Contacts of the strand formed by residues 545 - 553 (chain A) in PDB entry 5JMO
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 545 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A THR* 4.0 11.0 - - - -
471A VAL* 2.8 41.0 + - - +
508A PRO* 3.6 6.5 - - - -
543A PRO 3.7 0.2 + - - -
544A SER* 1.3 75.2 - - - +
546A GLU* 1.3 61.6 + - - -
547A TRP* 3.6 2.6 + - - -
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Residues in contact with GLU 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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468A ARG* 3.2 49.7 + - + +
469A LYS 3.4 10.9 + - - +
470A THR* 3.8 16.2 + - - +
506A VAL 4.1 0.5 - - - +
507A SER 3.9 2.6 - - - +
508A PRO* 3.3 27.0 - - + +
545A GLY* 1.3 71.9 - - - -
547A TRP* 1.3 69.5 + - - +
548A VAL* 4.2 5.4 + - + +
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Residues in contact with TRP 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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454A ILE* 6.4 0.4 - - + -
467A VAL 3.9 0.7 - - - +
468A ARG* 3.5 1.2 - - - -
469A LYS* 2.9 35.4 + - + +
471A VAL* 3.8 16.9 - - + +
484A LEU* 4.0 19.7 - - + -
487A ALA* 4.2 10.8 - - + -
505A LEU* 3.6 40.8 - - + -
506A VAL 3.4 16.2 - - - -
507A SER* 3.8 19.1 - - - -
508A PRO* 3.3 22.7 - - + +
535A THR* 5.6 1.8 - - + -
538A SER* 4.8 3.6 - - - -
543A PRO* 2.9 34.9 + - + +
545A GLY 3.9 0.7 - - - -
546A GLU* 1.3 75.5 - - - +
548A VAL* 1.3 66.3 + - - +
549A LEU 4.3 0.2 - - - -
566A PHE* 5.8 4.3 - - + -
568A LEU* 3.7 30.8 - - + +
570A LEU* 3.8 16.5 - - + +
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Residues in contact with VAL 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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466A GLU* 4.0 11.2 - - + +
467A VAL 3.5 8.7 - - - +
468A ARG* 3.6 44.9 - - + +
504A HIS 3.8 0.5 - - - +
505A LEU* 3.4 7.4 - - - +
506A VAL* 2.8 52.8 + - + +
546A GLU* 4.3 9.4 - - + +
547A TRP* 1.3 80.8 - - - +
549A LEU* 1.3 71.4 + - - +
550A GLU* 4.0 14.0 + - + +
566A PHE* 5.7 0.2 - - - -
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Residues in contact with LEU 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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465A LEU 3.8 0.7 - - - +
466A GLU* 3.3 4.7 - - - -
467A VAL* 2.9 38.7 + - + +
489A ALA* 4.7 2.0 - - + -
491A LEU* 3.8 26.2 - - + -
503A ILE* 3.7 20.6 - - + -
504A HIS 3.5 13.9 - - - +
505A LEU* 4.3 8.0 - - + +
515A LEU* 4.3 11.7 - - + -
547A TRP 4.3 0.4 - - - -
548A VAL* 1.3 73.0 - - - +
550A GLU* 1.3 61.5 + - - +
551A ILE* 4.0 23.3 - - + +
563A LEU* 4.3 8.7 - - + -
566A PHE* 3.6 39.4 - - + -
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Residues in contact with GLU 550 (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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464A ARG* 3.2 36.3 + - + +
465A LEU 3.4 4.5 - - - +
466A GLU* 4.8 4.3 - - + +
502A ALA 3.8 0.5 - - - +
503A ILE* 3.2 6.1 - - - +
504A HIS* 2.8 51.4 + - + +
506A VAL* 4.1 17.6 - - - +
512A ARG* 3.2 31.0 + - - -
548A VAL* 4.2 14.9 - - + +
549A LEU* 1.3 76.9 - - - +
551A ILE* 1.3 63.5 + - - +
552A GLU* 4.3 5.1 - - - +
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Residues in contact with ILE 551 (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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461A ILE* 3.9 19.7 - - + +
464A ARG* 3.4 2.8 - - - +
465A LEU* 2.7 57.1 + - + +
491A LEU* 4.7 3.4 - - + -
493A LEU* 4.3 11.7 - - + -
501A LEU* 3.8 26.0 - - + -
502A ALA 3.5 5.2 - - - +
503A ILE* 4.2 15.9 - - + -
549A LEU* 4.0 20.6 - - + -
550A GLU* 1.3 78.8 - - - +
552A GLU* 1.3 61.6 + - - +
563A LEU* 3.9 35.9 - - + -
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Residues in contact with GLU 552 (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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461A ILE* 5.5 0.9 - - - -
462A GLY 5.4 0.2 - - - -
463A LYS 3.5 9.9 - - - +
464A ARG* 4.2 26.4 + - + -
501A LEU* 3.4 10.9 - - - -
502A ALA* 2.9 54.8 + - + +
504A HIS* 3.9 19.5 + - - -
512A ARG* 4.3 6.4 + - - -
550A GLU* 5.0 4.7 - - - +
551A ILE* 1.3 76.9 - - - +
553A ASN* 1.3 64.8 + - - +
554A THR* 3.5 10.5 + - + +
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Residues in contact with ASN 553 (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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461A ILE* 5.5 0.2 - - - +
462A GLY 3.9 8.7 + - - +
463A LYS* 2.9 51.8 + - + +
495A TYR* 3.1 24.3 + - - +
500A ASP* 3.8 6.1 - - - +
501A LEU* 5.0 0.2 - - - -
552A GLU* 1.3 72.2 - - - +
554A THR* 1.3 59.2 + - - +
555A SER* 3.0 20.9 + - - +
557A ALA 3.1 25.9 + - - -
559A ASN* 3.0 31.6 + - - +
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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