Contacts of the helix formed by residues 431 - 444 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393H TRP* 5.2 3.6 - - - -
397H LEU* 3.9 11.5 - - - +
430H SER* 1.3 79.6 - - - +
432H LYS* 1.3 62.3 + - - +
433H THR 3.6 1.6 - - - -
434H THR* 3.4 19.6 - - - -
435H LEU* 2.9 26.9 + - - +
547H PHE* 3.3 16.7 - - - -
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Residues in contact with LYS 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418G LYS* 4.8 4.8 - - - +
540G ARG* 6.1 0.9 - - - +
424H PHE* 3.9 16.3 - - + +
426H GLY 3.2 28.9 - - - +
427H PRO 2.9 21.7 + - - -
428H ILE* 4.8 0.2 - - - +
429H ASP* 3.5 16.9 - - - +
430H SER* 3.0 22.2 + - - +
431H GLY* 1.3 72.2 - - - +
433H THR* 1.3 67.2 + - - +
434H THR 2.9 4.7 + - - -
435H LEU* 3.0 1.6 + - - +
436H ALA* 2.7 39.2 + - - +
474H ASP* 4.8 3.4 - - - -
527H THR* 4.9 7.2 - - + -
528H MET 3.9 4.0 - - - +
529H ASN* 3.3 20.9 - - - +
547H PHE* 3.4 26.6 - - + -
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Residues in contact with THR 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418G LYS* 5.5 4.8 + - - -
499G ASP* 5.8 0.4 - - - -
502G ASP* 4.3 20.3 + - + +
504G SER* 3.6 27.7 - - - +
505G VAL* 5.1 3.1 - - + -
540G ARG* 4.8 4.5 + - - -
432H LYS* 1.3 86.9 + - - +
434H THR* 1.3 56.8 + - - +
436H ALA* 4.6 0.2 - - - -
437H ALA* 3.1 25.3 - - - +
473H GLU* 3.1 35.0 + - - +
474H ASP* 4.4 9.2 + - - -
527H THR* 5.5 0.8 - - - +
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Residues in contact with THR 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504G SER* 5.5 0.7 - - - -
393H TRP* 3.9 14.0 - - + -
394H LEU* 4.8 2.7 - - + -
397H LEU* 5.3 0.9 - - + -
431H GLY* 3.4 21.3 + - - -
432H LYS 2.9 0.6 - - - -
433H THR* 1.3 82.0 - - - +
435H LEU* 1.3 60.5 + - - +
438H ALA* 3.5 7.6 + - - +
569H ILE* 3.2 51.4 - - + +
570H GLN* 3.5 25.1 - - + +
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Residues in contact with LEU 435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394H LEU* 5.5 4.9 - - + -
397H LEU* 4.4 6.3 - - + -
398H LEU* 4.1 3.4 - - + -
401H MET* 3.8 35.0 - - + -
404H VAL* 6.4 1.3 - - + -
405H VAL* 5.5 1.1 - - + -
424H PHE* 3.5 27.4 - - + -
431H GLY 2.9 15.5 + - - +
432H LYS 3.9 0.9 - - - +
434H THR* 1.3 75.3 - - - +
436H ALA* 1.3 63.3 + - - +
437H ALA 2.9 5.1 + - - -
438H ALA* 3.1 2.4 + - + +
439H LEU* 2.9 51.4 + - + +
545H ILE* 5.6 1.8 - - + -
547H PHE* 3.6 14.4 - - + -
569H ILE 5.4 0.4 - - - -
575H LEU* 4.2 20.0 - - + -
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Residues in contact with ALA 436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424H PHE* 3.8 14.0 - - + -
432H LYS 2.7 20.7 + - - +
433H THR* 4.6 0.2 - - - -
435H LEU* 1.3 72.9 - - - +
437H ALA* 1.3 57.7 + - - +
439H LEU* 4.2 6.6 - - - +
440H LEU* 3.7 14.6 + - - +
471H VAL* 3.7 22.8 - - + +
473H GLU* 3.8 12.8 - - - +
525H ILE* 4.6 7.1 - - + +
527H THR* 3.7 27.1 - - + -
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Residues in contact with ALA 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504G SER* 3.1 31.2 - - - +
505G VAL* 3.9 12.8 - - + +
433H THR* 3.1 22.4 + - - +
434H THR 4.1 3.6 - - - +
435H LEU 2.9 0.6 - - - -
436H ALA* 1.3 78.8 - - - +
438H ALA* 1.3 66.7 + - - +
440H LEU* 3.0 21.4 + - - +
