Contacts of the strand formed by residues 547 - 558 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517B ASN* 2.8 43.2 + - - -
518B VAL* 3.8 14.6 - - + -
541B ASN* 3.7 16.6 - - - -
543B SER* 3.7 13.5 - - - -
545B ASN* 3.4 29.8 + - + -
546B ARG* 1.3 78.3 - - - +
548B THR* 1.3 66.8 + - - +
549B ILE* 4.9 6.3 - - + -
576B THR* 3.4 6.3 - - - +
577B LEU* 2.9 38.2 + - + +
612B ILE* 3.7 16.8 - - + -
614B GLU* 3.6 22.4 - - + +
615B THR* 3.8 27.4 - - + +
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Residues in contact with THR 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B ARG* 5.3 6.3 - - - +
547B TYR* 1.3 78.4 - - - +
549B ILE* 1.3 66.0 + - - +
575B VAL 3.6 4.5 - - - -
576B THR* 3.6 23.1 - - + +
612B ILE* 3.7 0.7 - - - +
613B ASN* 2.8 53.1 + - - +
614B GLU* 2.6 29.6 + - - +
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Residues in contact with ILE 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518B VAL* 4.3 4.5 - - + -
539B PHE* 4.2 17.9 - - + -
547B TYR* 4.9 3.6 - - + -
548B THR* 1.3 81.8 - - - +
550B THR* 1.3 68.7 + - - +
551B ALA* 4.1 1.8 - - + +
573B PHE 4.0 0.2 - - - +
574B ASP* 3.3 6.6 - - - +
575B VAL* 2.9 44.8 + - + +
577B LEU* 3.4 38.8 - - + -
610B ALA* 3.7 26.2 - - + -
611B ARG 3.4 10.3 - - - +
612B ILE* 3.7 28.0 - - + -
613B ASN* 4.6 3.1 - - - +
619B LEU* 4.7 0.9 - - + -
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Residues in contact with THR 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ILE* 1.3 72.0 - - - +
551B ALA* 1.4 60.9 + - - +
552B TYR* 3.3 39.4 - - + +
572B THR* 3.9 10.5 - - - +
573B PHE 3.5 2.7 - - - -
574B ASP* 2.6 23.4 + - - +
610B ALA* 3.3 0.9 - - - -
611B ARG* 2.9 53.7 + - - +
613B ASN* 4.8 5.9 + - - +
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Residues in contact with ALA 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B PHE* 4.1 10.3 - - + -
549B ILE* 4.1 2.4 - - + -
550B THR* 1.4 72.5 - - - +
552B TYR* 1.3 64.5 + - - +
572B THR* 3.1 8.1 + - - -
573B PHE* 2.8 71.6 + - + -
608B VAL* 4.9 5.2 - - + -
609B THR 3.3 9.6 - - - +
610B ALA* 3.9 11.0 - - + -
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Residues in contact with TYR 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ASP* 3.1 36.8 + - - +
358B GLY* 3.8 6.1 - - - -
359B ASN* 3.4 55.0 - - - +
550B THR* 3.3 32.2 - - + +
551B ALA* 1.3 75.1 - - - +
553B LEU* 1.3 58.9 + - - +
554B SER* 4.1 0.8 + - - +
570B LYS* 3.7 4.0 - - - +
571B GLU 3.4 3.4 - - - -
572B THR* 3.5 26.0 - - + -
573B PHE* 5.6 1.6 - - - -
607B PHE 3.6 1.0 - - - +
608B VAL* 3.4 7.8 - - - +
609B THR* 2.7 46.5 + - - +
611B ARG* 3.1 17.2 + - - -
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Residues in contact with LEU 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B LEU* 4.0 31.0 - - + -
537B ILE* 5.1 4.9 - - + -
552B TYR* 1.3 73.2 - - - +
554B SER* 1.3 79.3 + - - +
555B ALA* 4.4 2.9 - - + +
569B LYS* 3.8 13.6 - - + +
570B LYS* 2.9 20.3 - - - -
571B GLU* 2.8 39.7 + - + +
573B PHE* 5.5 4.2 - - + -
587B VAL* 4.2 30.1 - - + -
589B ILE* 5.7 0.7 - - + -
606B PHE* 4.2 10.5 - - + -
607B PHE 3.3 13.2 - - - +
608B VAL* 4.2 12.6 - - + +
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Residues in contact with SER 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B ASN* 5.7 1.1 - - - -
360B VAL* 5.6 8.1 - - - +
552B TYR* 4.1 0.6 - - - -
553B LEU* 1.3 75.6 - - - +
555B ALA* 1.3 60.5 + - - +
556B ASN* 3.9 9.9 + - - -
567B GLU* 2.6 28.3 + - - +
569B LYS 3.6 4.3 - - - -
570B LYS* 4.0 6.1 - - - -
605B HIS 3.7 1.0 - - - +
606B PHE* 3.5 2.3 - - - -
607B PHE* 2.9 51.4 + - - +
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Residues in contact with ALA 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B LEU* 4.2 5.1 - - + -
554B SER* 1.3 73.3 + - - +
556B ASN* 1.3 56.1 + - - +
567B GLU* 3.3 4.7 - - - +
568B PHE* 2.8 45.7 + - + -
569B LYS* 2.8 25.7 + - + +
605B HIS 3.2 3.8 - - - -
606B PHE* 3.4 34.5 - - + -
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Residues in contact with ASN 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B SER* 6.3 1.0 - - - -
554B SER* 3.9 8.9 + - - -
555B ALA* 1.3 74.4 - - - +
557B ILE* 1.3 65.8 + - - +
558B THR* 4.2 8.9 - - + +
564B PRO* 3.6 23.7 - - + +
566B ALA 3.2 8.7 - - - +
567B GLU* 3.3 27.2 + - - +
568B PHE* 3.8 7.0 - - - -
604B LEU* 3.3 5.5 - - - -
605B HIS* 2.8 44.5 + - + +
607B PHE* 4.4 22.0 - - - -
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Residues in contact with ILE 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B ASN* 1.3 73.4 - - - +
558B THR* 1.3 64.2 + - - +
564B PRO* 3.6 0.9 - - - +
565B LYS* 2.9 33.3 + - - -
566B ALA* 2.9 36.3 + - + +
568B PHE* 3.5 26.7 - - + -
594B TYR* 5.3 2.0 - - + +
597B GLN* 3.2 58.8 - - + +
598B LEU* 4.3 4.5 - - + +
599B LEU* 3.9 26.9 - - + +
603B SER 3.9 8.1 - - - +
604B LEU* 4.6 6.5 - - + -
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Residues in contact with THR 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B ASN* 4.6 3.5 + - - -
556B ASN* 4.1 3.4 - - + +
557B ILE* 1.3 80.9 - - - +
559B PHE* 1.4 74.9 + - - +
562B GLY* 3.7 20.4 - - - +
563B VAL 3.2 9.6 - - - -
564B PRO* 3.8 12.1 - - + -
565B LYS 4.5 0.7 - - - +
599B LEU* 3.9 18.7 - - - +
600B GLU 4.9 0.9 - - - +
603B SER* 3.1 36.5 + - - +
604B LEU 4.3 2.3 + - - -
605B HIS* 3.6 29.1 - - + +
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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