Contacts of the strand formed by residues 354 - 359 (chain A) in PDB entry 5O5E
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 GLU 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A LYS* 3.8 8.5 - - - +
323A THR* 3.4 37.6 + - + +
324A LYS* 5.0 0.4 + - + -
347A GLN* 5.7 1.7 + - - -
348A SER 3.4 11.7 - - - +
349A GLU* 4.0 19.3 - - + +
353A GLY* 1.3 71.9 - - - -
355A PHE* 1.3 62.4 + - - +
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Residues in contact with PHE 355 (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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320A LYS* 5.3 6.7 - - + -
321A PHE* 3.3 16.4 - - - +
322A LYS* 3.7 37.0 - - + +
323A THR* 4.7 1.6 - - - +
347A GLN* 3.6 7.1 + - - +
348A SER* 2.8 47.2 + - - +
350A THR* 3.1 39.5 - - + -
352A ASP* 3.9 18.2 - - + -
353A GLY 3.8 8.5 - - - -
354A GLU* 1.3 73.7 - - - +
356A THR* 1.4 69.2 + - - +
357A GLU* 4.3 0.7 - - + -
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Residues in contact with THR 356 (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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319A SER 3.4 5.2 - - - +
320A LYS* 3.4 2.5 - - - -
321A PHE* 2.8 58.8 + - + -
323A THR* 3.4 14.7 + - - -
326A LEU* 5.5 2.2 - - + -
334A LEU* 4.3 12.1 - - + -
345A VAL* 3.8 26.0 - - + -
346A HIS 4.0 3.4 - - - -
347A GLN* 3.3 21.0 + - + +
355A PHE* 1.4 76.1 + - - +
357A GLU* 1.3 59.5 + - - +
358A CYS 3.6 3.8 + - - +
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Residues in contact with GLU 357 (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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318A TYR* 3.7 18.1 - - + -
319A SER 3.9 0.2 - - - -
320A LYS* 3.8 24.2 - - + +
344A THR 3.5 5.9 - - - +
345A VAL* 4.6 0.4 - - - -
346A HIS* 2.9 46.2 + - + +
348A SER* 5.7 2.9 + - - +
355A PHE* 4.3 0.6 - - + -
356A THR* 1.3 70.7 - - - +
358A CYS* 1.3 61.3 + - - +
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Residues in contact with CYS 358 (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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297A ILE* 4.9 2.2 - - + -
318A TYR* 3.4 4.6 - - - -
319A SER* 2.8 39.6 + - - +
321A PHE* 4.5 7.0 - - + -
334A LEU* 3.9 28.9 - - + -
343A VAL* 3.9 20.6 - - - -
344A THR 3.8 4.0 - - - -
345A VAL* 4.3 7.6 - - + +
356A THR* 3.6 4.1 + - + -
357A GLU* 1.3 74.2 - - - +
359A ASN* 1.3 74.7 + - - +
361A MET* 3.8 20.6 - - - -
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Residues in contact with ASN 359 (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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288A TYR* 3.1 26.9 + - - -
292A GLN* 4.8 1.2 + - - +
316A MET* 3.3 26.6 - - - +
317A SER 3.9 2.6 - - - +
318A TYR* 3.6 13.9 - - + -
319A SER* 5.4 0.6 - - - -
342A LEU 3.8 7.3 + - - -
343A VAL* 4.2 3.8 - - - +
344A THR* 3.2 30.8 + - - +
358A CYS* 1.3 87.6 - - - +
360A ASN* 1.3 72.2 + - - +
361A MET* 3.2 9.7 + - - +
365A ASN* 3.5 20.9 + - - +
366A LEU* 4.8 1.0 - - - +
369A LYS* 5.2 1.8 - - - +
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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