441H GLU* 3.4 6.4 + - - +
570H GLN* 4.3 9.1 - - + +
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Residues in contact with ALA 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394H LEU* 5.8 0.9 - - + -
434H THR 3.5 11.9 + - - +
435H LEU* 3.1 4.6 + - - +
437H ALA* 1.3 79.4 - - - +
439H LEU* 1.3 58.3 + - - +
441H GLU* 3.1 3.6 + - - -
442H LEU* 2.9 24.4 + - - +
569H ILE 4.4 3.6 - - - +
570H GLN* 3.7 21.2 + - - -
571H SER 3.5 19.5 - - - +
572H GLY* 3.4 9.2 - - - +
575H LEU* 3.5 22.4 - - + -
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Residues in contact with LEU 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405H VAL* 4.5 15.5 - - + -
408H PHE* 4.4 26.2 - - + -
424H PHE* 3.6 20.0 - - + -
435H LEU* 2.9 36.0 + - + +
436H ALA 4.4 3.6 - - - +
438H ALA* 1.3 77.1 - - - +
440H LEU* 1.3 62.0 + - - +
442H LEU* 3.6 13.9 - - + +
443H CYS* 3.0 29.3 + - - +
469H LEU* 4.7 3.1 - - + +
525H ILE* 3.5 28.0 - - + -
575H LEU* 3.5 20.2 - - + +
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Residues in contact with LEU 440 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505G VAL* 4.8 12.6 - - + -
506G LYS* 5.1 9.9 - - + +
436H ALA 3.7 11.9 + - - +
437H ALA 3.0 15.3 + - - +
439H LEU* 1.3 80.4 - - - +
441H GLU* 1.3 56.5 + - + +
444H GLY* 2.8 30.0 + - - -
445H GLY 3.4 33.0 + - - +
446H LYS* 3.4 8.1 - - - +
447H ALA* 3.8 29.4 - - + +
469H LEU* 3.5 25.1 - - + -
471H VAL* 3.5 13.2 - - + +
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Residues in contact with GLU 441 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506G LYS* 5.2 10.4 + - - -
364H ARG* 2.8 49.6 + - - +
368H LEU* 3.7 7.1 - - + +
371H ARG* 3.4 22.9 + - - +
437H ALA 3.4 5.1 + - - +
438H ALA* 3.1 8.1 + - - +
440H LEU* 1.3 78.0 - - + +
442H LEU* 1.3 61.5 + - - +
443H CYS 3.3 0.7 - - - -
570H GLN 5.0 1.4 - - - +
571H SER* 3.6 12.0 + - - -
572H GLY* 2.8 29.9 + - - +
573H ILE* 4.1 2.9 + - - +
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Residues in contact with LEU 442 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364H ARG* 3.5 6.4 - - - +
365H PHE* 3.9 12.8 - - + -
368H LEU* 3.5 27.6 - - + +
405H VAL* 3.7 25.1 - - + -
409H LEU* 4.3 11.0 - - + -
438H ALA 2.9 15.3 + - - +
439H LEU* 3.2 11.2 + - + +
441H GLU* 1.3 78.2 - - - +
443H CYS* 1.3 60.6 + - - +
572H GLY* 3.6 20.4 - - - +
575H LEU* 3.6 26.2 - - + -
576H LEU* 3.8 11.7 - - + +
579H LEU* 3.8 23.3 - - + -
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Residues in contact with CYS 443 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360H MET 5.4 0.3 - - - +
361H LEU* 3.7 26.6 - - + +
364H ARG* 3.2 20.3 - - - +
408H PHE* 3.9 15.3 - - - -
409H LEU* 3.5 31.9 - - - -
412H MET* 5.2 0.4 - - - -
439H LEU 3.0 14.7 + - - +
442H LEU* 1.3 83.2 - - - +
444H GLY* 1.3 59.8 + - - +
468H PHE* 3.8 10.6 - - + +
469H LEU* 3.5 28.3 - - + -
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Residues in contact with GLY 444 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364H ARG* 4.2 17.7 - - - -
440H LEU 2.8 22.2 + - - -
441H GLU 4.1 0.4 + - - -
442H LEU 3.8 0.4 - - - -
443H CYS* 1.3 74.4 - - - +
445H GLY* 1.3 58.0 + - - -
468H PHE* 3.3 23.7 - - - +
469H 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