Contacts of the helix formed by residues 440 - 458 (chain K) in PDB entry 5A31
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 THR 440 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H PHE* 5.4 3.5 - - - -
247K PHE* 5.2 6.6 - - + -
248K LYS* 5.9 1.6 - - + -
277K GLU 5.5 3.4 - - - +
278K LEU* 4.8 17.7 - - + -
438K GLU* 3.8 28.6 - - + +
439K VAL* 1.3 75.6 + - - +
441K VAL* 1.3 64.2 + - - +
442K ASP 3.6 0.7 - - - -
443K LYS* 4.0 21.6 + - + +
444K TRP* 3.9 32.4 + - - +
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Residues in contact with VAL 441 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H ALA* 3.7 16.4 - - + -
87H GLU* 5.2 11.4 - - + +
90H GLN* 6.0 0.4 - - + +
97H PHE* 5.9 2.5 - - - -
439K VAL* 3.7 22.0 + - + +
440K THR* 1.3 73.8 - - - +
442K ASP* 1.3 66.7 - - - +
443K LYS 3.3 0.2 + - - -
444K TRP* 3.4 2.1 + - - -
445K GLU* 3.3 18.0 + - - +
474K LEU* 3.4 57.2 - - + +
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Residues in contact with ASP 442 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440K THR 3.6 0.2 - - - -
441K VAL* 1.3 78.2 - - - +
443K LYS* 1.3 65.5 + - - +
444K TRP 3.4 0.2 + - - -
445K GLU* 3.5 18.5 + - - +
446K PRO* 3.6 7.8 - - - +
474K LEU 5.6 2.7 - - - -
475K ILE* 5.9 2.3 - - - +
5W LYS* 4.1 23.6 + - - +
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Residues in contact with LYS 443 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247K PHE* 3.2 33.7 - - + -
277K GLU* 3.3 49.4 + - - +
403K PHE* 4.0 18.8 - - + -
440K THR* 4.0 21.4 + - + +
441K VAL 3.2 1.0 - - - -
442K ASP* 1.3 78.9 - - - +
444K TRP* 1.3 77.6 + - + +
446K PRO* 2.9 21.7 - - - +
3W ARG* 6.0 0.4 - - - -
5W LYS* 4.3 31.4 - - + +
6W PRO* 3.7 18.1 - - + +
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Residues in contact with TRP 444 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H PHE* 4.4 14.6 - + + -
245K CYS* 6.2 0.2 - - + -
247K PHE* 6.3 0.4 - - - -
402K PRO* 3.6 37.7 - - + +
403K PHE* 3.5 35.4 - + - -
406K HIS* 4.3 11.9 - - + -
428K ALA* 5.7 0.2 - - + -
432K ILE* 2.9 32.6 - - + +
440K THR* 3.9 23.1 + - - +
441K VAL 3.4 4.1 + - - +
442K ASP 3.3 0.2 - - - -
443K LYS* 1.3 93.2 - - + +
445K GLU* 1.3 65.4 + - - +
446K PRO 3.2 2.5 - - - -
447K LEU* 2.9 48.1 + - + +
448K LEU* 3.4 8.5 + - - +
474K LEU* 4.5 3.6 - - - -
6W PRO* 3.5 28.9 - - + -
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Residues in contact with GLU 445 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441K VAL 3.3 13.6 + - - +
442K ASP* 3.6 18.5 - - - +
444K TRP* 1.3 78.1 - - - +
446K PRO* 1.4 74.4 - - + +
448K LEU* 3.4 5.7 + - - +
449K ASN* 3.3 23.0 + - - +
471K ALA* 4.1 18.6 - - - +
474K LEU* 4.1 17.2 - - + +
475K ILE* 3.9 27.5 - - + +
478K ASN* 3.7 6.0 + - - -
481K THR* 4.5 0.3 + - - -
8W ARG* 2.9 39.0 + - - -
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Residues in contact with PRO 446 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406K HIS* 4.5 0.2 - - - -
442K ASP 3.6 6.1 - - - +
