Contacts of the helix formed by residues 435 - 457 (chain E) in PDB entry 5X8Q
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 GLU 435 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E LEU* 4.3 2.2 - - + +
345E CYS* 3.3 39.7 + - - +
348E ASP* 2.9 11.2 + - - +
433E LEU 5.1 0.2 - - - -
434E GLN* 1.3 81.9 - - + +
436E LYS* 1.3 63.7 + - - +
437E ARG* 3.3 2.7 - - - -
438E LYS* 2.5 56.3 + - + +
439E VAL* 3.3 15.7 + - - +
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Residues in contact with LYS 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428E ALA* 3.6 22.2 + - - +
429E HIS* 5.3 3.2 - - - +
433E LEU* 4.1 31.9 - - + +
434E GLN 3.5 3.7 + - - +
435E GLU* 1.3 72.3 - - - +
437E ARG* 1.3 60.5 + - + +
439E VAL* 3.1 10.1 + - - +
440E GLU* 2.9 47.0 + - + +
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Residues in contact with ARG 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435E GLU 3.3 0.8 - - - -
436E LYS* 1.3 80.3 - - + +
438E LYS* 1.3 57.8 + - + +
440E GLU* 3.0 35.7 + - - +
441E GLN* 3.1 31.0 + - - +
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Residues in contact with LYS 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E GLU* 3.7 27.5 + - - -
344E LEU* 4.3 15.9 - - + -
435E GLU* 2.5 58.9 + - + +
437E ARG* 1.3 76.9 - - + +
439E VAL* 1.3 63.3 + - - +
441E GLN* 3.4 7.3 + - - +
442E LEU* 3.2 26.9 + - - +
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Residues in contact with VAL 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E LEU* 4.1 24.9 - - + -
348E ASP* 4.6 1.8 - - - +
352E LEU* 4.2 10.3 - - + -
426E ILE* 3.9 4.6 - - + +
427E ASN 3.7 16.8 - - - +
428E ALA* 3.6 28.0 - - - +
433E LEU* 3.9 29.2 - - + -
435E GLU 3.3 13.7 + - - +
436E LYS 3.1 6.8 + - - +
438E LYS* 1.3 73.0 - - - +
440E GLU* 1.3 59.0 + - - +
442E LEU* 3.1 7.8 + - - +
443E GLN* 2.8 26.9 + - - +
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Residues in contact with GLU 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428E ALA* 3.4 20.9 - - + +
436E LYS* 2.9 34.6 + - - +
437E ARG* 3.0 46.5 + - - +
438E LYS 3.3 0.2 - - - -
439E VAL* 1.3 76.4 - - - +
441E GLN* 1.3 59.9 + - + +
443E GLN* 3.2 5.1 + - - +
444E TYR* 2.7 33.9 + - + +
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Residues in contact with GLN 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437E ARG 3.1 14.6 + - - +
438E LYS* 3.8 7.2 - - - +
439E VAL 3.2 0.2 - - - -
440E GLU* 1.3 81.1 - - + +
442E LEU* 1.3 64.5 + - + +
444E TYR* 3.8 14.6 - - - +
445E ASN* 3.0 49.7 + - - +
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Residues in contact with LEU 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E SER* 5.8 1.1 - - - +
340E GLY* 3.4 49.4 - - - +
341E PHE* 3.8 4.9 - - - +
344E LEU* 3.7 20.4 - - + -
426E ILE* 3.7 21.1 - - + -
438E LYS 3.2 11.9 + - - +
439E VAL 3.1 8.1 + - - +
441E GLN* 1.3 79.5 - - + +
443E GLN* 1.3 61.9 + - - +
445E ASN* 3.5 11.7 + - + +
446E LEU* 3.2 27.8 + - + +
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Residues in contact with GLN 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E LEU* 3.9 18.5 + - + +
426E ILE* 3.1 33.3 + - + +
427E ASN* 3.6 15.7 - - - +
428E ALA* 3.1 24.4 + - - +
429E HIS* 4.4 13.7 - - - -
439E VAL 2.8 16.3 + - - +
440E GLU* 3.6 5.8 - - - +
442E LEU* 1.3 76.9 - - - +
444E TYR* 1.3 58.6 + - - +
446E LEU* 3.2 6.7 + - - +
447E GLU* 2.9 43.6 + - - +
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Residues in contact with TYR 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440E GLU 2.7 21.7 + - - +
441E GLN* 3.8 17.5 - - - +
443E GLN* 1.3 73.9 - - - +
445E ASN* 1.3 69.3 + - - +
447E GLU* 3.2 14.3 + - + +
448E LEU* 3.0 66.8 + - + +
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Residues in contact with ASN 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E ILE* 5.3 3.0 - - + +
273E LEU* 3.6 19.4 - - + +
441E GLN* 3.0 38.1 + - - +
442E LEU* 3.8 13.9 - - + +
444E TYR* 1.3 84.4 - - - +
446E LEU* 1.3 56.4 + - - +
448E LEU* 3.5 14.1 + - - +
449E ALA* 3.1 28.1 + - - +
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Residues in contact with LEU 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E LEU* 4.2 18.6 - - + -
277E VAL* 3.9 27.6 - - + -
338E LEU* 5.6 2.5 - - + -
419E LEU* 4.5 12.4 - - + +
422E ALA* 4.1 23.3 - - + +
423E LEU* 3.8 17.1 - - + +
426E ILE* 3.7 34.5 - - + -
442E LEU* 3.2 16.8 + - + +
443E GLN 3.2 7.4 + - - +
