Contacts of the helix formed by residues 517 - 536 (chain B) in PDB entry 4EMX
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 SER 517 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B THR 4.0 0.2 + - - -
516B LEU* 1.3 75.7 - - - +
518B GLU* 1.3 66.3 + - - +
519B LYS* 3.9 8.7 + - - +
520B GLU* 3.1 39.5 + - - +
521B ARG* 2.9 22.2 + - - +
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Residues in contact with GLU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B LEU 3.9 0.6 + - - -
517B SER* 1.3 71.2 - - - +
519B LYS* 1.3 58.8 + - + +
521B ARG* 3.0 30.6 + - - +
522B GLN* 2.9 56.0 + - - +
525B LYS* 4.9 6.2 + - - -
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Residues in contact with LYS 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B GLU* 4.5 14.1 + - - -
404B GLN* 4.9 6.3 + - - +
428B ARG* 3.1 32.1 + - - +
432B LYS* 5.6 5.3 - - - +
517B SER* 3.3 8.3 + - - +
518B GLU* 1.3 78.3 - - + +
520B GLU* 1.3 63.4 + - + +
522B GLN* 3.3 26.7 + - - +
523B ILE* 3.1 33.7 + - + +
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Residues in contact with GLU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 4.0 33.2 + - - +
516B LEU* 3.4 32.0 - - + +
517B SER* 3.1 41.1 + - - +
519B LYS* 1.3 76.8 - - + +
521B ARG* 1.3 61.8 + - - +
523B ILE* 3.4 12.4 + - + +
524B LYS* 3.2 24.4 + - - +
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Residues in contact with ARG 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B ILE* 2.9 42.0 + - + +
514B CYS* 3.2 17.5 + - - +
516B LEU* 2.8 31.5 + - + +
517B SER 2.9 14.1 + - - +
518B GLU* 3.0 36.0 + - - +
520B GLU* 1.3 74.6 - - - +
522B GLN* 1.3 63.6 + - - +
524B LYS* 3.2 17.7 + - - +
525B LYS* 3.2 24.5 + - + +
555B VAL* 4.1 22.4 - - + -
559B CYS* 5.3 2.0 - - - -
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Residues in contact with GLN 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B TYR* 3.6 44.9 - - + +
404B GLN* 5.1 0.3 - - - +
428B ARG* 3.2 21.1 + - - +
518B GLU* 2.9 39.6 + - - +
519B LYS* 3.3 23.7 + - - +
521B ARG* 1.3 76.0 - - - +
523B ILE* 1.3 52.8 + - - +
525B LYS* 3.0 16.6 + - - +
526B GLN* 2.8 39.0 + - - +
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Residues in contact with ILE 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 4.9 14.8 - - - +
424B VAL* 4.3 11.5 - - + +
428B ARG* 3.3 30.9 - - - +
519B LYS* 3.1 28.7 + - + +
520B GLU* 3.5 13.0 - - + +
521B ARG 3.3 0.2 - - - -
522B GLN* 1.3 74.8 - - - +
524B LYS* 1.3 52.5 + - + +
526B GLN* 3.7 7.9 - - - +
527B THR* 2.7 48.0 + - - +
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Residues in contact with LYS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 6.3 0.9 - - - +
509B PHE* 4.2 11.7 - - + -
512B ASP* 4.7 9.9 + - - -
513B ILE* 3.9 32.5 - - + +
516B LEU* 4.2 15.0 - - + +
520B GLU 3.2 15.7 + - - +
521B ARG 3.2 10.6 + - - +
523B ILE* 1.3 77.4 - - + +
525B LYS* 1.3 56.8 + - - +
527B THR* 3.2 12.4 - - + +
528B ALA* 3.1 25.5 + - - +
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Residues in contact with LYS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B TYR* 3.9 27.1 + - - +
509B PHE* 4.8 15.0 - - + -
513B ILE* 5.8 0.7 - - + -
518B GLU* 4.9 5.2 + - - -
521B ARG* 3.2 27.4 + - + +
522B GLN* 3.0 21.1 + - - +
524B LYS* 1.3 76.1 - - + +
526B GLN* 1.3 59.8 + - - +
528B ALA* 3.1 9.0 + - - +
529B LEU* 2.9 26.5 + - - +
548B MET* 3.8 14.2 - - + +
551B PHE* 4.8 7.3 - - + +
552B ALA* 4.1 37.9 + - + +
555B VAL* 5.2 11.5 - - + +
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Residues in contact with GLN 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B TYR* 3.8 14.2 - - + -
404B GLN* 3.2 35.8 + - - +
405B ASN* 3.2 28.5 + - - +
408B LEU* 3.6 16.1 - - + +
424B VAL* 4.0 7.9 - - + -
428B ARG* 2.8 39.8 + - - +
522B GLN 2.8 19.8 + - - +
523B ILE* 3.9 3.8 - - - +
525B LYS* 1.3 69.2 - - - +
527B THR* 1.3 65.3 + - - +
529B LEU* 3.7 3.0 - - - +
530B VAL* 3.0 29.3 + - - +
548B MET* 4.0 9.2 - - + -
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Residues in contact with THR 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B THR* 3.9 14.7 - - + +
424B VAL* 3.8 16.3 - - - +
506B THR* 6.0 1.8 - - + +
523B ILE* 2.7 31.0 + - - +