443K LYS 2.9 28.7 - - - +
444K TRP 3.3 0.4 - - - -
445K GLU* 1.4 88.9 - - + +
447K LEU* 1.3 60.2 + - - +
449K ASN* 3.7 1.7 - - + +
450K ASN* 2.8 35.7 + - - +
5W LYS* 6.3 0.2 - - + -
6W PRO* 3.5 33.2 - - + +
7W THR 4.2 3.8 - - - +
8W ARG* 3.4 31.9 - - + -
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Residues in contact with LEU 447 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H PHE* 5.7 1.1 - - + -
406K HIS* 3.6 27.4 - - + -
425K PHE* 3.9 31.0 - - + +
428K ALA* 4.3 9.0 - - + -
429K LEU* 4.0 26.7 - - + +
432K ILE* 4.0 19.3 - - + -
444K TRP* 2.9 38.5 + - + +
446K PRO* 1.3 81.3 - - - +
448K LEU* 1.3 68.9 + - + +
450K ASN* 3.2 2.1 + - - +
451K LEU* 3.0 25.5 + - + +
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Residues in contact with LEU 448 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H VAL* 4.3 2.7 - - + -
97H PHE* 3.8 27.6 - - + -
429K LEU* 4.6 18.4 - - + -
444K TRP 3.4 9.1 + - - +
445K GLU 3.8 4.7 - - - +
446K PRO 3.3 0.4 - - - -
447K LEU* 1.3 79.6 - - + +
449K ASN* 1.3 63.7 + - - +
451K LEU* 3.3 7.3 + - + +
452K GLY 3.0 18.5 + - - -
467K TYR* 3.6 23.9 - - + +
470K GLN* 3.9 36.1 - - + +
471K ALA* 3.9 17.3 - - + +
474K LEU* 3.9 24.2 - - + -
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Residues in contact with ASN 449 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445K GLU* 3.3 18.9 + - - +
446K PRO* 3.7 8.7 - - + +
448K LEU* 1.3 77.5 - - - +
450K ASN* 1.3 62.2 + - - +
452K GLY* 3.2 2.9 + - - -
453K HIS* 3.0 41.1 + - - -
468K HIS* 4.0 16.6 + - + -
471K ALA* 4.1 10.2 - - + +
480K SER* 4.4 4.6 + - - -
481K THR* 4.7 5.7 + - - +
484K ALA* 5.4 0.2 - - - +
8W ARG* 2.7 43.7 - - - +
9W LEU 3.9 9.6 + - - -
10W GLU* 5.0 0.4 + - - -
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Residues in contact with ASN 450 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406K HIS* 3.0 19.4 + - - +
410K VAL* 3.8 9.3 - - - +
425K PHE* 3.9 15.9 - - + -
446K PRO 2.8 20.1 + - - +
447K LEU 3.6 4.0 - - - +
449K ASN* 1.3 71.4 - - - +
451K LEU* 1.3 61.7 + - - +
453K HIS* 3.2 6.4 + - - +
454K VAL* 3.0 23.0 + - - +
7W THR 2.9 26.7 + - - -
8W ARG* 3.6 2.7 - - - +
9W LEU* 2.6 51.6 + - + +
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Residues in contact with LEU 451 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422K GLU* 4.4 2.5 - - + -
425K PHE* 3.8 33.0 - - + +
426K LEU* 4.1 22.4 - - + -
429K LEU* 3.5 35.7 - - + -
447K LEU* 3.0 20.1 + - + +
448K LEU* 3.6 7.9 - - - +
450K ASN* 1.3 76.9 - - - +
452K GLY* 1.3 60.0 + - - +
454K VAL* 3.4 15.5 - - + +
455K CYS* 3.0 35.2 + - - -
467K TYR* 3.7 23.1 - - + -
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Residues in contact with GLY 452 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448K LEU 3.0 11.5 + - - -
449K ASN 3.6 4.3 - - - -
451K LEU* 1.3 74.4 - - - +
453K HIS* 1.3 60.6 + - - +
455K CYS 3.3 1.4 + - - -
456K ARG* 3.0 19.8 + - - +
464K ALA* 3.5 15.1 - - - +
467K TYR* 3.8 19.3 - - - +
