Contacts of the helix formed by residues 321 - 332 (chain E) in PDB entry 1SID
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 MET 321 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317E ASN* 5.3 0.2 + - - -
319E TYR 4.3 0.2 + - - -
320E PRO* 1.3 66.5 - - - +
322E ALA* 1.3 69.4 + - - +
324E LEU* 2.9 17.6 + - - +
325E ILE* 2.8 41.0 + - + +
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Residues in contact with ALA 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320E PRO* 4.2 9.0 - - + +
321E MET* 1.3 83.0 - - - +
323E SER* 1.3 69.0 + - - +
325E ILE* 2.9 6.3 + - - +
326E SER* 2.9 20.5 + - - -
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Residues in contact with SER 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E TYR* 5.3 3.6 - - - +
320E PRO* 2.7 34.6 + - - +
322E ALA* 1.3 77.6 - - - +
324E LEU* 1.3 55.9 + - - +
326E SER* 2.9 6.7 + - - -
327E SER* 2.6 45.0 + - - -
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Residues in contact with LEU 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E ASN* 4.0 22.2 - - - +
319E TYR* 4.0 24.2 - - + -
320E PRO 2.9 25.3 + - - +
321E MET* 2.9 14.1 + - - +
323E SER* 1.3 76.1 - - - +
325E ILE* 1.3 69.0 + - + +
327E SER* 3.3 8.2 + - - +
328E LEU* 2.8 21.3 + - - +
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Residues in contact with ILE 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321E MET* 2.8 57.8 + - + +
322E ALA* 3.4 6.7 - - - +
324E LEU* 1.3 73.4 - - + +
326E SER* 1.3 68.7 + - - +
328E LEU* 2.6 31.4 + - + +
329E PHE* 2.7 43.4 + - + -
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Residues in contact with SER 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322E ALA 2.9 9.1 + - - -
323E SER* 2.9 12.5 + - - -
325E ILE* 1.3 84.3 - - - +
327E SER* 1.3 54.7 + - - -
329E PHE* 2.9 5.8 + - - +
330E ASN* 2.6 51.1 + - - +
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Residues in contact with SER 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323E SER* 2.6 30.6 + - - -
324E LEU* 3.4 11.4 + - - +
326E SER* 1.3 72.9 - - - +
328E LEU* 1.3 67.7 + - - +
330E ASN* 2.9 14.2 + - - +
331E ASN* 2.8 23.8 + - - +
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Residues in contact with LEU 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324E LEU 2.8 12.1 + - - +
325E ILE* 2.6 30.4 + - + +
327E SER* 1.3 72.0 - - - +
329E PHE* 1.3 77.2 + - + +
331E ASN* 3.1 15.2 + - - +
332E MET* 3.2 28.0 + - + +
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Residues in contact with PHE 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325E ILE* 2.7 39.8 + - + -
326E SER* 2.9 11.1 + - - +
328E LEU* 1.3 78.3 - - + +
330E ASN* 1.3 54.4 + - - +
331E ASN 2.6 5.1 + - - -
332E MET* 2.4 46.7 + - + +
333E LEU* 3.0 21.9 - - + +
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Residues in contact with ASN 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E SER* 2.6 34.0 + - - +
327E SER* 3.5 5.4 - - - +
329E PHE* 1.3 71.9 - - - +
331E ASN* 1.3 61.1 + - - +
333E LEU* 3.3 26.1 + - - +
335E GLN* 5.5 10.3 + - - +
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Residues in contact with ASN 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327E SER* 2.8 30.1 + - - +
328E LEU* 3.3 11.2 + - - +
329E PHE 2.6 5.3 + - - -
330E ASN* 1.3 75.0 + - - +
332E MET* 1.3 72.7 + - + +
333E LEU 4.1 2.8 - - - +
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Residues in contact with MET 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E LEU* 3.2 33.2 + - - +
329E PHE* 2.4 33.0 + - + +
331E ASN* 1.3 80.5 - - + +
333E LEU* 1.3 77.9 + - + +
334E PRO* 3.2 6.8 - - - +
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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