Contacts of the strand formed by residues 551 - 555 (chain A) in PDB entry 1GXD
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 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A TYR* 3.3 33.8 - - + +
542A ALA* 5.1 0.2 - - + -
543A PHE 3.1 11.0 + - - +
544A ASN* 4.8 1.9 - - - +
550A LYS* 1.3 76.5 + - - +
552A TYR* 1.3 68.6 + - - +
553A ILE* 3.8 25.6 - - + -
561A ARG* 3.7 7.4 - - - -
562A TYR* 3.2 42.9 + - + +
564A GLU* 3.1 24.3 - - - +
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Residues in contact with TYR 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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542A ALA* 3.3 21.1 - - - -
543A PHE* 3.0 32.4 + + + -
545A TRP* 2.9 38.3 + + - -
548A ASN* 3.1 26.1 + - - -
550A LYS* 4.3 5.4 - - + -
551A THR* 1.3 78.4 - - - +
553A ILE* 1.3 61.5 + - - +
554A PHE* 3.5 16.1 + - + -
559A PHE* 3.9 9.9 - + - -
560A TRP 3.5 14.4 - - - +
561A ARG* 4.0 16.7 + - + -
581A TRP* 4.1 4.9 - + - -
187C GLU* 4.6 1.4 + - - -
188C PHE* 2.8 57.8 + + - -
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Residues in contact with ILE 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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506A PHE* 4.3 10.5 - - + -
530A LEU* 4.0 22.7 - - + -
532A LEU* 3.7 39.9 - - + -
539A VAL* 4.2 24.5 - - + -
541A ALA 3.7 3.1 - - - +
542A ALA* 4.2 8.7 - - + -
551A THR* 3.8 22.2 - - + -
552A TYR* 1.3 69.1 - - - +
554A PHE* 1.3 60.8 + - - +
555A ALA* 3.6 3.9 + - + -
559A PHE 3.6 1.0 - - - -
560A TRP* 2.8 46.2 + - + +
561A ARG 5.2 0.7 - - - +
562A TYR* 4.5 15.7 - - + -
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Residues in contact with PHE 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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539A VAL* 3.8 1.7 - - - +
540A ASP* 3.2 10.6 + - + +
541A ALA* 2.8 43.6 + - + +
543A PHE* 3.1 38.1 - + - -
552A TYR* 3.5 12.8 - - + -
553A ILE* 1.3 70.5 - - - +
555A ALA* 1.3 60.7 + - - +
556A GLY 4.3 0.9 - - - +
559A PHE* 3.4 22.4 - - + +
577A ILE* 5.4 4.3 - - + -
581A TRP* 3.0 41.7 - + - -
584A ILE* 5.2 8.3 - - + -
587A ASN* 6.1 1.8 - - - -
588A LEU* 5.4 9.6 - - + +
591A VAL* 3.7 24.2 - - + -
602A PHE* 3.7 15.9 - + - -
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Residues in contact with ALA 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 5.8 1.1 - - + -
535A ASP* 5.2 3.6 - - - +
538A ARG 4.4 16.8 - - - +
539A VAL* 4.5 11.4 - - + -
540A ASP* 3.7 7.2 - - - +
553A ILE* 3.6 3.7 + - + +
554A PHE* 1.3 76.7 - - - +
556A GLY* 1.3 61.6 + - - +
558A LYS* 2.7 28.5 + - - +
560A TRP* 3.4 28.7 - - + -
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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