Contacts of the strand formed by residues 552 - 558 (chain A) in PDB entry 5ID6
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 552 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A ARG* 3.4 6.1 - - - +
549A TYR* 2.8 62.3 + - - -
550A GLY* 4.9 1.6 - - - -
551A SER* 1.3 90.4 - - - +
553A TYR* 1.3 61.4 + - - +
554A TYR* 3.1 36.0 - - + +
703A GLN* 4.2 22.7 - - - +
709A PHE* 5.1 9.0 - - + +
711A ASP* 5.9 3.8 - - - +
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Residues in contact with TYR 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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546A ILE* 5.1 5.6 - - + -
547A LEU 3.4 5.8 - - - +
548A ARG* 3.6 47.6 + - + -
550A GLY 5.6 0.2 - - - -
551A SER* 3.5 23.6 - - - -
552A LYS* 1.3 74.0 - - - +
554A TYR* 1.3 71.4 + - - +
682A PHE* 5.1 2.2 - + - -
703A GLN* 3.5 3.7 - - - +
704A ILE* 3.1 35.2 + - + +
709A PHE* 4.0 15.6 - + - -
724A PHE* 3.6 36.6 - + + -
725A LYS* 4.6 17.9 + - + +
728A PHE* 3.5 36.1 - + - +
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Residues in contact with TYR 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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24A VAL* 4.3 8.7 - - + -
546A ILE* 3.3 9.7 - - - +
547A LEU* 2.5 55.5 + - + +
549A TYR* 4.0 19.1 - - + +
552A LYS* 3.1 55.8 - - + +
553A TYR* 1.3 79.1 - - - +
555A LEU* 1.3 61.0 + - - +
556A ALA 4.1 0.2 - - - -
578A TYR* 4.4 5.6 - + - -
701A MSE 3.4 40.6 - - + -
702A PHE 3.3 6.7 - - - +
703A GLN* 3.5 32.8 + - + +
704A ILE* 3.4 6.7 - - - +
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Residues in contact with LEU 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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21A ALA* 5.1 1.8 - - + -
531A MSE 3.7 9.6 - - + -
534A TRP* 3.7 27.4 - - + -
544A ALA* 4.3 10.3 - - + -
545A THR 3.6 15.0 - - - +
546A ILE* 4.8 1.3 - - + +
554A TYR* 1.3 73.8 - - - +
556A ALA* 1.3 60.3 + - - +
557A ILE* 4.4 12.1 - - + -
700A TYR 3.7 1.4 - - - +
701A MSE 3.4 4.9 - - - +
702A PHE* 2.8 50.0 + - + +
704A ILE* 3.6 16.9 - - + +
744A LEU* 4.2 27.1 - - + -
796A LEU* 4.2 24.2 - - + -
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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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544A ALA* 3.3 3.1 - - - -
545A THR* 2.8 56.5 + - + +
547A LEU* 3.8 25.8 - - + -
554A TYR 4.1 0.2 + - - -
555A LEU* 1.3 73.4 - - - +
557A ILE* 1.3 62.0 + - - +
558A MSE 3.7 4.4 - - - +
566A LEU* 4.7 1.1 - - + -
699A LEU* 4.3 17.0 - - + -
700A TYR 3.4 6.3 - - - +
701A MSE 4.6 2.9 - - + +
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Residues in contact with ILE 557 (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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525A PHE* 3.6 39.7 - - + -
530A PHE* 3.7 31.0 - - + -
543A ARG* 3.4 11.0 - - + +
544A ALA* 4.5 2.5 - - + -
555A LEU* 4.4 12.6 - - + -
556A ALA* 1.3 75.2 - - - +
558A MSE 1.3 67.5 + - - +
699A LEU* 4.1 2.0 - - - +
700A TYR* 2.7 56.4 + - + +
702A PHE* 3.8 22.0 - - + -
744A LEU* 4.0 9.0 - - + -
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Residues in contact with MSE 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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539A GLU* 3.8 26.0 - - + +
543A ARG* 2.9 39.7 + - + +
544A ALA 3.9 4.0 - - - +
545A THR* 3.4 42.4 - - + +
556A ALA 3.7 12.6 - - - +
557A ILE* 1.3 79.6 - - - +
559A ASP* 1.3 70.4 + - - +
560A LYS 3.7 0.5 + - - -
562A TYR 4.3 3.6 - - - +
563A ALA* 3.9 27.4 - - - +
565A CYS* 4.1 6.5 - - - -
566A LEU* 3.5 14.8 - - + -
698A LYS 4.1 0.2 - - - -
699A LEU* 3.7 19.1 - - + -
700A TYR* 4.5 0.4 - - - -
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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