Contacts of the helix formed by residues 519 - 539 (chain B) in PDB entry 2ETM
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 ASP 519 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B SER 4.1 2.4 + - - +
518B LEU* 1.3 79.6 - - - +
520B LEU* 1.3 69.6 + - - +
521B ALA* 3.5 9.2 - - - +
522B SER* 3.1 32.2 + - - -
523B LEU* 3.4 10.5 + - - +
687B GLN* 3.3 27.5 - - - +
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Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ASP* 1.3 71.8 - - - +
521B ALA* 1.3 55.9 + - - +
522B SER 2.7 1.2 + - - -
523B LEU* 2.5 39.7 + - + +
524B ILE* 2.8 18.0 + - + +
616B LEU* 4.0 26.5 - - + -
646B ASN* 3.3 33.0 - - + +
647B CYS* 5.0 0.2 - - - -
648B PRO* 3.6 21.8 - - + -
683B GLU* 3.8 33.9 - - + +
687B GLN* 3.9 4.4 - - - +
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Residues in contact with ALA 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ASP* 3.5 7.4 - - - +
520B LEU* 1.3 77.7 - - - +
522B SER* 1.3 57.6 + - - +
524B ILE* 4.7 3.1 - - - +
525B LEU* 3.0 27.3 + - - +
680B LEU* 3.6 11.1 - - - +
683B GLU* 4.1 7.1 + - - +
684B LYS* 4.2 24.6 - - + +
687B GLN* 3.1 28.2 - - - +
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Residues in contact with SER 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B LEU* 3.5 26.8 - - - +
519B ASP* 3.1 24.6 + - - -
520B LEU 2.7 5.1 + - - -
521B ALA* 1.3 74.5 - - - +
523B LEU* 1.3 65.4 + - - -
525B LEU* 3.2 8.9 + - - +
526B TYR* 3.0 38.1 + - - -
557B ASN 4.8 0.3 + - - -
558B ASP* 4.3 12.3 + - - -
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Residues in contact with LEU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B LEU* 3.9 24.2 - - + -
518B LEU* 4.2 17.0 - - + +
519B ASP 3.7 13.9 - - - +
520B LEU* 2.5 26.1 + - + +
522B SER* 1.3 72.5 - - - +
524B ILE* 1.3 63.1 + - - +
526B TYR* 2.9 20.9 + - + +
527B ALA* 3.2 9.7 + - - +
615B ILE* 3.6 33.4 - - + +
616B LEU* 4.0 24.2 - - + +
618B HIS* 3.8 28.7 - - + +
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Residues in contact with ILE 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B LEU* 2.8 28.8 + - + +
521B ALA 4.3 3.6 - - - +
523B LEU* 1.3 72.0 - - - +
525B LEU* 1.3 57.0 + - - +
527B ALA* 3.2 7.6 + - - +
528B TYR* 2.9 26.9 + - - +
616B LEU* 4.6 2.0 - - + -
648B PRO* 4.1 13.2 - - + -
651B LEU* 3.8 18.8 - - + -
676B LEU* 4.3 14.8 - - + +
679B ILE* 4.1 20.9 - - + -
680B LEU* 3.8 32.5 - - + +
683B GLU* 3.6 33.9 - - + -
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Residues in contact with LEU 525 (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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521B ALA 3.0 21.6 + - - +
522B SER* 3.4 10.5 - - - +
523B LEU 3.1 0.4 - - - -
524B ILE* 1.3 78.9 - - - +
526B TYR* 1.3 55.7 + - + +
528B TYR* 3.9 5.1 - - + +
529B GLN* 2.7 67.0 + - + +
558B ASP* 4.0 33.0 - - + +
680B LEU* 3.8 27.3 - - + +
684B LYS* 6.4 0.9 - - + -
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Residues in contact with TYR 526 (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 LEU* 4.7 5.8 - - + -
510B PHE* 3.8 14.7 - + - -
511B LEU* 4.4 14.1 - - + -
518B LEU* 3.8 30.9 - - + +
522B SER* 3.0 31.4 + - - -
523B LEU* 2.9 12.3 + - + +
525B LEU* 1.3 79.7 - - + +
527B ALA* 1.3 66.4 + - - +