468K HIS* 3.5 22.3 - - - -
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Residues in contact with HIS 453 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413K PHE* 4.3 17.3 - + + -
449K ASN* 3.0 36.2 + - - +
450K ASN 3.3 10.3 - - - +
452K GLY* 1.3 75.0 - - - +
454K VAL* 1.3 62.3 + - - +
456K ARG* 3.3 42.3 + - - +
457K LYS* 3.2 24.3 + - - +
468K HIS* 3.8 10.2 + - - -
484K ALA* 4.4 5.2 - - + -
9W LEU* 3.8 27.5 + - + -
10W GLU* 3.8 23.2 - - - -
11W LEU* 3.8 16.9 - - + +
15W ASP* 4.5 2.2 - - - -
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Residues in contact with VAL 454 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413K PHE* 3.5 32.3 - - + -
418K TRP* 3.7 17.5 - - + +
421K ALA* 3.6 22.4 - - + -
422K GLU* 3.7 33.7 - - + +
425K PHE* 4.4 5.6 - - + -
450K ASN 3.0 12.1 + - - +
451K LEU* 3.4 21.3 - - + +
452K GLY 3.4 0.2 - - - -
453K HIS* 1.3 75.3 - - - +
455K CYS* 1.3 61.4 + - - +
457K LYS* 3.1 5.3 + - - +
458K LEU* 3.0 31.1 + - - +
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Residues in contact with CYS 455 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422K GLU* 3.7 24.5 - - - -
426K LEU* 6.3 0.2 - - - -
451K LEU* 3.0 29.7 + - - +
452K GLY 3.7 4.3 - - - +
453K HIS 3.3 0.2 - - - -
454K VAL* 1.3 77.6 - - - +
456K ARG* 1.3 59.4 + - - +
458K LEU* 3.3 4.8 + - - +
459K LYS 3.2 3.8 + - - -
460K LYS* 3.0 38.2 + - + +
463K GLU* 4.0 17.3 - - - +
464K ALA* 3.9 15.7 - - + +
467K TYR* 4.0 21.1 - - - -
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Residues in contact with ARG 456 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452K GLY 3.0 10.1 + - - +
453K HIS* 3.4 50.5 + - - +
455K CYS* 1.3 75.3 - - - +
457K LYS* 1.3 78.0 + - - +
459K LYS* 3.2 14.4 + - - +
461K TYR* 4.0 15.1 - - + -
464K ALA* 3.7 6.1 - - - +
468K HIS* 4.9 0.8 + - - -
484K ALA* 4.8 5.9 - - - +
487K TYR* 3.5 22.0 - - - -
488K ILE* 3.4 32.8 - - + +
491K LEU* 3.8 13.9 - - + -
11W LEU* 3.9 15.8 - - - +
15W ASP* 3.2 28.7 + - - +
18W GLU* 3.4 21.7 + - - +
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Residues in contact with LYS 457 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413K PHE* 4.1 16.9 - - + -
418K TRP* 3.7 59.2 - - + +
453K HIS 3.2 11.2 + - - +
454K VAL 3.1 8.5 + - - +
456K ARG* 1.3 98.7 - - - +
458K LEU* 1.3 61.9 + - - +
459K LYS* 3.1 12.6 + - - +
14W ASP 5.6 0.8 + - - -
15W ASP* 4.1 21.7 + - - +
18W GLU* 3.7 30.2 + - + +
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Residues in contact with LEU 458 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418K TRP* 3.6 39.5 - - + +
419K LYS* 4.9 19.5 - - + +
422K GLU* 3.2 30.1 - - + +
454K VAL 3.0 24.6 + - - +
455K CYS 3.3 9.6 + - - +
457K LYS* 1.3 74.5 - - - +
459K LYS* 1.3 68.0 + - - +
460K LYS* 3.5 24.4 + - + +
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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
------------------------------------------------------------
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