Contacts of the helix formed by residues 407 - 418 (chain Z) in PDB entry 5L4K
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 MET 407 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399Z LEU* 3.2 30.4 - - + +
400Z TYR 4.9 2.0 - - - +
402Z ASN 3.5 20.2 - - - +
403Z LYS* 3.8 26.2 + - + -
404Z ASP 3.4 6.2 + - - +
405Z HIS 3.2 0.6 - - - -
406Z GLY* 1.3 78.5 - - - +
408Z LEU* 1.3 59.5 + - - +
410Z ALA 3.9 0.7 - - - -
411Z ALA* 2.9 31.2 + - - +
437Z GLU* 3.8 24.5 - - + +
439Z TYR* 3.7 39.7 - - + +
440Z ILE* 3.7 26.9 - - + -
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Residues in contact with LEU 408 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405Z HIS* 3.5 28.3 + - + +
407Z MET* 1.3 77.2 - - - +
409Z SER* 1.3 66.7 + - - +
411Z ALA 3.2 0.7 + - - -
412Z ALA* 3.0 24.7 + - + +
439Z TYR* 3.5 41.6 + - + +
442Z SER* 4.1 16.8 - - - +
443Z GLY* 3.8 14.3 - - - +
446Z LEU* 5.4 6.1 - - + -
476Z THR* 5.7 2.2 - - + -
795Z GLY* 3.3 27.8 - - - +
796Z LEU* 5.7 7.9 - - + -
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Residues in contact with SER 409 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372Z LEU* 4.2 14.0 - - - +
375Z SER* 4.0 14.8 + - - +
376Z PHE* 4.8 15.6 - - - -
405Z HIS 3.3 15.3 + - - -
406Z GLY* 5.4 0.9 - - - -
408Z LEU* 1.3 77.5 - - - +
410Z ALA* 1.3 57.7 + - - +
412Z ALA* 3.6 1.9 + - - +
413Z SER* 2.9 29.5 + - - -
416Z MET* 4.8 0.7 - - - +
794Z ALA 3.8 7.0 + - - -
795Z GLY* 3.3 22.2 + - - -
798Z THR* 4.5 13.8 - - - +
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Residues in contact with ALA 410 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371Z ASN* 5.1 0.2 - - - +
375Z SER* 3.8 17.4 + - - -
398Z TRP* 4.4 11.2 - - + -
399Z LEU* 3.9 25.0 - - + +
402Z ASN* 4.9 0.7 - - - +
406Z GLY 3.4 21.0 + - - +
407Z MET 3.7 1.4 + - - -
408Z LEU 3.2 0.4 - - - -
409Z SER* 1.3 81.0 - - - +
411Z ALA* 1.3 58.1 + - - +
413Z SER* 2.9 21.6 + - - +
414Z LEU* 3.5 15.6 - - - +
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Residues in contact with ALA 411 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399Z LEU* 4.1 11.4 - - + +
407Z MET 2.9 20.2 + - - +
408Z LEU 3.2 0.4 + - - -
410Z ALA* 1.3 75.7 - - - +
412Z ALA* 1.3 63.3 + - - +
413Z SER 3.3 0.2 - - - -
414Z LEU* 3.5 20.2 + - + +
429Z ILE* 5.5 0.2 - - - +
432Z TYR* 6.3 0.7 - - + -
440Z ILE* 3.7 30.7 - - + +
443Z GLY* 3.3 19.6 - - - +
444Z ALA* 3.9 4.1 + - + +
447Z ALA* 3.5 9.9 - - - +
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Residues in contact with ALA 412 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408Z LEU* 3.0 20.1 + - + +
409Z SER 4.0 0.2 - - - +
411Z ALA* 1.3 72.3 - - - +
413Z SER* 1.3 57.5 + - - +
414Z LEU 3.0 5.2 - - - -
415Z GLY* 2.9 19.2 + - - -
416Z MET* 3.1 13.7 + - - +
443Z GLY* 3.4 15.8 + - - +
446Z LEU* 4.4 11.7 - - + -
447Z ALA* 3.9 3.5 - - - +
450Z ILE* 3.8 5.7 - - + +
798Z THR* 3.8 32.5 - - + +
