Contacts of the strand formed by residues 366 - 370 (chain A) in PDB entry 2PU1
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 SER 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A GLN* 2.6 32.9 + - - -
338A ASN 3.1 5.0 + - - -
339A SER* 2.9 14.8 + - - -
340A LEU 2.9 21.7 + - - -
361A MET* 5.7 0.2 - - - -
364A GLY 4.0 0.6 + - - -
365A TRP* 1.3 79.8 - - - +
367A VAL* 1.3 64.8 + - - +
390A SER 5.9 0.2 - - - -
392A GLN* 3.6 14.0 + - - -
425A PHE* 3.8 20.2 - - - -
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU* 3.4 9.9 - - + +
342A LEU* 3.8 37.2 - - + -
357A SER* 3.9 25.4 - - - +
360A CYS* 4.2 12.6 - - + -
361A MET* 3.9 20.9 - - + +
366A SER* 1.3 83.1 - - - +
368A MET* 1.3 62.7 + - - +
369A VAL* 4.4 5.2 - - + +
388A LEU* 4.7 0.9 - - + -
390A SER* 2.8 42.7 + - - +
392A GLN* 3.7 10.9 - - - +
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Residues in contact with MET 368 (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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147A CYS* 4.0 24.5 - - + -
167A MET* 5.3 2.7 - - + +
241A CYS* 4.8 3.8 - - + -
289A SER* 4.1 12.1 - - - +
291A GLU* 5.3 1.6 - - - +
314A GLN* 3.8 10.8 - - - +
316A VAL* 4.9 5.2 - - + -
339A SER* 4.4 5.1 + - - +
340A LEU 2.8 10.4 + - - +
341A LEU* 3.4 22.0 - - + +
342A LEU 2.9 23.2 + - - -
366A SER 4.3 0.2 - - - -
367A VAL* 1.3 71.7 - - - +
369A VAL* 1.3 71.2 + - - +
392A GLN* 3.3 33.0 + - + +
393A ILE 4.1 1.3 - - - -
394A LYS* 3.7 36.6 - - - +
428A TRP* 4.3 3.8 - - + -
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Residues in contact with VAL 369 (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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342A LEU* 3.8 16.8 - - + +
367A VAL* 3.8 2.4 - - + -
368A MET* 1.3 72.9 - - - +
370A SER* 1.3 60.3 + - - +
381A ILE* 3.7 41.5 - - + +
384A LEU* 4.4 10.3 - - + -
385A VAL* 3.7 35.2 - - + +
388A LEU* 4.0 22.4 - - + -
390A SER* 4.5 4.3 - - - +
392A GLN 3.1 5.3 + - - -
393A ILE* 3.3 7.7 - - + +
394A LYS 2.9 24.6 + - - -
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Residues in contact with SER 370 (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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341A LEU* 3.5 34.4 - - - +
342A LEU 3.0 18.0 + - - +
343A LYS* 3.6 10.8 - - - +
344A ILE* 5.2 0.7 + - - +
369A VAL* 1.3 77.8 - - - +
371A HIS* 1.3 80.4 + - - +
381A ILE* 3.8 19.2 - - - +
394A LYS* 3.3 27.5 - - - -
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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