Contacts of the helix formed by residues 431 - 444 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393J TRP* 5.2 3.4 - - - -
397J LEU* 3.9 12.2 - - - +
430J SER* 1.3 80.3 - - - +
432J LYS* 1.3 62.4 + - - +
433J THR 3.6 1.3 - - - -
434J THR* 3.4 19.6 - - - -
435J LEU* 2.9 26.0 + - - +
547J PHE* 3.3 16.7 - - - -
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Residues in contact with LYS 432 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418I LYS* 4.7 5.1 - - - +
540I ARG* 5.7 2.2 - - - +
424J PHE* 3.9 16.1 - - + +
426J GLY 3.2 28.7 - - - +
427J PRO 2.9 21.6 + - - -
428J ILE* 4.8 0.4 - - - +
429J ASP* 3.6 15.4 - - - +
430J SER* 2.9 23.9 + - - +
431J GLY* 1.3 73.6 - - - +
433J THR* 1.3 66.0 + - - +
434J THR 2.9 5.7 + - - -
435J LEU* 3.0 1.6 + - - +
436J ALA* 2.7 38.6 + - - +
474J ASP* 4.8 3.1 - - - -
527J THR* 4.9 7.9 - - + -
528J MET 3.9 3.4 - - - +
529J ASN* 3.3 20.9 - - - +
547J PHE* 3.4 26.6 - - + -
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Residues in contact with THR 433 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418I LYS* 5.4 5.3 + - - -
499I ASP* 5.4 1.1 - - - -
502I ASP* 3.8 26.8 + - + +
504I SER* 3.6 24.2 - - - +
505I VAL* 5.2 3.1 - - + -
540I ARG* 4.4 6.3 + - - -
431J GLY 3.6 0.2 - - - -
432J LYS* 1.3 87.0 + - - +
434J THR* 1.3 58.8 + - - +
436J ALA* 4.6 0.2 - - - -
437J ALA* 3.1 24.0 - - - +
473J GLU* 3.1 35.2 + - - +
474J ASP* 4.4 7.1 + - - -
527J THR* 5.7 0.9 + - - -
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Residues in contact with THR 434 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504I SER* 5.3 2.0 + - - -
393J TRP* 3.9 14.1 - - + -
394J LEU* 4.8 1.8 - - + -
397J LEU* 5.3 1.6 - - + -
431J GLY* 3.4 21.0 - - - -
432J LYS 2.9 0.8 - - - -
433J THR* 1.3 81.2 - - - +
435J LEU* 1.3 61.1 + - - +
437J ALA 4.1 0.2 - - - -
438J ALA* 3.5 8.0 + - - +
569J ILE* 3.2 52.2 - - + +
570J GLN* 3.5 26.1 - - + +
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Residues in contact with LEU 435 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394J LEU* 5.5 4.9 - - + -
397J LEU* 4.4 6.1 - - + -
398J LEU* 4.1 3.4 - - + -
401J MET* 3.8 35.4 - - + -
404J VAL* 6.4 1.6 - - + -
405J VAL* 5.5 1.1 - - + -
424J PHE* 3.5 27.8 - - + -
431J GLY 2.9 16.8 + - - +
432J LYS 3.9 0.9 - - - +
434J THR* 1.3 75.2 - - - +
436J ALA* 1.3 63.0 + - - +
437J ALA 2.9 5.9 + - - -
438J ALA* 3.1 2.2 + - + +
439J LEU* 2.9 51.2 + - + +
545J ILE* 5.6 1.3 - - + -
547J PHE* 3.6 14.6 - - + -
569J ILE 5.4 0.7 - - - -
575J LEU* 4.3 20.2 - - + -
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Residues in contact with ALA 436 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424J PHE* 3.8 14.0 - - + -
432J LYS 2.7 20.7 + - - +
433J THR* 4.6 0.7 - - - -
435J LEU* 1.3 74.0 - - - +
437J ALA* 1.3 57.5 + - - +
439J LEU* 4.2 6.6 - - - +
440J LEU* 3.7 14.6 + - - +
471J VAL* 3.7 22.9 - - + +
473J GLU* 3.8 11.9 - - - +
525J ILE* 4.6 7.5 - - + +
527J THR* 3.7 27.6 - - + -
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Residues in contact with ALA 437 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504I SER* 3.0 31.9 - - - +
505I VAL* 3.6 15.3 - - + -
433J THR 3.1 22.7 + - - +
434J THR 4.1 3.1 - - - +
435J LEU 2.9 0.6 - - - -
436J ALA* 1.3 79.8 - - - +
438J ALA* 1.3 65.6 + - - +
439J LEU 3.2 0.2 - - - -
440J LEU* 3.1 19.9 + - - +
441J GLU* 3.4 6.4 + - - +