529B GLN* 3.2 8.8 + - - +
530B LEU* 2.9 29.9 + - - +
554B VAL* 5.9 0.4 - - + -
556B SER 5.0 0.9 - - - -
557B ASN* 2.5 34.1 + - - -
558B ASP* 4.4 3.4 - - - -
559B CYS 4.4 6.1 - - - -
560B VAL* 3.3 37.2 - - + +
615B ILE* 4.3 14.4 - - + -
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Residues in contact with ALA 527 (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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523B LEU 3.2 10.1 + - - +
524B ILE* 3.2 12.3 + - - +
526B TYR* 1.3 75.6 - - - +
528B TYR* 1.3 64.2 + - - +
530B LEU* 3.0 8.6 + - - +
531B SER 2.9 19.2 + - - -
608B PHE* 3.6 7.9 - - - -
612B MET* 4.0 25.4 - - + -
615B ILE* 4.3 14.2 - - + +
616B LEU* 6.3 1.8 - - + -
651B LEU* 5.7 3.4 - - + -
676B LEU* 4.0 16.4 - - + -
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Residues in contact with TYR 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B HIS* 6.4 0.4 - - - -
524B ILE 2.9 16.1 + - - +
525B LEU* 3.9 8.3 - - + +
527B ALA* 1.3 77.6 - - - +
529B GLN* 1.3 67.3 + - + +
531B SER* 2.8 24.2 + - - -
532B THR* 3.0 33.3 - - + +
673B LYS* 3.2 43.9 - - + +
676B LEU* 3.9 14.9 - - + +
677B SER* 3.5 31.1 + - - -
680B LEU* 4.4 21.8 - - + -
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Residues in contact with GLN 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B HIS* 3.4 44.5 + - + +
525B LEU* 2.7 44.2 + - + +
526B TYR* 3.2 8.8 + - - +
528B TYR* 1.3 82.7 - - + +
530B LEU* 1.3 61.8 + - - +
532B THR* 2.7 25.1 + - - -
533B ALA 3.3 4.0 + - - -
558B ASP 3.1 22.0 + - - +
559B CYS* 3.2 4.2 + - - -
560B VAL* 3.0 36.1 + - + +
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Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B HIS 5.3 1.3 - - - +
507B LEU* 4.7 0.7 - - + -
526B TYR 2.9 12.6 + - - +
527B ALA* 3.3 7.6 - - - +
529B GLN* 1.3 78.6 - - - +
531B SER* 1.3 56.5 + - - +
533B ALA* 3.1 6.1 + - - +
534B LEU* 2.9 33.6 + - + +
547B ILE* 5.9 2.0 - - + -
552B VAL* 3.6 46.0 - - + -
560B VAL* 4.2 11.0 - - + +
562B LEU* 4.3 23.3 - - + +
608B PHE* 3.8 16.2 - - + -
611B CYS* 3.9 13.2 - - - -
615B ILE* 3.7 29.8 - - + -
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Residues in contact with SER 531 (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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527B ALA 2.9 5.3 + - - -
528B TYR* 2.8 17.4 + - - -
529B GLN 3.2 0.2 - - - -
530B LEU* 1.3 73.6 - - - +
532B THR* 1.3 60.6 + - - +
534B LEU* 3.8 7.4 - - - +
535B ALA* 2.8 31.7 + - - +
608B PHE* 3.7 13.8 - - - -
669B PHE* 4.2 8.1 - - - +
672B LEU 4.8 0.2 - - - -
673B LYS* 3.4 29.3 - - - +
676B LEU* 3.5 26.5 - - - +
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Residues in contact with THR 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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480B HIS* 3.2 23.0 + - - -
482B HIS* 3.5 9.4 - - + -
528B TYR* 3.0 51.7 + - + +
529B GLN* 2.7 17.8 + - - -
531B SER* 1.3 78.3 + - - +
533B ALA* 1.3 60.4 + - - +
535B ALA* 3.9 1.9 - - - +
536B TYR* 3.2 21.7 + - - +
673B LYS* 4.0 25.1 + - - -
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Residues in contact with ALA 533 (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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480B HIS* 3.7 9.9 - - - -