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Residues in contact with SER 413 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375Z SER* 3.1 30.4 + - - -
378Z ASN* 4.5 9.5 + - - -
379Z GLY* 4.4 3.0 - - - -
409Z SER 2.9 15.6 + - - -
410Z ALA* 2.9 18.2 + - - +
411Z ALA 3.3 0.2 - - - -
412Z ALA* 1.3 74.7 - - - +
414Z LEU* 1.3 62.3 + - - +
415Z GLY 3.3 0.4 - - - -
416Z MET* 3.5 21.7 - - - +
417Z ILE* 3.5 28.4 + - - +
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Residues in contact with LEU 414 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378Z ASN* 5.4 2.2 - - - +
391Z LEU 4.5 4.0 - - - +
392Z THR* 3.7 40.8 - - + +
395Z GLY 5.4 4.9 - - - +
396Z ASN* 4.2 2.2 - - - +
399Z LEU* 4.1 22.7 - - + -
410Z ALA 3.5 16.6 - - - +
411Z ALA* 3.6 12.6 - - + +
412Z ALA 3.0 1.4 - - - -
413Z SER* 1.3 81.6 - - - +
415Z GLY* 1.3 60.6 + - - +
417Z ILE* 4.3 2.2 - - + -
418Z LEU* 3.5 27.7 + - - +
429Z ILE* 3.8 16.1 - - + +
432Z TYR* 3.4 37.0 - - + -
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Residues in contact with GLY 415 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412Z ALA 2.9 5.8 + - - -
414Z LEU* 1.3 77.9 - - - +
416Z MET* 1.3 62.9 + - - +
417Z ILE 3.3 0.2 - - - -
418Z LEU 2.8 25.5 - - - +
429Z ILE* 4.2 3.4 - - - -
447Z ALA* 3.3 34.6 - - - +
450Z ILE* 2.9 17.1 - - - +
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Residues in contact with MET 416 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375Z SER 3.9 9.4 - - - +
376Z PHE* 4.0 22.2 - - + +
379Z GLY* 3.6 23.3 - - - +
380Z PHE* 4.6 5.8 - - + -
383Z ALA* 3.7 12.3 - - - +
409Z SER 4.8 0.2 - - - +
412Z ALA 3.1 12.0 + - - +
413Z SER* 3.5 31.6 - - - +
414Z LEU 3.5 0.4 - - - -
415Z GLY* 1.3 77.6 - - - +
417Z ILE* 1.3 61.7 + - - +
419Z LEU* 3.2 19.1 - - - +
450Z ILE* 3.7 19.7 - - + -
798Z THR* 3.8 29.6 - - + +
800Z LEU* 5.7 0.4 - - - -
801Z VAL* 3.9 22.9 - - + -
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Residues in contact with ILE 417 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378Z ASN* 3.4 47.6 - - - +
379Z GLY* 4.0 2.5 - - - -
382Z ASN* 3.8 28.9 - - + +
383Z ALA* 4.4 3.1 - - - +
385Z PHE* 4.6 3.8 + - - -
387Z GLN* 3.8 14.1 - - - +
388Z ASP 3.7 28.9 - - - +
391Z LEU* 4.4 3.6 - - + -
392Z THR* 3.5 21.5 - - + -
413Z SER 3.5 15.7 + - - +
414Z LEU 4.5 0.2 - - - +
415Z GLY 3.3 0.4 - - - -
416Z MET* 1.3 77.6 - - - +
418Z LEU* 1.3 65.3 + - + +
419Z LEU* 2.7 17.2 + - - +
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Residues in contact with LEU 418 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387Z GLN* 4.9 10.1 - - + +
388Z ASP 4.7 4.0 - - - +
389Z LYS* 6.0 1.1 - - - -
392Z THR* 4.0 20.9 - - + +
414Z LEU 3.5 20.5 + - - +
415Z GLY 2.8 15.3 + - - +
417Z ILE* 1.3 89.9 - - + +
419Z LEU* 1.3 55.5 + - - +
421Z ASP* 3.1 24.9 - - - +
425Z GLY* 4.4 8.3 - - - +
428Z GLN* 3.5 37.0 - - + -
429Z ILE* 4.7 4.3 - - + -
432Z TYR* 6.4 1.1 - - + -
451Z VAL* 3.4 27.6 - - + +
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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