Contacts of the strand formed by residues 558 - 563 (chain A) in PDB entry 4Y5U
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 THR 558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551A LEU* 4.1 5.1 - - + +
554A GLU* 4.2 14.6 - - + +
555A PRO* 2.5 40.2 + - + +
556A ASP 3.2 1.1 + - - -
557A GLY* 1.3 75.7 - - - +
559A PHE* 1.3 64.8 + - - +
575A HIS* 3.4 1.7 - - - +
576A VAL* 2.9 35.0 + - - +
614A ASN* 3.1 23.2 + - + +
615A LEU 4.6 0.2 - - - -
616A TYR* 4.1 25.6 - - + +
618A LYS* 4.6 8.3 - - - +
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Residues in contact with PHE 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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551A LEU* 4.6 1.8 - - - -
557A GLY 3.6 6.5 - - - -
558A THR* 1.3 77.1 - - - +
560A LEU* 1.3 70.3 + - - +
561A LEU* 4.8 2.7 - - + -
573A ILE* 4.1 14.4 - - + -
574A ALA 3.3 14.8 - - - +
575A HIS* 3.5 11.4 - - + +
606A ILE* 3.8 35.0 - - + -
612A LEU* 3.5 27.1 - - + -
614A ASN* 3.1 28.4 + - - -
615A LEU* 3.5 29.8 - - + +
616A TYR* 2.9 28.4 + - - +
621A LYS* 4.4 8.3 - - + -
625A PHE* 3.9 10.5 - + - -
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Residues in contact with LEU 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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539A ILE* 4.5 22.2 - - + -
542A ILE* 4.9 2.0 - - + -
547A VAL* 3.7 31.0 - - + -
550A LEU* 4.3 16.6 - - + -
551A LEU* 3.6 34.8 - - + -
559A PHE* 1.3 78.4 - - - +
561A LEU* 1.3 67.6 + - - +
562A ARG* 4.4 12.6 - - + -
573A ILE* 3.5 6.2 - - - +
574A ALA* 3.0 46.2 + - + +
615A LEU* 4.1 6.5 - - + -
616A TYR* 4.5 9.6 - - + -
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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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532A TYR* 6.1 0.4 - - + -
537A LEU* 3.4 27.2 + - + +
538A ILE* 3.6 13.0 - - + +
539A ILE* 3.3 11.2 + - - +
540A GLY 3.2 18.5 + - - -
559A PHE* 4.8 2.0 - - + -
560A LEU* 1.3 83.4 - - - +
562A ARG* 1.3 60.8 + - - +
571A ILE* 3.7 11.7 - - + -
572A THR 3.5 5.2 - - - +
573A ILE* 3.8 26.9 - - + -
602A LEU* 4.1 34.8 - - + -
606A ILE* 4.3 15.0 - - + -
615A LEU* 4.7 6.3 - - + +
625A PHE* 4.5 9.4 - - + -
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Residues in contact with ARG 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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540A GLY* 3.5 15.0 - - - +
542A ILE* 3.1 31.0 + - + -
543A SER 3.9 3.6 - - - -
544A LYS* 3.4 31.9 - - - +
547A VAL* 4.0 23.3 - - - -
560A LEU* 4.4 7.0 - - + -
561A LEU* 1.3 74.9 - - - +
563A PHE* 1.3 68.5 + - - +
565A ASP* 2.6 33.7 + - - -
571A ILE* 3.5 8.6 - - - +
572A THR* 2.9 49.0 + - + +
574A ALA* 4.8 8.1 - - + -
588A ASN* 4.9 2.8 - - - +
641B PTR 3.1 29.9 + - - -
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Residues in contact with PHE 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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459A PHE* 5.2 1.3 - + - -
517A TRP* 4.2 16.3 - - + -
521A VAL* 3.8 23.1 - - + -
524A LEU* 4.2 4.7 - - + -
525A THR* 4.0 19.3 - - + -
529A LEU* 4.2 9.2 - - + -
533A TRP* 4.5 11.7 - + - -
538A ILE* 4.3 9.6 - - + -
540A GLY* 3.1 40.4 + - - +
541A PHE* 3.7 35.7 - + - -
542A ILE 4.7 1.2 - - - +
562A ARG* 1.3 92.0 + - - +
564A SER* 1.3 62.2 + - - +
565A ASP* 3.6 6.1 + - - +
570A GLY 3.4 8.1 - - - +
571A ILE* 3.8 22.0 - - + -
572A THR* 4.5 0.9 - - - -
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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