Contacts of the strand formed by residues 540 - 548 (chain A) in PDB entry 5JPM
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 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A SER* 4.4 9.2 + - - -
512A ARG* 4.7 3.1 + - - +
537A LEU 3.5 9.3 + - - +
539A PRO* 1.3 82.9 - - - +
541A PHE* 1.3 61.1 + - - +
542A TYR* 5.7 2.1 - - - -
559A ARG* 4.8 11.9 - - - +
560A VAL 3.4 7.0 - - - -
561A ASP* 3.4 26.5 - - - -
562A VAL* 4.3 0.7 - - - +
629A ASN* 3.5 25.3 + - - -
632A ASP* 4.7 6.1 + - - -
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Residues in contact with PHE 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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489A LEU* 4.7 4.5 - - + -
491A LEU* 5.9 0.7 - - + -
509A ILE* 3.7 27.8 - - + -
510A LEU 3.2 15.5 - - - +
511A SER* 4.3 2.0 - - - -
531A VAL* 4.5 12.3 - - + -
533A VAL* 3.9 21.8 - - + -
537A LEU* 3.7 41.7 - - + +
540A SER* 1.3 74.5 - - - +
542A TYR* 1.3 69.6 + - - +
543A PHE* 4.0 7.1 + + + -
559A ARG* 3.7 1.9 - - - -
560A VAL* 2.9 66.0 + - + -
562A VAL* 3.8 20.2 - - + -
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Residues in contact with TYR 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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508A MET 3.7 1.0 - - - +
509A ILE* 3.6 7.1 - - - +
510A LEU* 2.9 55.2 + - + +
540A SER* 5.7 2.5 - - - -
541A PHE* 1.3 78.1 - - - +
543A PHE* 1.3 60.1 + - - +
544A VAL* 3.9 5.8 + - + -
557A SER* 5.1 7.4 - - - -
558A LEU 3.8 3.6 - - - -
559A ARG* 3.6 38.1 + - + -
632A ASP* 3.5 33.5 + - - -
634A GLY* 3.3 26.0 + - - -
636A GLY 2.8 28.9 + - - -
638A GLY* 4.8 5.8 - - - -
649A ALA 4.2 10.1 - - - -
650A ALA* 4.3 18.2 - - + -
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Residues in contact with PHE 543 (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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475A ILE* 4.0 14.4 - - + -
491A LEU* 3.6 32.3 - - + -
493A LEU* 4.1 11.9 - - + -
507A TYR* 3.6 38.6 - + + -
508A MET 3.8 2.0 - - - -
509A ILE* 3.5 20.0 - - + -
529A VAL* 4.0 16.6 - - + -
531A VAL* 3.8 19.5 - - + -
541A PHE* 4.0 9.3 + + + -
542A TYR* 1.3 69.8 - - - +
544A VAL* 1.3 60.3 + - - +
545A ALA* 3.8 21.9 + - + -
557A SER* 3.2 3.5 - - - -
558A LEU* 2.8 44.5 + - + +
560A VAL* 5.1 2.0 - - + -
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Residues in contact with VAL 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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506A TYR 4.1 0.2 - - - +
507A TYR* 3.2 2.9 - - - +
508A MET* 2.9 50.9 + - + +
510A LEU* 4.0 20.0 - - + -
542A TYR* 4.5 3.1 - - + -
543A PHE* 1.3 77.2 - - - +
545A ALA* 1.3 65.0 + - - +
546A PHE* 5.1 0.8 - - + -
555A ALA* 5.3 1.8 - - + -
556A ASN 3.9 8.3 - - - +
557A SER* 3.9 10.5 - - - -
646A VAL* 5.4 3.1 - - + +
647A PHE* 3.7 35.4 - - + -
650A ALA* 3.8 27.6 - - + -
652A LEU* 5.2 0.7 - - + -
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Residues in contact with ALA 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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473A LEU* 3.3 16.8 - - + +
475A ILE* 4.0 3.1 - - + -
493A LEU* 3.9 16.8 - - + -
505A TYR* 5.8 0.2 - - + -
506A TYR 3.2 9.9 - - - +
507A TYR* 4.0 5.6 - - + -
543A PHE* 3.8 22.2 - - + -
544A VAL* 1.3 75.7 - - - +
546A PHE* 1.3 65.5 + - - +
555A ALA* 3.4 1.9 - - - +
556A ASN 3.1 31.3 + - - +
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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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24A LEU* 3.7 21.1 - - + -
26A PHE* 3.9 31.9 - + - -
42A GLN* 3.9 10.5 - - + -
473A LEU* 3.8 4.6 - - - +
505A TYR* 3.9 2.9 - - - +
506A TYR* 2.8 71.3 + + + +
508A MET* 4.4 11.4 - - + -
544A VAL 5.1 0.4 - - - -
545A ALA* 1.3 81.0 - - - +
547A TYR* 1.3 68.8 + - - +
548A TYR* 4.5 13.2 - + - -
553A PRO* 5.3 3.8 - - + -
554A VAL 3.2 15.3 - - - +
555A ALA* 3.5 14.4 - - + -
647A PHE* 4.3 18.6 - + + -
654A PHE* 6.2 0.9 - + - -
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Residues in contact with TYR 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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470A PRO 4.6 0.9 + - - -
471A GLY* 4.2 3.6 - - - -
472A PHE 3.2 28.2 + - - -
473A LEU* 4.0 11.7 - - + -
495A ALA* 3.8 18.6 - - + +
496A VAL 4.2 3.3 + - - -
499A GLY* 5.6 4.2 + - - -
500A ALA* 3.9 20.9 + - + -
502A PHE* 3.5 42.0 - + + -
504A HIS 4.3 5.6 - - - +
505A TYR* 4.1 17.9 - + + -
506A TYR* 5.1 2.9 - - - -
546A PHE* 1.3 79.1 - - - +
548A TYR* 1.3 66.8 + - - +
549A HIS* 4.3 3.4 - + + -
553A PRO* 3.7 2.3 - - - +
554A VAL* 2.7 73.6 + - + +
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Residues in contact with TYR 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 3.5 22.9 - - - -
24A LEU* 3.3 41.0 - - + +
44A GLN* 3.7 33.0 - - + +
500A ALA* 3.9 2.6 - - - +
501A THR* 5.2 1.0 + - - +
502A PHE* 3.7 24.3 + - + +
506A TYR* 5.9 4.5 - + + -
546A PHE* 4.5 9.9 - + - -
547A TYR* 1.3 83.7 - - - +
549A HIS* 1.3 59.9 + - - +
550A GLY 4.1 1.7 + - - +
551A ASP* 3.7 11.2 - - - +
552A HIS 3.4 19.1 - - - -
553A PRO* 3.4 34.3 - - + +
654A PHE* 3.9 4.9 - + - -
656A ASP* 3.0 23.0 + - - +
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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
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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