Contacts of the strand formed by residues 549 - 556 (chain A) in PDB entry 1HWL
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 LYS 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A LEU 4.1 0.2 - - - -
545A CYS* 3.3 6.9 - - - +
546A LEU 2.9 31.2 + - - +
547A ASP* 3.7 13.9 - - + +
548A GLU* 1.3 84.9 - - - +
550A GLU* 1.3 65.3 + - - +
551A PHE* 3.8 25.1 - - + -
837A GLN* 3.3 23.3 + - - +
840A ARG* 5.5 3.6 - - - +
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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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543A PRO* 3.6 28.5 - - + +
544A LEU 3.3 3.1 - - - -
545A CYS* 4.0 20.0 - - - -
549A LYS* 1.3 80.7 - - - +
551A PHE* 1.3 68.3 + - - +
552A GLN* 4.4 3.3 + - - +
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Residues in contact with PHE 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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542A GLY* 3.9 1.2 - - - -
543A PRO* 3.3 6.5 - - - +
544A LEU* 2.8 55.5 + - + +
546A LEU* 3.9 22.7 - - + -
549A LYS* 3.8 33.2 - - + -
550A GLU* 1.3 79.2 - - - +
552A GLN* 1.3 64.6 + - - +
553A VAL* 3.7 7.7 + - + -
820A MET 6.0 0.2 - - - -
821A LEU* 3.8 32.1 - - + -
837A GLN* 3.5 31.9 - - + -
841A ILE* 3.6 30.5 - - + -
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Residues in contact with GLN 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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540A VAL* 3.9 14.7 - - + +
541A ALA 4.0 1.3 - - - -
542A GLY 4.0 12.1 - - - +
543A PRO* 3.5 29.9 - - - +
550A GLU* 5.5 3.3 - - - +
551A PHE* 1.3 74.1 + - - +
553A VAL* 1.3 60.6 + - - +
554A PRO* 3.3 6.9 - - - +
820A MET* 3.7 15.0 + - + +
821A LEU* 3.3 15.2 - - - +
499B LEU* 3.6 34.1 - - + +
502B LYS* 4.1 27.9 + - + +
503B LEU* 4.0 20.2 - - + +
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Residues in contact with VAL 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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540A VAL* 3.4 5.0 - - - +
541A ALA* 2.8 45.3 + - + +
544A LEU* 4.3 9.2 - - + -
551A PHE* 4.2 16.4 - - + +
552A GLN* 1.3 71.6 - - - +
554A PRO* 1.3 74.4 - - + +
555A MET* 3.7 5.7 + - + +
570A CYS* 5.7 1.1 - - - -
760A ILE* 3.7 32.3 - - + -
821A LEU* 4.1 1.3 - - + -
841A ILE* 4.2 18.4 - - + -
845A THR* 3.7 25.8 - - + +
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Residues in contact with PRO 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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538A VAL* 4.2 4.9 - - + -
539A GLY 3.5 7.4 - - - +
540A VAL* 4.7 1.6 - - + -
552A GLN 3.3 10.8 - - - +
553A VAL* 1.3 92.8 - - + +
555A MET* 1.3 63.7 + - - +
760A ILE* 3.9 9.5 - - - +
763A ALA* 3.8 10.5 - - + +
764A CYS* 4.1 12.3 - - - -
817A CYS* 3.8 46.9 - - + +
820A MET* 3.9 15.2 - - + -
821A LEU* 3.9 13.0 - - + -
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Residues in contact with MET 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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537A PRO 3.6 0.2 - - - +
538A VAL* 3.5 3.3 - - - +
539A GLY* 2.8 37.6 + - - +
541A ALA* 3.9 26.5 - - - -
553A VAL* 4.0 7.6 - - + +
554A PRO* 1.3 78.5 - - - +
556A ALA* 1.3 62.0 + - - +
557A THR* 3.6 6.7 + - + +
562A LEU* 3.9 23.3 - - + +
563A VAL* 4.1 17.0 - - + -
566A THR* 3.5 28.5 - - - +
756A ILE* 4.1 17.5 - - + -
759A ALA* 3.8 24.0 - - + -
760A ILE* 4.3 9.9 - - + -
763A ALA* 4.4 0.4 - - - -
845A THR* 4.6 4.9 - - - -
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Residues in contact with ALA 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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536A ILE* 3.8 13.7 - - + +
537A PRO 3.2 8.5 - - - +
538A VAL* 4.2 9.6 - - + +
555A MET* 1.3 67.9 - - - +
557A THR* 1.3 61.7 + - - +
758A THR* 5.6 0.3 - - - +
759A ALA* 2.9 26.0 + - - +
762A ILE* 3.5 37.0 - - + +
763A ALA* 3.6 20.0 - - + +
534B MET* 4.5 1.1 - - + -
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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