Contacts of the helix formed by residues 535 - 549 (chain B) in PDB entry 5ULM
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 LYS 535 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491B HIS* 4.9 9.6 - - + -
492B MET* 4.9 16.3 - - + +
495B ILE* 4.1 22.7 - - + +
533B VAL* 2.9 12.1 + - + +
534B ALA* 1.3 78.9 - - + +
536B GLN* 1.3 64.0 + - - +
537B GLU 3.1 2.9 - - - -
538B LEU* 3.0 33.1 + - + +
539B VAL* 3.2 14.7 + - - +
592B LEU* 4.1 12.6 - - + -
594B ASP* 3.9 19.9 + - - -
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Residues in contact with GLN 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B HIS* 3.1 28.2 + - - -
522B LYS* 4.6 7.9 - - - +
532B PRO* 4.7 11.7 - - + -
533B VAL* 2.7 34.5 + - - +
534B ALA 3.4 0.8 - - - -
535B LYS* 1.3 69.5 - - - +
537B GLU* 1.3 54.1 + - + +
539B VAL* 3.1 17.7 + - - +
540B ASP* 2.8 67.5 + - - +
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Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ALA 4.9 3.1 + - - +
535B LYS 3.1 0.2 - - - -
536B GLN* 1.3 79.5 - - + +
538B LEU* 1.3 56.8 + - - +
540B ASP* 3.5 10.2 + - - +
541B PHE* 3.0 25.8 + - - +
591B VAL* 3.7 17.3 - - + +
592B LEU* 3.8 39.8 + - + +
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Residues in contact with LEU 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ILE* 3.7 28.7 - - + -
535B LYS* 3.0 30.4 + - - +
537B GLU* 1.3 76.5 - - - +
539B VAL* 1.3 65.7 + - - +
541B PHE* 3.5 2.8 + - + +
542B TRP* 3.1 33.0 + - - +
572B PRO* 3.6 38.4 - - + -
591B VAL* 3.8 20.0 - - + +
592B LEU* 4.1 30.7 - - + +
594B ASP* 5.5 1.6 - - - +
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Residues in contact with VAL 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B HIS* 3.4 37.9 - - + +
494B VAL* 4.4 16.2 - - + -
495B ILE* 3.9 20.4 - - + -
522B LYS* 4.2 21.1 - - - +
535B LYS 3.2 9.0 + - - +
536B GLN* 3.1 18.9 + - - +
538B LEU* 1.3 78.4 - - - +
540B ASP* 1.3 60.9 + - - +
542B TRP* 3.4 3.1 + - - +
543B MET* 3.0 29.9 + - + +
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Residues in contact with ASP 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B LYS* 4.9 5.7 + - - -
536B GLN* 2.8 53.6 + - - +
537B GLU* 3.7 8.9 - - - +
539B VAL* 1.3 73.2 - - - +
541B PHE* 1.3 64.3 + - - +
543B MET* 3.4 5.4 + - - +
544B ASP* 2.9 25.3 + - - +
574B TYR* 4.7 1.6 - - - +
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Residues in contact with PHE 541 (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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537B GLU 3.0 18.8 + - - +
538B LEU* 3.7 6.7 - - - +
539B VAL 3.3 0.2 - - - -
540B ASP* 1.3 75.3 - - - +
542B TRP* 1.3 86.1 + + - +
544B ASP* 3.1 4.5 + - - +
545B PHE* 2.7 51.4 + + + +
560B PRO* 3.6 13.9 - - + -
561B VAL 3.3 18.2 - - - -
562B LEU* 3.9 7.2 - - + -
572B PRO* 3.7 26.0 - - + -
573B SER 3.3 25.1 - - - -
574B TYR* 3.7 31.2 + + + +
591B VAL* 4.3 11.0 - - + -
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Residues in contact with TRP 542 (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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494B VAL* 5.4 0.4 - - + -
495B ILE* 3.7 38.6 - - + +
498B SER* 3.6 35.0 - - - +
499B GLU* 3.5 38.6 - - + -
502B PHE* 4.1 6.1 - - + -
538B LEU* 3.1 26.8 + - + +
539B VAL* 4.1 4.0 - - - +
540B ASP 3.3 0.2 - - - -
541B PHE* 1.3 89.7 - + - +
543B MET* 1.3 65.9 + - + +
545B PHE* 3.7 28.4 - + + +
546B LEU* 2.9 36.7 + - + +
562B LEU* 3.6 39.0 - - + -
570B TYR 6.0 0.2 - - - -
572B PRO* 4.2 12.8 - - + +