570J GLN* 4.3 7.1 - - + +
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Residues in contact with ALA 438 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394J LEU* 5.9 0.4 - - + -
434J THR 3.5 11.9 + - - +
435J LEU* 3.1 5.6 + - + +
437J ALA* 1.3 77.7 - - - +
439J LEU* 1.3 58.1 + - - +
441J GLU* 3.1 3.4 + - - -
442J LEU* 2.9 24.4 + - - +
569J ILE 4.4 3.8 - - - +
570J GLN* 3.7 21.9 + - - -
571J SER 3.5 19.3 - - - +
572J GLY* 3.4 8.8 - - - +
575J LEU* 3.5 22.2 - - + -
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Residues in contact with LEU 439 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405J VAL* 4.5 14.8 - - + -
408J PHE* 4.4 26.9 - - + -
424J PHE* 3.6 20.9 - - + -
435J LEU* 2.9 34.6 + - + +
436J ALA* 4.4 3.8 - - - +
438J ALA* 1.3 76.4 - - - +
440J LEU* 1.3 63.6 + - - +
442J LEU* 3.6 12.6 - - + +
443J CYS* 3.0 29.1 + - - +
469J LEU* 4.7 2.7 - - + +
525J ILE* 3.5 28.7 - - + -
575J LEU* 3.5 21.1 - - + -
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Residues in contact with LEU 440 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505I VAL* 4.6 13.7 - - + -
506I LYS* 4.9 9.6 - - + +
436J ALA 3.7 11.6 + - - +
437J ALA 3.1 15.2 + - - +
439J LEU* 1.3 80.0 - - - +
441J GLU* 1.3 56.3 + - + +
444J GLY* 2.8 29.6 + - - -
445J GLY 3.4 32.0 + - - +
446J LYS* 3.4 7.6 - - + +
447J ALA* 3.8 29.4 - - + +
469J LEU* 3.5 24.7 - - + -
471J VAL* 3.5 13.9 - - + -
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Residues in contact with GLU 441 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506I LYS* 5.0 12.6 + - - -
364J ARG* 2.8 49.6 + - - +
368J LEU* 3.7 7.0 - - + +
371J ARG* 3.4 24.2 + - - +
437J ALA 3.4 5.9 + - - +
438J ALA* 3.1 7.8 + - - +
440J LEU* 1.3 78.3 - - - +
442J LEU* 1.3 60.7 + - - +
443J CYS 3.3 0.2 - - - -
570J GLN 5.0 1.0 - - - +
571J SER* 3.6 11.6 + - - -
572J GLY* 2.8 30.8 + - - +
573J ILE* 4.1 3.3 + - - +
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Residues in contact with LEU 442 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364J ARG* 3.5 6.9 - - - +
365J PHE* 4.0 13.6 - - + -
368J LEU* 3.5 27.0 - - + +
405J VAL* 3.7 24.2 - - + -
409J LEU* 4.4 11.2 - - + -
438J ALA 2.9 16.0 + - - +
439J LEU* 3.2 11.4 + - + +
441J GLU* 1.3 78.9 - - - +
443J CYS* 1.3 59.9 + - - +
572J GLY* 3.6 20.4 - - - +
575J LEU* 3.6 27.4 - - + -
576J LEU* 3.8 12.3 - - + +
579J LEU* 3.8 23.3 - - + -
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Residues in contact with CYS 443 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360J MET 5.4 0.3 - - - +
361J LEU* 3.7 26.2 - - + +
364J ARG* 3.2 20.0 - - - +
408J PHE* 4.0 14.6 - - - -
409J LEU* 3.5 32.1 - - - -
439J LEU* 3.0 14.9 + - - +
442J LEU* 1.3 84.2 - - - +
444J GLY* 1.3 59.8 + - - +
468J PHE* 3.8 11.3 - - + +
469J LEU* 3.5 28.5 - - + -
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Residues in contact with GLY 444 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364J ARG* 4.2 17.5 - - - -
440J LEU 2.8 22.9 + - - -
441J GLU 4.1 0.4 + - - -
442J LEU 3.8 0.4 - - - -
443J CYS* 1.3 75.9 - - - +
445J GLY* 1.3 57.5 + - - -
468J PHE* 3.4 23.4 - - - +
469J LEU* 3.4 13.2 - - - +
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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
------------------------------------------------------------
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