Contacts of the helix formed by residues 324 - 338 (chain C) in PDB entry 1SA0
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 VAL 324 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B THR* 3.8 12.3 - - - +
322C ASP* 6.0 1.3 - - - +
323C VAL* 1.3 83.5 - - - +
325C PRO* 1.3 78.1 - - + +
326C LYS* 3.1 17.7 + - + +
327C ASP* 3.2 25.8 + - - +
328C VAL 3.6 5.5 + - - -
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Residues in contact with PRO 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B THR* 3.4 26.2 - - + -
323C VAL 4.2 1.1 - - - +
324C VAL* 1.3 92.1 - - + +
326C LYS* 1.3 61.9 + - - +
327C ASP 2.9 0.3 + - - -
328C VAL* 3.0 13.6 + - + +
329C ASN* 2.9 34.0 + - - +
353C VAL* 6.5 0.2 - - + -
355C ILE* 3.7 27.5 - - + -
357C TYR* 5.7 4.3 - - - +
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Residues in contact with LYS 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B THR* 4.0 23.5 - - + +
221B THR* 3.3 21.5 + - - +
324C VAL* 3.1 11.8 - - + -
325C PRO* 1.3 76.7 - - - +
327C ASP* 1.3 65.7 + - - +
329C ASN* 3.8 7.0 - - - +
330C ALA* 3.7 17.0 + - - +
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Residues in contact with ASP 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C VAL* 3.9 34.7 - - + +
289C ALA* 5.8 0.7 - - + +
323C VAL* 5.2 0.5 - - - -
324C VAL* 3.2 24.9 + - - +
325C PRO 3.0 0.4 - - - -
326C LYS* 1.3 80.8 - - - +
328C VAL* 1.3 55.3 + - - +
329C ASN 2.8 5.6 + - - -
330C ALA* 2.8 7.2 + - - +
331C ALA* 2.7 36.9 + - + +
373C ARG* 5.7 0.5 + - - -
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Residues in contact with VAL 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C VAL* 4.7 2.7 - - + -
319C TYR* 3.7 32.3 + - + +
323C VAL* 3.4 31.2 - - + -
324C VAL 3.6 3.1 + - - +
325C PRO* 3.0 15.5 + - + +
327C ASP* 1.3 78.0 - - - +
329C ASN* 1.3 65.0 + - - +
331C ALA* 3.7 8.1 + - - +
332C ILE* 3.2 36.1 + - + +
353C VAL* 3.6 30.1 - - + -
355C ILE* 5.2 2.9 - - + -
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Residues in contact with ASN 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B TYR* 4.2 15.1 + - - -
325C PRO* 2.9 22.3 + - - +
326C LYS* 3.8 8.7 - - - +
327C ASP 2.8 0.6 + - - -
328C VAL* 1.3 81.0 - - - +
330C ALA* 1.3 57.6 + - - +
331C ALA 3.0 3.8 - - - -
332C ILE* 2.8 29.4 + - - +
333C ALA* 2.9 13.8 + - - +
353C VAL* 5.9 1.8 - - - +
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Residues in contact with ALA 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C LYS 3.7 9.8 + - - +
327C ASP* 2.8 11.9 + - - +
329C ASN* 1.3 75.7 - - - +
331C ALA* 1.3 50.7 + - - +
333C ALA* 3.9 11.0 - - - +
334C THR* 2.7 35.3 + - - +
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C VAL 4.4 1.8 - - - +
289C ALA* 3.8 35.1 - - + +
292C THR* 4.0 19.7 - - + +
293C ASN* 6.1 0.3 - - - -
327C ASP 2.7 19.8 + - - +
328C VAL* 3.7 9.6 - - - +
330C ALA* 1.3 72.5 - - - +
332C ILE* 1.3 58.6 + - - +
334C THR* 3.6 5.4 + - - -
335C ILE* 3.0 30.0 + - - +
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Residues in contact with ILE 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C THR* 5.1 4.0 - - + -
296C PHE* 6.4 1.1 - - + -
317C LEU* 4.2 24.2 - - + -
328C VAL* 3.2 34.4 + - + +
329C ASN* 2.8 15.5 + - - +
331C ALA* 1.3 74.5 - - - +
333C ALA* 1.3 69.8 + - - +
335C ILE* 2.8 18.1 + - + +
336C LYS* 3.1 28.7 + - + +
351C PHE* 4.8 26.2 - - + -
353C VAL* 4.2 13.0 - - + -
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Residues in contact with ALA 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C ASN 2.9 13.9 + - - +
330C ALA* 3.9 10.8 - - - +
332C ILE* 1.3 83.0 - - - +
334C THR* 1.3 63.4 + - + +
336C LYS* 3.2 13.7 + - - +
337C THR* 3.4 15.0 + - - -
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Residues in contact with THR 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C ALA* 5.6 3.3 - - - +
293C ASN* 5.4 3.2 + - - +
330C ALA 2.7 22.1 + - - +
331C ALA* 3.6 7.6 + - - -
333C ALA* 1.3 77.0 - - + +
335C ILE* 1.3 59.0 + - - +
336C LYS 3.1 6.1 + - - -
337C THR* 3.7 22.1 + - - +
338C LYS* 4.2 6.2 + - - +
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Residues in contact with ILE 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C THR* 4.9 8.3 - - + +
293C ASN* 4.7 15.9 - - - +
296C PHE* 4.7 27.1 - - + +
331C ALA 3.0 19.5 + - - +
332C ILE* 2.8 13.2 + - + +
334C THR* 1.3 76.0 - - - +
336C LYS* 1.3 59.6 + - + +
339C ARG* 3.1 23.7 - - - +
341C ILE* 6.2 0.2 - - - -
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Residues in contact with LYS 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ILE* 3.1 19.4 + - + +
333C ALA* 3.7 9.4 - - - +
334C THR 3.1 0.4 - - - -
335C ILE* 1.3 82.7 - - - +
337C THR* 1.3 64.6 + - - +
338C LYS 3.5 1.3 + - - -
339C ARG* 3.7 7.5 + - - +
341C ILE* 3.5 42.4 - - + +
349C THR* 3.5 33.8 + - - +
351C PHE* 4.2 24.5 - - + -
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Residues in contact with THR 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ALA 3.4 13.0 + - - -
334C THR* 3.7 18.2 + - - +
336C LYS* 1.3 78.5 - - - +
338C LYS* 1.3 61.5 + - + +
339C ARG 4.0 0.7 + - - +
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Residues in contact with LYS 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C THR 4.2 6.6 + - - +
337C THR* 1.3 80.0 - - + +
339C ARG* 1.3 60.4 + - - +
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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