Contacts of the strand formed by residues 339 - 343 (chain D) in PDB entry 2O1S
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 LEU 339 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328D TRP* 4.7 0.2 - - + -
329D LEU* 4.1 11.0 - - + +
332D THR* 3.5 34.5 - - + -
333D ALA* 4.0 11.9 - - + +
336D ASP* 3.0 9.1 + - - +
338D LYS* 1.3 74.8 - - - +
340D MSE 1.3 83.9 + - - +
341D ALA* 4.0 4.5 - - + +
355D PHE* 3.9 27.4 - - + -
362D ARG* 2.8 31.7 + - - +
386D LYS 3.4 7.2 - - - -
388D ILE* 3.7 26.9 - - + -
465D TYR* 3.3 14.6 + - + +
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Residues in contact with MSE 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C LYS* 3.9 19.1 - - + -
337D ASN 3.5 22.2 - - - +
338D LYS 3.6 7.4 - - - +
339D LEU* 1.3 89.2 - - - +
341D ALA* 1.3 55.1 + - - +
342D ILE* 4.8 1.1 - - - +
361D ASP 3.9 3.8 - - - +
362D ARG* 3.5 33.4 - - - +
364D PHE* 3.9 16.2 - - + -
380D LEU* 3.9 26.9 - - + -
385D TYR* 3.5 31.4 - - + -
386D LYS 3.2 4.1 + - - +
387D PRO* 3.2 5.9 - - + +
388D ILE* 2.6 36.0 + - - +
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Residues in contact with ALA 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D PHE* 5.8 0.7 - - + -
329D LEU* 4.0 22.0 - - + -
339D LEU* 4.0 4.4 - - + +
340D MSE 1.3 73.2 - - - +
342D ILE* 1.3 64.2 + - - +
352D MSE 5.1 7.2 - - - -
355D PHE* 3.6 28.3 - - + -
362D ARG 2.8 9.3 + - - +
363D TYR* 3.5 6.1 - - + -
364D PHE* 3.0 25.8 + - - -
388D ILE* 3.4 7.9 - - + +
390D ALA* 6.3 0.4 - - + -
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Residues in contact with ILE 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D MSE 4.8 0.9 - - - +
341D ALA* 1.3 81.2 - - - +
343D THR* 1.3 63.2 + - - +
352D MSE 5.1 1.6 - - - -
364D PHE* 3.5 12.8 - - + +
366D VAL* 4.3 11.4 - - + -
373D ALA* 3.9 30.1 - - + +
376D PHE* 3.6 26.9 - - + -
377D ALA* 3.5 34.3 - - + -
380D LEU* 3.8 13.7 - - + -
387D PRO* 4.4 4.5 - - + -
388D ILE 2.6 15.3 + - - +
389D VAL* 3.6 6.6 - - + +
390D ALA* 2.7 35.9 + - - +
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Residues in contact with THR 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D ILE* 1.3 75.1 - - - +
344D PRO* 1.3 71.7 - - - +
345D ALA 3.1 4.5 + - - -
346D MSE 3.3 23.3 + - - +
347D ARG 4.4 0.2 - - - +
350D SER* 4.7 0.3 + - - -
352D MSE 3.2 32.6 - - + +
363D TYR* 3.5 34.3 - - + +
364D PHE 3.0 6.3 + - - +
365D ASP* 4.1 8.3 - - + -
366D VAL* 3.2 23.5 + - - +
390D ALA 3.7 4.0 + - - -
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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