Contacts of the strand formed by residues 558 - 565 (chain A) in PDB entry 2WIN
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 GLN 558 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A GLN* 3.9 6.1 + - - -
553A PRO* 5.6 0.2 - - - +
556A GLY 4.9 2.5 - - - +
557A GLN* 1.3 95.2 + - - +
559A MET* 1.3 63.7 + - - +
770B ASN* 3.1 29.2 + - - +
771B ILE 3.3 7.6 - - - +
772B PHE* 3.1 45.9 - - + -
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Residues in contact with MET 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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545A SER* 3.7 28.7 - - - +
547A GLN* 3.1 15.5 - - - +
553A PRO* 4.4 13.0 - - + -
558A GLN* 1.3 79.5 - - - +
560A THR* 1.3 71.8 + - - +
561A LEU* 5.2 3.4 - - + -
770B ASN* 3.8 5.4 - - - +
771B ILE* 3.3 47.0 + - + +
773B LEU* 3.8 31.4 - - + -
799B PHE* 5.1 2.0 - - + -
801B VAL* 3.9 29.6 - - + -
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Residues in contact with THR 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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545A SER 3.8 0.3 - - - -
546A GLY* 2.7 44.3 + - - -
547A GLN* 3.1 18.4 + - - +
559A MET* 1.3 81.2 - - - +
561A LEU* 1.3 60.1 + - - +
768B LEU* 3.8 37.0 - - + -
769B MET 3.1 8.1 - - - +
770B ASN* 4.3 6.9 + - + +
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Residues in contact with LEU 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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543A VAL* 3.8 24.7 - - + -
544A LYS 3.5 16.8 - - - +
545A SER* 4.9 0.9 - - - -
559A MET* 4.6 6.7 - - + +
560A THR* 1.3 77.1 - - - +
562A LYS* 1.3 64.2 + - - +
563A ILE* 3.6 7.2 + - + +
573A LEU* 4.7 12.3 - - + -
750B LEU* 4.4 7.4 - - + -
767B LYS 3.3 4.0 - - - +
769B MET* 2.6 40.6 + - + +
771B ILE* 4.3 26.0 - - + -
782B ILE* 3.8 28.0 - - + -
799B PHE* 4.2 16.2 - - + -
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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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543A VAL* 3.6 4.2 - - - +
544A LYS* 3.1 59.9 + - + +
545A SER 4.8 5.6 + - - -
546A GLY* 3.8 15.4 + - - +
548A SER* 6.1 3.2 - - - -
560A THR 4.0 0.2 - - - -
561A LEU* 1.3 72.3 - - - +
563A ILE* 1.3 66.5 + - - +
564A GLU* 3.4 29.3 + - + +
766B THR* 3.7 22.0 - - + -
767B LYS 3.6 4.0 - - - -
768B LEU* 3.8 18.4 - - + -
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Residues in contact with ILE 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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541A LEU* 4.1 22.4 - - + -
542A VAL 3.5 4.5 - - - +
543A VAL* 4.4 14.1 - - + -
561A LEU* 3.8 11.0 - - + +
562A LYS* 1.3 80.9 - - - +
564A GLU* 1.3 62.4 + - - +
565A GLY 3.7 0.9 + - - -
571A VAL* 4.6 10.8 - - + -
573A LEU* 3.8 36.8 - - + -
754B GLU* 5.4 2.9 - - + -
756B LEU* 3.9 16.7 - - + +
765B SER 3.5 1.2 - - - +
766B THR* 3.3 5.4 - - - -
767B LYS* 3.0 41.5 + - + +
769B MET* 3.8 17.3 - - + -
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Residues in contact with GLU 564 (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 SER* 3.8 3.0 + - - +
541A LEU* 3.4 4.3 + - - -
542A VAL* 2.8 52.9 + - + +
544A LYS* 3.7 24.0 + - + +
562A LYS* 3.4 29.8 + - + +
563A ILE* 1.3 72.3 - - - +
565A GLY* 1.3 58.0 + - - +
764B ILE* 3.9 20.2 - - + +
765B SER 3.4 4.9 - - - -
766B THR* 4.0 15.2 + - - +
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Residues in contact with GLY 565 (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 SER 3.4 11.9 - - - -
541A LEU* 3.8 8.7 - - - -
564A GLU* 1.3 74.9 - - - +
566A ASP* 1.3 65.4 + - - -
756B LEU* 3.5 21.3 - - - +
764B ILE* 3.6 7.6 - - - -
765B SER* 2.9 30.7 + - - +
786B SER* 5.9 0.2 - - - -
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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