445E ASN* 1.3 76.9 - - - +
447E GLU* 1.3 60.6 + - - +
449E ALA* 3.9 1.9 - - - +
450E PHE* 2.9 32.2 + - - +
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Residues in contact with GLU 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E LEU* 3.8 20.6 - - + -
443E GLN* 2.9 35.3 + - - +
444E TYR* 3.2 15.2 + - + +
446E LEU* 1.3 76.3 - - - +
448E LEU* 1.3 52.9 + - - +
450E PHE* 3.7 1.9 - - - +
451E HIS* 2.8 38.4 + - - +
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Residues in contact with LEU 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E ILE* 4.2 19.2 - - + +
444E TYR* 3.0 62.4 + - + +
445E ASN* 3.6 15.9 - - - +
447E GLU* 1.3 77.4 - - - +
449E ALA* 1.3 58.5 + - - +
451E HIS* 3.8 7.7 - - - +
452E HIS* 2.9 30.7 + - - +
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Residues in contact with ALA 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E ILE* 3.9 25.3 - - + +
273E LEU* 4.2 14.6 - - + -
274E VAL* 3.7 26.5 - - + +
419E LEU* 4.8 4.7 - - + -
445E ASN 3.1 15.1 + - - +
446E LEU* 3.9 3.8 - - - +
448E LEU* 1.3 79.8 - - - +
450E PHE* 1.3 63.7 + - - +
452E HIS* 3.5 2.8 + - - +
453E HIS* 3.0 23.2 + - - +
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Residues in contact with PHE 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412E PHE* 6.2 0.4 - + - -
416E GLU* 3.8 30.1 - - + -
419E LEU* 3.7 33.4 - - + +
420E TYR* 3.7 25.1 - + + -
423E LEU* 3.6 22.7 - - + -
446E LEU 2.9 18.9 + - - +
447E GLU* 3.8 3.4 - - - +
449E ALA* 1.3 77.4 - - - +
451E HIS* 1.3 51.7 + - - +
453E HIS* 3.0 3.7 + - + -
454E LEU* 2.8 63.6 + - + +
462E ILE* 5.1 0.9 - - + -
463E LEU* 4.0 31.0 - - + -
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Residues in contact with HIS 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447E GLU 2.8 22.8 + - - +
448E LEU* 3.8 8.4 - - - +
450E PHE* 1.3 72.4 - - - +
452E HIS* 1.3 62.8 + - - +
454E LEU* 3.3 9.8 + - + +
455E CYS* 3.0 41.4 + - - -
460E GLN* 5.0 8.7 - - + +
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Residues in contact with HIS 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E LEU* 5.5 9.4 - - + -
270E ILE* 3.6 26.0 - - + +
271E GLU* 3.7 31.0 + - + +
274E VAL* 5.8 3.6 - - + -
448E LEU 2.9 18.1 + - - +
449E ALA 3.6 4.7 - - - +
451E HIS* 1.3 77.4 - - - +
453E HIS* 1.3 66.7 - + + +
455E CYS* 3.1 8.8 + - - +
456E LYS* 3.0 42.7 + - + +
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Residues in contact with HIS 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274E VAL* 4.0 22.9 - - + -
413E SER* 4.8 5.6 - - - -
415E ASP* 3.2 37.8 + - + +
416E GLU* 4.8 10.8 - - + +
419E LEU* 4.4 14.7 - - + +
449E ALA 3.0 14.5 + - - +
450E PHE* 3.4 9.4 - - + +
452E HIS* 1.3 80.5 - + + +
454E LEU* 1.3 57.1 + - - +
456E LYS* 3.5 23.0 - - - +
457E THR* 2.7 43.6 + - + -
297G SER* 3.3 24.9 + - - -
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Residues in contact with LEU 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416E GLU* 4.4 7.2 - - + +
450E PHE* 2.8 54.3 + - + +
451E HIS* 3.8 9.6 - - + +
452E HIS 3.3 0.2 - - - -
453E HIS* 1.3 75.3 - - - +
455E CYS* 1.3 55.2 + - - +
457E THR* 3.4 3.3 + - - +
458E HIS* 3.0 7.8 + - - -
459E ARG* 2.7 63.8 + - + +
460E GLN* 3.9 17.7 + - + +
462E ILE* 3.9 12.6 - - + -
463E LEU* 4.3 24.2 - - + -
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Residues in contact with CYS 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E HIS* 3.0 47.7 + - - +
452E HIS* 3.1 10.3 + - - +
454E LEU* 1.3 74.5 - - - +
456E LYS* 1.3 65.9 + - - +
458E HIS* 3.3 20.3 + - - -
460E GLN* 3.6 25.8 + - - +
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Residues in contact with LYS 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E GLU* 4.2 22.4 + - - +
452E HIS* 3.0 35.1 + - + +
453E HIS* 3.5 23.5 - - - +
455E CYS* 1.3 76.9 - - - +
457E THR* 1.3 63.5 + - + +
458E HIS* 3.3 11.9 + - - -
297G SER* 3.5 46.0 + - - +
298G ASN* 4.8 5.1 - - - +
299G ILE* 4.7 11.1 + - - +
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Residues in contact with THR 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416E GLU* 4.5 2.9 + - - +
453E HIS* 2.7 34.3 + - + +
454E LEU* 3.4 5.9 + - - -
455E CYS 3.2 0.2 - - - -
456E LYS* 1.3 77.3 - - + +
458E HIS* 1.3 71.8 + - - +
459E ARG* 3.4 26.7 - - - +
297G SER* 3.4 40.6 - - - +
299G ILE* 4.2 20.0 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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