Contacts of the strand formed by residues 547 - 558 (chain A) in PDB entry 1EX0
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 TYR 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516A SER* 3.4 21.3 + - - -
518A VAL* 3.8 27.8 - - + -
541A ASN* 3.6 18.6 - - - -
543A SER* 3.6 13.4 + - - -
545A ASN* 3.0 32.8 + - - -
546A ARG* 1.3 77.8 - - - +
548A THR* 1.3 64.8 + - - +
549A ILE* 4.1 9.3 + - + +
576A THR* 3.2 6.1 - - - +
577A LEU* 2.7 43.0 + - + +
612A ILE* 3.6 17.9 - - + -
614A GLU* 3.1 25.1 - - + +
615A THR* 3.7 29.1 - - + +
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Residues in contact with THR 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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546A ARG* 6.0 3.6 - - + +
547A TYR* 1.3 75.7 - - - +
549A ILE* 1.3 60.3 + - - +
575A VAL 3.5 5.4 - - - -
576A THR* 3.8 20.2 - - + +
613A ASN* 2.7 53.7 + - - +
614A GLU* 2.7 30.3 + - - +
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Residues in contact with ILE 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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518A VAL* 4.4 7.0 - - + -
539A PHE* 4.3 17.0 - - + -
547A TYR* 4.5 7.6 - - + -
548A THR* 1.3 80.1 - - - +
550A THR* 1.3 68.0 + - - +
551A ALA* 4.2 5.8 - - + +
573A PHE 3.6 1.2 - - - +
574A ASP* 3.6 3.5 - - - +
575A VAL* 2.7 49.5 + - + +
577A LEU* 3.5 33.2 - - + -
610A ALA* 3.7 28.0 - - + -
611A ARG 3.5 7.2 - - - +
612A ILE* 3.9 29.6 - - + -
613A ASN* 4.7 0.9 - - - -
619A LEU* 4.7 1.6 - - + -
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Residues in contact with THR 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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357A ASP 5.2 2.2 - - - -
548A THR 4.3 0.2 + - - -
549A ILE* 1.3 75.9 - - - +
551A ALA* 1.3 61.7 + - - +
552A TYR* 3.3 35.9 - - + +
572A THR* 3.7 17.7 - - - +
573A PHE 3.5 1.8 - - - +
574A ASP* 3.4 19.4 + - - +
610A ALA* 3.3 1.9 - - - -
611A ARG* 3.0 33.7 + - - -
613A ASN* 4.2 14.6 + - - -
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Residues in contact with ALA 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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537A ILE* 5.6 0.9 - - + -
539A PHE* 4.1 21.8 - - + -
549A ILE* 4.1 2.9 - - + -
550A THR* 1.3 72.2 - - - +
552A TYR* 1.3 63.7 + - - +
572A THR* 3.2 6.1 - - - -
573A PHE* 2.8 50.6 + - + +
575A VAL* 5.2 0.9 - - + -
608A VAL* 4.9 7.9 - - + -
609A THR 3.3 4.3 - - - +
610A ALA* 3.4 19.5 - - + -
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Residues in contact with TYR 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASP* 3.3 48.9 + - - +
358A GLY* 3.7 5.2 - - - -
359A ASN* 3.2 44.0 - - - +
360A VAL 5.7 0.2 - - - +
550A THR* 3.3 38.9 - - + +
551A ALA* 1.3 72.6 - - - +
553A LEU* 1.3 61.2 + - - +
554A SER* 3.9 2.9 + - - -
571A GLU 3.4 3.4 - - - +
572A THR* 3.7 24.9 - - + -
573A PHE* 5.0 0.4 - - - -
607A PHE* 3.3 5.9 - - - +
608A VAL* 3.4 5.0 - - - -
609A THR* 2.6 45.2 + - - +
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Residues in contact with LEU 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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535A LEU* 4.0 35.0 - - + -
537A ILE* 4.9 0.2 - - + -
552A TYR* 1.3 73.0 - - - +
554A SER* 1.3 78.6 + - - +
555A ALA* 4.2 4.5 - - + -
569A LYS* 4.6 22.4 - - + +
570A LYS* 3.1 8.0 - - - +
571A GLU* 2.7 40.4 + - + +
573A PHE* 3.7 23.6 - - + -
587A VAL* 4.2 20.2 - - + -
589A ILE* 5.3 1.6 - - + -
606A PHE* 4.3 9.2 - - + -
607A PHE 3.5 10.1 - - - +
608A VAL* 4.1 14.1 - - + -
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Residues in contact with SER 554 (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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359A ASN* 6.0 3.8 - - - -
360A VAL* 5.5 8.2 - - - +
552A TYR* 3.9 3.1 + - - -
553A LEU* 1.3 77.1 - - - +
555A ALA* 1.3 59.2 + - - +
556A ASN* 3.6 13.0 + - - -
567A GLU* 2.6 29.2 + - - +
569A LYS 3.8 2.7 - - - -
605A HIS 3.7 0.9 - - - +
606A PHE* 3.4 1.7 - - - -
607A PHE* 2.8 54.3 + - - +
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Residues in contact with ALA 555 (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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553A LEU* 4.2 6.5 - - + -
554A SER* 1.3 73.9 + - - +
556A ASN* 1.3 55.7 + - - +
567A GLU* 3.4 3.1 - - - -
568A PHE* 2.7 46.2 + - + -
569A LYS* 2.9 26.8 + - + +
589A ILE* 6.1 0.2 - - + -
605A HIS 3.1 4.7 - - - -
606A PHE* 3.6 31.4 - - + -
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Residues in contact with ASN 556 (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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554A SER* 3.6 20.0 + - - -
555A ALA* 1.3 80.8 - - - +
557A ILE* 1.3 68.6 - - - +
558A THR* 4.2 5.8 - - + -
564A PRO* 4.2 20.1 - - + +
566A ALA 3.2 5.4 - - - +
567A GLU* 3.1 29.7 + - - +
568A PHE* 3.7 6.9 - - - -
604A LEU* 3.3 6.8 - - - -
605A HIS* 2.8 41.7 + - + +
607A PHE* 4.8 12.3 - - - -
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Residues in contact with ILE 557 (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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556A ASN* 1.3 72.5 - - - +
558A THR* 1.3 59.7 + - - +
564A PRO* 3.5 3.6 - - - +
565A LYS* 2.8 31.6 + - + -
566A ALA* 3.0 23.0 + - + +
568A PHE* 3.7 25.8 - - + -
594A TYR* 4.3 5.6 - - + +
597A GLN* 3.2 50.0 - - + +
598A LEU* 4.1 8.5 - - + -
599A LEU* 3.8 27.6 - - + +
603A SER 4.0 6.1 - - - +
604A LEU* 3.9 11.4 - - + -
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Residues in contact with THR 558 (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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371A ASN* 4.4 3.8 + - - -
556A ASN* 3.7 6.7 + - + +
557A ILE* 1.3 81.8 - - - +
559A PHE* 1.3 72.4 + - - +
562A GLY* 3.6 21.9 - - - +
563A VAL 3.2 9.4 - - - -
564A PRO* 3.9 8.7 - - + -
599A LEU* 3.5 20.5 - - - +
600A GLU 4.9 0.5 - - - +
603A SER* 3.1 38.1 + - - +
604A LEU 4.3 2.6 + - - -
605A HIS* 3.6 29.4 - - + +
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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