Contacts of the strand formed by residues 557 - 563 (chain A) in PDB entry 3H44
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 557 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552A LYS* 3.7 17.0 - - - +
553A ASP 3.7 0.2 - - - -
554A THR* 3.0 33.9 + - - +
556A MET* 1.3 81.6 - - - +
558A LYS* 1.3 60.9 + - - +
559A LEU 4.0 0.9 - - - -
724A HIS* 4.2 2.7 - - - -
725A ILE* 3.1 13.5 - - - -
742A MET* 3.8 24.9 - - - +
746A GLU* 2.8 27.8 + - - -
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Residues in contact with LYS 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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550A LEU* 3.5 21.5 - - + +
552A LYS 3.2 3.1 - - - -
553A ASP* 3.8 21.6 + - - +
557A SER* 1.3 76.2 - - - +
559A LEU* 1.3 59.4 + - - +
560A TRP* 3.6 19.8 - - - +
724A HIS* 4.0 18.6 - - + +
725A ILE 2.9 7.7 + - - -
726A GLU* 3.4 39.0 - - + +
727A ALA* 3.2 21.8 + - - -
914A GLN* 5.6 0.6 - - - +
916A TYR* 3.6 19.2 + - - -
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Residues in contact with LEU 559 (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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550A LEU* 3.4 6.3 - - - +
551A ILE* 2.9 56.2 + - + -
552A LYS* 2.9 24.9 + - + +
557A SER 4.0 1.0 - - - -
558A LYS* 1.3 70.2 - - - +
560A TRP* 1.3 81.0 + - - +
561A PHE* 4.8 0.9 - - + -
727A ALA* 3.9 15.0 - - + +
729A LEU* 3.5 24.7 - - + -
738A ALA* 4.0 12.6 - - + +
739A LEU* 4.0 12.3 - - + +
742A MET* 3.5 33.4 - - + -
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Residues in contact with TRP 560 (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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548A PRO* 3.8 14.4 - - + -
549A ALA 3.5 2.9 - - - -
550A LEU* 3.7 45.3 - - + -
558A LYS* 3.6 27.4 + - - +
559A LEU* 1.3 77.9 - - - +
561A PHE* 1.3 61.2 + - - +
726A GLU* 2.8 28.2 + - + +
727A ALA 2.8 22.0 + - - +
728A LEU* 3.4 7.6 - - + -
729A LEU 2.8 26.3 + - - -
911A ILE* 4.0 25.6 - - + -
916A TYR* 3.3 36.7 - + + -
918A PHE* 3.5 24.9 - + - -
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Residues in contact with PHE 561 (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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541A GLU* 4.1 4.7 - - - -
544A ALA* 6.2 4.0 - - - -
545A THR* 5.6 0.3 + - - -
547A TYR 4.4 0.3 - - - +
548A PRO* 3.1 4.7 - - - +
549A ALA* 2.8 37.1 + - + +
551A ILE* 3.6 33.0 - - + -
559A LEU* 4.8 1.3 - - + -
560A TRP* 1.3 76.2 - - - +
562A LYS* 1.3 66.4 + - - +
563A GLN* 3.4 28.5 - - + -
728A LEU* 4.5 0.4 - - - -
729A LEU 3.2 12.6 - - - +
733A ILE* 3.5 26.7 - - + -
734A THR 3.8 9.2 - - - -
735A LYS* 3.4 36.6 - - + -
738A ALA* 3.7 19.7 - - + -
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Residues in contact with LYS 562 (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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545A THR 3.4 17.3 - - - +
546A PRO* 2.9 30.9 + - - +
547A TYR 4.3 2.0 - - - +
548A PRO* 3.9 14.8 - - + +
561A PHE* 1.3 82.9 - - - +
563A GLN* 1.3 73.5 + - - +
565A ASP* 2.7 37.7 + - - +
566A LYS* 4.2 3.4 - - - +
728A LEU* 4.8 1.2 - - + +
729A LEU 3.1 7.1 + - - +
730A HIS* 3.2 37.2 + - + +
731A GLY 3.3 9.9 + - - -
903A GLU* 3.1 24.7 + - - -
907A TYR* 4.0 10.8 - - + +
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Residues in contact with GLN 563 (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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538A LEU* 3.9 11.9 + - - +
539A PRO 2.9 26.9 + - - -
540A LEU* 3.4 19.5 - - + +
541A GLU* 2.8 36.8 + - - +
544A ALA* 4.1 12.9 - - + +
545A THR 5.1 0.5 - - - +
561A PHE* 3.4 17.8 - - + -
562A LYS* 1.3 85.4 - - - +
564A ASP* 1.3 68.3 + - - +
565A ASP* 3.3 5.7 + - - +
731A GLY 3.6 7.6 - - - +
732A ASN* 5.4 2.6 + - - +
733A ILE 3.4 24.9 + - - +
734A THR* 4.4 11.9 - - - +
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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