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Residues in contact with MET 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LEU* 4.5 5.6 - - + -
486B VAL* 4.5 9.2 - - + -
494B VAL* 3.6 28.9 - - + -
498B SER* 3.7 15.0 - - - +
518B ILE* 3.7 36.3 - - + -
522B LYS* 3.8 29.4 - - - +
539B VAL* 3.0 23.5 + - + +
540B ASP* 3.8 5.2 - - - +
542B TRP* 1.3 78.2 - - + +
544B ASP* 1.3 61.8 + - - +
546B LEU* 4.1 9.5 - - + +
547B VAL* 3.0 34.1 + - + +
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Residues in contact with ASP 544 (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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540B ASP 2.9 19.0 + - - +
541B PHE 3.3 4.7 - - - +
543B MET* 1.3 77.0 - - - +
545B PHE* 1.3 57.1 + - - +
547B VAL* 4.0 4.3 - - - +
548B GLU* 2.9 35.5 + - - +
558B ARG* 4.8 2.8 + - - -
560B PRO* 3.9 10.7 - - - +
574B TYR* 2.8 36.2 + - - +
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Residues in contact with PHE 545 (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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502B PHE* 3.6 39.3 - + + -
541B PHE* 2.7 35.4 + + + +
542B TRP* 3.7 25.8 - + + +
543B MET 3.3 0.2 - - - -
544B ASP* 1.3 74.0 - - - +
546B LEU* 1.3 68.0 + - + +
548B GLU* 3.3 0.3 + - - +
549B ALA* 3.0 30.3 + - + +
560B PRO* 3.5 35.0 - - + +
561B VAL* 4.3 2.5 - - - -
562B LEU* 4.0 16.6 - - + -
636B TYR 4.4 0.7 - - - -
637B PHE 3.9 4.5 - - - -
638B CYS* 3.5 38.2 - - + +
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Residues in contact with LEU 546 (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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482B LEU* 3.7 22.7 - - + -
498B SER* 3.6 43.3 - - - +
501B LEU* 4.4 10.1 - - + -
502B PHE* 5.0 3.8 - - + +
511B LEU* 3.9 23.6 - - + +
514B ILE* 6.0 0.4 - - + -
515B VAL* 3.6 23.2 - - + +
518B ILE* 5.2 4.5 - - + -
542B TRP* 2.9 19.4 + - + +
543B MET* 4.3 9.2 - - + +
545B PHE* 1.3 91.9 - - + +
547B VAL* 1.3 62.9 + - + +
549B ALA* 3.3 17.9 + - + +
550B THR* 3.5 5.2 + - - +
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Residues in contact with VAL 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B VAL* 4.1 23.6 - - + +
518B ILE* 5.7 7.6 - - + -
519B LEU* 4.1 27.8 - - + -
543B MET* 3.0 26.8 + - + +
544B ASP* 4.1 4.7 - - - +
546B LEU* 1.3 72.9 - - + +
548B GLU* 1.3 64.2 + - - +
550B THR* 2.8 26.2 + - - +
551B LYS* 3.7 26.9 + - - +
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Residues in contact with GLU 548 (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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544B ASP* 2.9 27.1 + - - +
545B PHE 3.7 3.1 - - - +
547B VAL* 1.3 76.9 - - - +
549B ALA* 1.3 56.9 + - - +
551B LYS* 3.0 43.3 + - - +
553B ASP 5.0 0.2 - - - +
554B VAL* 4.8 4.2 - - - +
555B THR 4.9 0.5 + - - -
556B VAL* 3.3 36.0 - - + +
560B PRO* 4.2 18.3 - - + +
638B CYS* 3.6 12.3 - - - -
642B HIS* 2.8 39.1 + - + +
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Residues in contact with ALA 549 (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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508B ALA* 5.5 6.6 - - - +
511B LEU* 3.7 20.2 - - + +
545B PHE* 3.0 16.4 + - + +
546B LEU* 3.3 14.8 - - + +
547B VAL 3.1 0.6 - - - -
548B GLU* 1.3 76.5 - - - +
550B THR* 1.3 57.8 + - - +
551B LYS 3.3 1.3 + - - +
638B CYS* 3.7 23.1 - - + +
639B THR* 3.2 25.6 - - - +
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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