Contacts of the helix formed by residues 535 - 547 (chain F) 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 GLY 535 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503F CYS* 3.4 27.7 - - - -
522F PHE* 4.6 2.8 - - - -
532F ARG* 4.5 1.4 - - - +
533F VAL 3.6 0.2 - - - -
534F GLU* 1.3 78.7 - - - +
536F MET* 1.3 71.2 + - - +
537F GLU* 3.4 5.2 - - - -
538F ILE* 3.3 20.6 + - - +
539F TYR* 3.3 9.0 + - - +
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Residues in contact with MET 536 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503F CYS* 5.4 1.1 - - - -
522F PHE* 5.0 6.7 - - + +
525F VAL* 4.0 21.8 - - + -
526F ARG* 3.5 34.5 - - + -
529F GLU 5.6 0.2 - - - +
532F ARG* 3.8 20.6 - - + +
533F VAL* 3.7 15.1 + - - +
534F GLU 3.4 3.8 - - - -
535F GLY* 1.3 87.3 - - - +
537F GLU* 1.3 60.3 + - - +
539F TYR* 3.0 15.8 + - + -
540F SER* 2.7 33.1 + - - -
555F LEU* 4.3 16.2 - - + -
559F LEU* 3.8 31.4 - - + -
568F GLU* 5.1 3.4 - - + +
572F ALA* 5.1 1.1 - - + -
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Residues in contact with GLU 537 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534F GLU 5.3 0.9 - - - +
535F GLY* 4.7 4.5 - - - +
536F MET* 1.3 75.6 - - - +
538F ILE* 1.3 66.6 + - + +
540F SER* 3.5 7.9 + - - -
541F THR* 3.0 31.0 + - - -
568F GLU* 4.8 10.9 + - - +
571F CYS* 4.0 19.6 - - + -
572F ALA 5.2 0.9 - - - +
575F ASN* 4.1 1.1 + - - +
600F TYR* 2.4 51.3 + - - +
602F TYR* 2.8 48.0 - - + +
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Residues in contact with ILE 538 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507F ARG* 3.6 39.0 - - + -
510F PHE* 4.1 36.4 - - + -
511F GLU* 5.6 2.9 - - - +
522F PHE* 3.5 29.2 - - + -
535F GLY* 3.3 7.9 + - - +
536F MET 3.1 0.4 - - - -
537F GLU* 1.3 83.9 - - + +
539F TYR* 1.3 62.9 + - - +
541F THR* 3.2 4.4 + - - -
542F THR* 2.8 28.4 + - - -
602F TYR* 4.3 24.9 - - + +
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Residues in contact with TYR 539 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519F GLU* 4.1 19.2 + - + -
522F PHE* 3.0 53.8 - + + -
523F SER* 4.5 13.5 - - - -
526F ARG* 4.3 14.5 - - + +
535F GLY 3.3 2.4 + - - +
536F MET* 3.0 24.3 + - - +
538F ILE* 1.3 77.6 - - - +
540F SER* 1.3 62.8 + - - +
542F THR* 3.3 4.3 - - - -
543F LEU* 3.2 50.7 + - + +
551F ALA* 5.4 3.8 + - - +
555F LEU* 3.8 36.7 - - + +
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Residues in contact with SER 540 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536F MET 2.7 18.4 + - - -
537F GLU* 3.5 4.9 + - - -
539F TYR* 1.3 70.5 - - - +
541F THR* 1.3 65.1 + - - +
543F LEU* 3.1 6.0 + - - +
544F TRP* 3.0 21.3 + - - +
552F LEU* 3.8 14.7 - - - +
555F LEU* 3.6 25.6 - - - -
572F ALA* 3.7 16.0 + - - -
575F ASN* 2.3 38.2 + - - +
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Residues in contact with THR 541 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510F PHE* 3.4 26.5 - - + -
537F GLU 3.0 16.2 + - - -
538F ILE 3.2 4.2 + - - -
540F SER* 1.3 78.4 + - - +
542F THR* 1.3 66.9 + - - +
544F TRP* 2.9 15.2 + - + +
545F HIS* 3.0 24.6 + - + +
575F ASN* 3.2 17.2 + - - +
602F TYR* 3.6 20.2 + - - +
606F LEU* 4.1 1.2 - - - +
492R ILE 5.4 0.7 - - - +
493R ARG* 3.7 26.5 - - + +
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Residues in contact with THR 542 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510F PHE* 3.1 30.6 - - - +
515F TYR* 3.7 18.3 - - + +
518F ALA* 4.2 8.7 - - + +
519F GLU* 3.5 38.6 - - + +
522F PHE* 4.3 3.3 - - - -
538F ILE 2.8 16.1 + - - -
539F TYR* 3.3 13.5 - - - +
541F THR* 1.3 72.9 - - - +
543F LEU* 1.3 64.9 + - + +
545F HIS* 3.1 14.8 + - - +
546F LEU* 3.2 13.9 + - + +
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Residues in contact with LEU 543 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519F GLU* 3.4 34.5 - - + +
539F TYR* 3.2 42.8 + - + +
540F SER 3.1 7.9 + - - +
542F THR* 1.3 79.0 - - - +
544F TRP* 1.3 58.1 + - - +
546F LEU* 3.2 5.6 + - + +
547F GLN 3.0 23.0 + - - -
548F LYS* 3.1 24.5 + - + +
551F ALA* 3.9 11.0 - - + +
552F LEU* 3.6 47.8 - - + +
555F LEU* 4.6 2.5 - - + -
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Residues in contact with TRP 544 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540F SER 3.0 11.9 + - - +
541F THR* 2.9 11.3 + - - +
543F LEU* 1.3 76.5 - - - +
545F HIS* 1.3 99.2 + + - +
547F GLN* 3.1 30.4 + - - +
552F LEU* 4.0 9.8 - - + +
575F ASN* 3.8 18.6 - - - -
578F SER* 3.6 10.0 + - - -
579F LEU* 3.9 25.7 - - + +
613F LEU* 5.6 7.6 - - + -
490R THR* 4.1 15.9 - - + -
493R ARG* 3.0 68.6 - - + +
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Residues in contact with HIS 545 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510F PHE* 4.0 7.8 - + - -
515F TYR* 3.6 46.6 + + + -
541F THR* 3.0 40.3 + - + +
542F THR 3.2 8.1 - - - +
544F TRP* 1.3 100.1 - + - +
546F LEU* 1.3 60.4 + - - +
547F GLN* 3.4 15.7 + - - +
490R THR 4.0 6.7 + - - -
491R ARG* 3.5 30.1 + - - -
492R ILE 4.1 11.6 + - - -
493R ARG* 4.4 0.2 - - - -
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Residues in contact with LEU 546 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515F TYR* 3.6 28.7 - - + +
516F MET* 3.9 26.0 - - + +
519F GLU* 4.0 22.0 - - + -
542F THR 3.2 12.4 + - - +
543F LEU* 3.2 7.4 + - + +
545F HIS* 1.3 75.8 - - - +
547F GLN* 1.3 70.1 + - - +
548F LYS* 3.3 43.7 + - + +
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Residues in contact with GLN 547 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543F LEU 3.0 4.2 + - - -
544F TRP* 3.1 23.3 + - - -
545F HIS* 3.4 18.3 + - - +
546F LEU* 1.3 81.1 - - - +
548F LYS* 1.3 55.6 + - - +
549F ASP* 2.5 28.2 + - - +
579F LEU* 3.3 27.3 - - - +
483R VAL 6.3 0.8 - - - -
484R SER* 5.4 5.7 + - - -
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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