482B HIS* 3.7 27.4 - - + +
483B ILE* 3.9 13.7 - - + +
529B GLN 3.3 7.4 + - - +
530B LEU* 3.1 12.1 + - - +
532B THR* 1.3 80.0 + - - +
534B LEU* 1.3 62.3 + - + +
536B TYR* 3.3 4.9 + - - +
537B LEU* 3.0 31.2 + - - +
562B LEU* 4.5 9.9 - - + -
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Residues in contact with LEU 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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530B LEU* 2.9 18.5 + - + +
531B SER 3.3 0.6 + - - +
533B ALA* 1.3 75.8 - - - +
535B ALA* 1.3 58.2 + - - +
537B LEU* 3.1 13.8 + - + +
538B GLU* 2.9 31.0 + - - +
544B HIS* 5.1 1.6 - - + -
547B ILE* 3.5 36.1 - - + -
562B LEU* 3.9 24.5 - - + -
604B ASP* 5.1 2.2 - - - +
608B PHE* 3.5 32.8 - - + -
669B PHE* 3.4 39.0 - - + -
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Residues in contact with ALA 535 (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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531B SER 2.8 18.5 + - - +
532B THR 3.9 4.5 - - - +
534B LEU* 1.3 75.4 - - - +
536B TYR* 1.3 57.9 + - - +
538B GLU* 3.7 6.0 - - - +
539B SER* 3.1 27.9 + - - -
669B PHE* 3.5 25.9 - - + +
670B THR* 4.4 6.6 + - - +
673B LYS* 4.1 24.7 - - + +
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Residues in contact with TYR 536 (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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477B GLN 3.8 1.6 + - - -
478B PHE* 3.4 34.0 - + + -
479B ASP* 3.1 35.0 + - - +
480B HIS* 4.0 22.2 - + + -
483B ILE* 3.6 20.4 - - + -
532B THR 3.2 17.0 + - - +
533B ALA 3.5 3.4 - - - +
534B LEU 3.1 0.4 - - - -
535B ALA* 1.3 82.3 - - - +
537B LEU* 1.3 62.1 + - - +
539B SER* 2.8 25.6 + - - -
540B LYS* 2.9 39.6 + - + +
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Residues in contact with LEU 537 (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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478B PHE* 3.4 52.7 - - + -
483B ILE* 3.8 11.9 - - + -
533B ALA 3.0 19.5 + - - +
534B LEU* 3.1 24.2 + - + +
536B TYR* 1.3 75.7 - - + +
538B GLU* 1.3 61.5 + - - +
539B SER 3.1 0.2 - - - -
540B LYS* 2.8 19.7 + - - +
542B PHE* 3.0 45.7 + - + +
544B HIS* 4.5 4.3 - - + -
562B LEU* 4.2 7.4 - - + -
565B PHE* 3.8 19.7 - - + -
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Residues in contact with GLU 538 (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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534B LEU 2.9 16.7 + - - +
535B ALA* 3.7 5.2 - - - +
537B LEU* 1.3 75.5 - - - +
539B SER* 1.3 58.6 + - - +
541B ARG* 2.8 26.3 + - - +
542B PHE 4.3 6.9 + - - -
601B SER* 4.4 17.2 - - - +
605B VAL* 5.4 0.9 - - - +
668B ARG* 3.3 51.1 + - - +
669B PHE* 3.5 34.2 + - + +
670B THR* 4.1 10.4 + - - -
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Residues in contact with SER 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ALA 3.1 15.9 + - - -
536B TYR* 2.8 22.5 + - - -
537B LEU 3.1 0.4 - - - -
538B GLU* 1.3 77.6 + - - +
540B LYS* 1.3 71.9 + - - +
541B ARG* 3.4 3.0 - - - +
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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
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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