Contacts of the helix formed by residues 321 - 332 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B GLU* 2.7 10.4 + - - +
112B LEU* 3.7 30.6 - - + +
321B MET* 4.4 1.6 - - + -
325B ILE* 4.2 24.9 - - + -
110F GLU* 4.7 3.8 - - - +
112F LEU* 3.2 45.1 - - + -
317F ASN* 4.7 12.6 - - - +
319F TYR* 3.7 5.9 + - + +
320F PRO* 1.3 65.5 - - - +
322F ALA* 1.3 52.5 + - - +
323F SER* 2.6 17.7 + - - -
324F LEU* 2.8 30.0 + - + +
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Residues in contact with ALA 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLU* 2.6 35.0 + - + +
112B LEU* 4.0 9.2 - - + +
117B LEU* 4.6 6.9 - - + +
317B ASN* 5.5 2.2 - - - +
321B MET* 4.6 7.0 - - + -
321F MET* 1.3 68.7 - - - +
323F SER* 1.3 53.5 + - - -
324F LEU* 2.7 13.2 - - - +
325F ILE* 2.6 43.4 + - + +
326F SER* 2.9 13.2 + - - -
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Residues in contact with SER 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B MET* 3.5 27.2 - - - +
110B GLU* 3.0 2.8 + - - -
370C VAL* 5.0 1.6 - - - +
373C PHE* 4.8 13.2 - - - -
319F TYR* 5.6 2.0 - - - -
320F PRO* 2.8 24.3 + - - -
321F MET 2.6 6.3 + - - -
322F ALA* 1.3 74.5 - - - +
324F LEU* 1.3 55.1 + - - +
326F SER* 3.0 14.9 - - - -
327F SER* 2.6 37.4 + - - -
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Residues in contact with LEU 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B MET* 3.8 29.4 - - + -
324B LEU* 4.0 23.1 - - + +
325B ILE* 4.5 13.5 - - + +
321F MET* 2.8 27.8 + - + +
322F ALA* 2.7 3.1 - - - -
323F SER* 1.3 82.0 + - - +
325F ILE* 1.3 74.9 + - + +
326F SER 3.1 0.2 - - - -
327F SER* 3.1 14.2 - - - +
328F LEU* 2.6 33.1 + - - +
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Residues in contact with ILE 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.6 24.5 - - + -
317B ASN* 3.3 27.4 - - - +
318B PRO* 3.6 11.0 - - + -
319B TYR* 3.8 9.9 - - + +
321B MET* 5.5 1.8 - - - -
324B LEU* 4.8 10.5 - - + -
322F ALA* 2.6 27.1 + - + +
324F LEU* 1.3 80.2 - - + +
326F SER* 1.3 61.8 + - - +
328F LEU* 3.0 25.1 + - + +
329F PHE* 2.9 66.1 + - + -
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Residues in contact with SER 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B MET* 4.6 6.1 - - - +
117B LEU* 5.6 1.0 - - - +
275B GLY* 4.8 2.7 - - - +
276B GLU* 3.6 23.6 + - - -
370C VAL* 4.4 14.1 - - - +
322F ALA 2.9 14.1 + - - -
323F SER* 3.0 17.0 + - - -
325F ILE* 1.3 81.4 - - - +
327F SER* 1.3 63.5 + - - +
329F PHE* 3.0 13.4 + - - +
330F ASN* 2.8 24.8 + - - +
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Residues in contact with SER 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C VAL* 4.8 7.7 - - - +
373C PHE* 5.7 5.7 - - - +
323F SER* 2.6 27.1 + - - -
324F LEU* 3.1 21.2 - - - -
326F SER* 1.3 72.4 - - - +
328F LEU* 1.3 52.7 + - - +
330F ASN* 2.8 27.9 + - - +
331F ASN* 2.9 21.4 + - - -
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Residues in contact with LEU 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B TYR* 3.5 36.1 - - + -
324B LEU* 4.7 17.7 - - + -
324F LEU 2.6 15.3 + - - +
325F ILE* 3.0 25.5 + - + +
327F SER* 1.3 72.5 - - - +
329F PHE* 1.3 63.0 + - + +
331F ASN* 2.9 16.0 + - + +
332F MET* 2.9 45.1 + - + +
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Residues in contact with PHE 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 5.4 1.6 - - + -
119B MET* 4.2 19.3 - - + -
274B LYS* 3.8 31.9 - - + -
275B GLY* 4.0 15.9 - - - +
276B GLU* 5.8 0.7 - - - -
318B PRO* 4.0 13.9 - - + -
319B TYR* 3.8 22.0 - + - -
325F ILE* 2.9 57.2 + - + -
326F SER* 3.0 11.2 + - - +
328F LEU* 1.3 77.6 - - + +
330F ASN* 1.3 58.5 + - - +
332F MET* 3.6 22.0 - - - -
333F LEU* 2.7 38.5 + - + +
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Residues in contact with ASN 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LYS* 4.2 16.9 + - - +
104B GLN* 4.9 2.8 - - - +
275B GLY* 3.9 18.9 - - - -
279B TYR* 5.9 0.2 + - - -
370C VAL* 3.8 24.8 - - + +
371C ASP* 5.4 3.9 + - - +
326F SER 2.8 9.1 + - - +
327F SER* 2.8 14.4 + - - +
329F PHE* 1.3 75.4 - - - +
331F ASN* 1.3 61.3 + - - +
333F LEU* 3.2 21.7 + - - +
335F GLN* 3.5 24.4 + - - +
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Residues in contact with ASN 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327F SER* 2.9 20.2 + - - +
328F LEU* 3.2 16.3 - - + +
330F ASN* 1.3 83.4 + - - +
332F MET* 1.3 67.8 + - - +
333F LEU 2.9 7.1 + - - -
334F PRO* 4.3 1.2 - - - +
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Residues in contact with MET 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLU* 5.3 0.2 - - - +
215B LYS* 5.5 2.4 - - - -
274B LYS* 3.2 29.4 - - - +
319B TYR* 5.4 6.1 - - - -
328F LEU* 2.9 31.6 + - + +
329F PHE* 3.5 36.3 - - - +
331F ASN* 1.3 75.7 - - - +
333F LEU* 1.3 72.0 + - + +
334F PRO* 3.0 13.5 - - - +
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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