Contacts of the strand formed by residues 539 - 549 (chain A) in PDB entry 5H65
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 GLN 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A LEU* 3.4 3.2 - - - -
381A HIS* 2.7 65.5 + - - +
383A PRO* 4.8 11.5 - - + +
537A PRO 4.0 0.2 + - - -
538A LEU* 1.3 73.6 - - - +
540A TYR* 1.3 69.6 + - - +
541A VAL* 3.8 16.5 - - - +
562A SER* 3.9 19.4 + - - -
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Residues in contact with TYR 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A VAL* 3.7 14.8 - - + -
379A LYS 3.4 4.0 - - - -
380A LEU* 3.7 24.0 - - + -
391A VAL* 3.8 18.6 - - + +
498A ILE* 4.7 4.0 - - + -
499A HIS* 2.6 36.2 + - - +
500A HIS* 4.9 4.0 - - - -
501A TYR* 3.4 16.9 - + - -
538A LEU 5.1 3.6 - - - -
539A GLN* 1.3 75.4 - - - +
541A VAL* 1.3 66.0 + - - +
562A SER* 3.3 20.6 - - - -
570A ALA* 3.4 17.7 - - - +
571A SER* 3.5 49.6 - - - +
574A LEU* 4.4 7.4 - - + +
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Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A SER 3.3 2.1 - - - +
378A VAL* 3.5 2.5 - - - -
379A LYS* 2.8 46.0 + - + +
381A HIS* 4.1 20.4 - - + +
388A LEU* 4.2 2.7 - - + -
539A GLN* 3.8 24.0 - - - +
540A TYR* 1.3 80.8 - - - +
542A PHE* 1.3 61.9 + - - +
543A VAL* 3.6 19.2 + - + -
560A MET* 4.4 12.8 - - + -
561A ASP* 3.5 23.8 - - - +
562A SER* 4.2 1.3 - - - +
570A ALA* 3.9 7.4 - - - +
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Residues in contact with PHE 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A SER* 3.4 24.7 - - - +
378A VAL* 4.1 7.2 - - + -
541A VAL* 1.3 69.8 - - - +
543A VAL* 1.3 59.8 + - - +
544A MET* 4.1 3.6 - - + -
559A LEU* 3.3 9.0 - - + +
560A MET* 3.3 7.3 - - - -
561A ASP* 2.8 42.7 + - - +
562A SER 3.8 3.8 - - - -
563A ASP* 5.7 0.4 - - - -
566A PHE* 3.8 33.4 - + + -
568A ILE* 3.5 25.6 - - + -
570A ALA* 3.7 16.2 - - + -
573A VAL* 3.9 32.3 - - + -
583A VAL* 4.1 27.1 - - + -
293B TRP* 4.6 3.6 - + - -
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A SER* 2.7 20.4 + - - -
379A LYS* 3.5 28.9 - - + -
388A LEU* 4.4 12.3 - - + -
541A VAL* 3.8 17.9 - - + -
542A PHE* 1.3 75.7 - - - +
544A MET* 1.3 71.0 + - - +
558A TYR* 5.6 0.2 - - + -
559A LEU 3.3 7.4 - - - +
560A MET* 4.3 10.3 - - + -
306B TYR* 3.3 31.1 - - + +
308B VAL* 4.2 18.4 - - + +
313B LEU* 4.5 13.9 - - + -
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Residues in contact with MET 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A TYR* 5.1 2.5 - - - -
370A LYS 3.4 9.4 - - - +
371A PRO* 4.0 4.5 - - + -
374A LEU* 4.0 21.5 - - + -
377A SER* 3.7 27.4 - - - +
542A PHE* 4.4 4.5 - - + -
543A VAL* 1.3 80.4 - - - +
545A THR* 1.3 58.5 + - - +
546A PHE* 3.7 30.5 - - + -
558A TYR* 3.4 7.1 - - - +
559A LEU* 2.8 41.1 + - + +
566A PHE* 3.5 31.6 - - + -
583A VAL* 4.5 5.6 - - + -
587A MET* 3.9 13.0 - - - +
306B TYR* 3.1 10.7 + - - -
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Residues in contact with THR 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A TYR* 3.3 3.8 - - - -
370A LYS* 2.8 60.4 + - - +
544A MET* 1.3 71.3 - - - +
546A PHE* 1.3 63.1 + - - +
547A THR* 4.1 0.7 + - - -
556A GLU* 3.9 37.0 - - + +
557A ALA 3.9 4.0 - - - +
558A TYR* 3.6 26.7 - - + -
306B TYR* 2.7 25.1 + - - -
308B VAL* 4.0 2.3 - - - +
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Residues in contact with PHE 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A LEU* 3.4 24.7 - - + -
368A SER 3.9 0.7 - - - -
369A TYR* 3.9 17.7 - - + -
544A MET* 3.7 36.8 - - + -
545A THR* 1.3 78.2 - - - +
547A THR* 1.3 61.2 + - - +
548A LEU* 3.8 11.3 + - + -
555A LEU 3.7 1.0 - - - +
556A GLU* 3.3 4.5 - - - +
557A ALA 2.8 41.6 + - - +
559A LEU* 4.3 9.9 - - + -
565A PHE* 3.8 36.3 - + - -
587A MET* 4.4 11.9 - - + -
603A LEU* 4.4 11.4 - - + -
624A ILE* 3.5 25.6 - - + -
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Residues in contact with THR 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A LEU* 3.7 2.5 - - - +
367A ARG* 3.0 38.9 + - + +
368A SER* 2.8 37.1 + - - +
369A TYR* 5.4 0.2 - - - -
370A LYS* 4.8 7.6 + - - -
545A THR 4.1 1.6 + - - -
546A PHE* 1.3 71.4 - - - +
548A LEU* 1.3 59.2 + - - +
554A VAL* 3.6 28.5 - - + -
555A LEU 3.5 5.8 - - - +
556A GLU* 4.1 15.8 + - + +
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Residues in contact with LEU 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A LEU* 3.6 8.5 - - + +
362A ILE* 3.9 25.4 - - + -
364A ALA* 4.0 15.0 - - + +
365A LYS 3.4 9.4 - - - +
366A LEU* 4.2 9.6 - - + -
546A PHE* 4.1 21.1 - - + +
547A THR* 1.3 73.0 - - - +
549A ASP* 1.3 61.5 + - - +
554A VAL* 3.3 7.5 - - - +
555A LEU* 2.8 42.4 + - + +
557A ALA* 3.7 26.0 - - + -
603A LEU* 4.1 24.7 - - + -
605A CYS* 4.8 3.8 - - - -
607A ILE* 4.5 4.0 - - + -
624A ILE* 5.1 3.1 - - + -
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Residues in contact with ASP 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A ALA* 3.8 1.5 - - - +
365A LYS* 2.8 45.6 + - - +
367A ARG* 2.9 38.8 + - + +
548A LEU* 1.3 75.3 - - - +
550A ASP* 1.3 56.0 + - - +
551A GLY* 2.8 34.3 + - - -
553A GLY 3.6 11.1 - - - +
554A VAL* 3.6 13.5 - - + +
597A ILE* 4.0 18.3 - - + +
602A TRP* 5.3 0.2 - - - -
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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
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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