524B LYS* 3.2 18.9 - - + +
526B GLN* 1.3 71.4 - - - +
528B ALA* 1.3 65.2 + - - +
530B VAL* 3.2 5.7 + - - +
531B GLU* 3.1 28.0 + - + +
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Residues in contact with ALA 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B THR 5.2 7.2 - - - +
507B PHE* 3.8 17.5 - - + -
509B PHE* 4.2 21.1 - - + -
524B LYS 3.1 10.3 + - - +
525B LYS* 3.1 9.8 + - - +
527B THR* 1.3 82.5 - - - +
529B LEU* 1.3 61.4 + - - +
531B GLU* 3.3 6.9 + - - +
532B LEU* 3.0 25.2 + - - +
551B PHE* 5.9 3.4 - - + -
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ASN* 3.9 22.2 - - + +
408B LEU* 3.6 21.5 - - + -
409B VAL* 4.1 21.5 - - + -
525B LYS 2.9 16.0 + - - +
526B GLN 3.7 6.1 - - - +
527B THR 3.3 0.2 - - - -
528B ALA* 1.3 73.7 - - - +
530B VAL* 1.3 64.3 + - - +
532B LEU* 3.4 11.1 + - + +
533B VAL* 3.1 33.0 + - + +
544B LEU* 4.3 29.4 - - + +
548B MET* 3.9 33.8 - - + -
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Residues in contact with VAL 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 3.3 27.8 - - + -
412B THR* 3.8 18.1 - - - +
420B THR* 3.5 29.2 - - + +
423B LEU* 4.0 21.3 - - + -
424B VAL* 3.8 15.7 - - + -
526B GLN 3.0 18.9 + - - +
527B THR 3.4 7.6 - - - +
529B LEU* 1.3 77.6 - - - +
531B GLU* 1.3 56.6 + - - +
533B VAL* 3.1 6.6 + - - +
534B LYS* 2.9 32.7 + - + +
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Residues in contact with GLU 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B THR* 2.5 33.1 + - + +
500B LYS* 2.8 38.4 + - - +
506B THR* 3.7 34.3 + - + +
507B PHE* 3.8 8.0 - - + -
527B THR* 3.1 21.1 + - + +
528B ALA* 3.3 9.1 + - - +
530B VAL* 1.3 75.0 - - - +
532B LEU* 1.3 56.9 + - - +
534B LYS* 3.7 7.5 - - - +
535B HIS* 3.1 26.3 + - - +
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Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B PHE* 3.9 21.3 - - + -
528B ALA 3.0 15.8 + - - +
529B LEU* 3.6 15.5 - - + +
531B GLU* 1.3 74.6 - - - +
533B VAL* 1.3 61.0 + - - +
534B LYS 3.3 0.2 - - - -
535B HIS* 3.8 11.5 - - + -
536B LYS* 2.9 34.8 + - + +
544B LEU* 4.1 22.2 - - + +
547B VAL* 3.7 39.7 - - + -
579B SER* 5.2 10.3 - - - +
580B GLN* 6.4 0.7 - - - -
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Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 5.2 0.2 - - + -
409B VAL* 4.3 20.6 - - + +
412B THR* 3.4 23.6 - - + -
413B LYS* 3.8 33.4 - - + -
529B LEU* 3.1 20.2 + - + +
530B VAL* 3.5 7.9 - - - +
532B LEU* 1.3 76.3 - - - +
534B LYS* 1.3 63.5 + - - +
535B HIS 3.2 0.2 - - - -
536B LYS 4.4 4.7 - - - -
537B PRO* 3.2 25.8 - - + +
544B LEU* 4.0 24.0 - - + -
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Residues in contact with LYS 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B THR* 4.1 9.0 - - + -
416B PRO* 3.2 26.2 - - + +
417B GLN 4.9 0.8 + - - -
418B VAL 2.7 23.1 + - - -
419B SER* 3.6 1.6 - - - +
420B THR* 2.7 35.3 + - - +
423B LEU* 4.1 6.3 - - - -
497B TYR* 3.4 29.7 - - + +
499B PRO* 3.6 2.6 - - - +
500B LYS* 3.0 51.6 + - + +
530B VAL* 2.9 28.0 + - - +
531B GLU* 3.7 8.5 + - - +
532B LEU 3.3 0.2 - - - -
533B VAL* 1.3 76.1 - - - +
535B HIS* 1.3 59.7 + - - +
537B PRO* 4.1 1.4 - - - +
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Residues in contact with HIS 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B PRO* 3.6 15.4 - - - +
500B LYS* 3.0 27.3 + - + +
501B GLU* 5.2 0.9 - - - +
502B PHE* 3.4 47.7 + + + +
507B PHE* 4.8 7.6 - + + -
531B GLU 3.1 17.7 + - - +
532B LEU* 3.9 14.6 - - + +
533B VAL 3.2 0.2 - - - -
534B LYS* 1.3 78.7 - - - +
536B LYS* 1.3 90.7 + - + +
537B PRO* 3.9 1.3 - - - +
580B GLN* 5.5 9.7 + - + +
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Residues in contact with LYS 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LEU* 2.9 21.0 + - + +
533B VAL* 3.5 6.6 - - - +
535B HIS* 1.3 112.8 - - + +
537B PRO* 1.4 59.0 - - - +
538B LYS* 3.1 5.4 - - + -
539B ALA* 3.0 33.8 + - + +
544B LEU* 5.1 1.0 - - - +
579B SER 5.6 2.9 - - - +
580B GLN* 3.9 23.1 + - - +
581B ALA 5.6 1.2 + - - -
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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
------------------------------------------------------------
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