3.6 20.4 - - + -
435I LEU* 2.9 37.8 + - + +
436I ALA 4.4 3.4 - - - +
438I ALA* 1.3 75.6 - - - +
440I LEU* 1.3 63.1 + - - +
442I LEU* 3.6 13.5 - - + +
443I CYS* 3.0 29.5 + - - +
469I LEU* 4.7 2.1 - - - +
525I ILE* 3.5 27.8 - - + -
575I LEU* 3.5 19.7 - - + +
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Residues in contact with LEU 440 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505H VAL* 4.8 11.0 - - + -
506H LYS* 5.1 10.5 - - + +
436I ALA 3.7 11.0 + - - +
437I ALA* 3.1 15.9 + - - +
439I LEU* 1.3 79.6 - - - +
441I GLU* 1.3 55.3 + - - +
444I GLY* 2.8 30.5 + - - -
445I GLY 3.4 32.7 + - - +
446I LYS* 3.4 8.1 - - - +
447I ALA* 3.8 29.4 - - + +
469I LEU* 3.5 24.7 - - + -
471I VAL* 3.5 14.1 - - + -
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Residues in contact with GLU 441 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506H LYS* 5.5 6.8 + - - -
364I ARG* 2.8 49.4 + - - +
368I LEU* 3.7 7.2 - - + +
371I ARG* 3.4 22.8 + - - +
437I ALA 3.4 6.0 + - - +
438I ALA* 3.1 7.9 + - - +
440I LEU* 1.3 78.7 - - + +
442I LEU* 1.3 60.6 + - - +
443I CYS 3.3 0.2 - - - -
570I GLN 5.0 1.0 - - - +
571I SER* 3.6 11.3 + - - -
572I GLY* 2.8 30.7 + - - +
573I ILE* 4.1 3.2 + - - +
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Residues in contact with LEU 442 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364I ARG* 3.5 7.1 - - - +
365I PHE* 3.9 12.8 - - + -
368I LEU* 3.5 26.8 - - + +
405I VAL* 3.7 26.0 - - + -
409I LEU* 4.3 12.1 - - + -
438I ALA 2.9 15.7 + - - +
439I LEU* 3.2 11.6 + - + +
441I GLU* 1.3 78.1 - - - +
443I CYS* 1.3 60.8 + - - +
572I GLY* 3.6 21.5 - - - +
575I LEU* 3.6 24.9 - - + -
576I LEU* 3.8 11.4 - - + +
579I LEU* 3.8 22.7 - - + -
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Residues in contact with CYS 443 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361I LEU* 3.7 25.9 - - + +
364I ARG* 3.2 20.6 - - - +
408I PHE* 3.9 14.6 - - - -
409I LEU* 3.5 31.4 - - - -
439I LEU* 3.0 15.6 + - - +
442I LEU* 1.3 83.6 - - - +
444I GLY* 1.3 58.8 + - - +
468I PHE* 3.8 12.3 - - + +
469I LEU* 3.5 28.7 - - + -
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Residues in contact with GLY 444 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364I ARG* 4.2 17.0 - - - -
440I LEU 2.8 22.8 + - - -
441I GLU 4.1 0.4 + - - -
442I LEU 3.8 0.2 - - - -
443I CYS* 1.3 75.7 - - - +
445I GLY* 1.3 59.0 + - - -
468I PHE* 3.3 23.8 - - - +
469I 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