Contacts of the helix formed by residues 306 - 316 (chain L) in PDB entry 3SWD
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 306 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232L ARG 5.2 1.1 - - - +
233L ILE* 3.6 32.3 - - + +
236L GLY* 3.4 30.5 - - - +
237L THR 3.7 2.5 - - - +
240L VAL* 3.8 9.6 - - + -
259L LEU* 5.7 0.7 - - + -
262L VAL* 4.1 12.1 - - + -
302L PHE* 3.8 15.3 - - + -
303L PRO* 3.0 27.8 + - + +
305L ASP* 1.3 78.5 - - - +
307L GLN* 1.3 64.5 - - - +
309L GLN* 3.3 44.1 + - + +
310L PHE* 3.1 34.6 + - + -
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Residues in contact with GLN 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296L THR* 3.9 15.7 - - + -
302L PHE* 4.1 6.3 - - + -
303L PRO 3.6 1.6 + - - -
304L THR 2.9 14.4 + - - +
305L ASP 3.4 0.2 - - - -
306L MET* 1.3 76.2 - - - +
308L ALA* 1.3 62.8 + - - +
310L PHE* 3.3 3.1 + - - -
311L THR* 2.9 36.0 + - - -
323L ILE* 3.5 25.4 - - + +
325L GLU* 2.9 28.7 + - + +
331L ARG* 3.0 31.1 + - - +
332L PHE* 3.7 17.7 - - + -
334L HIS* 3.0 28.7 + - - -
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Residues in contact with ALA 308 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304L THR 4.6 1.4 + - - -
307L GLN* 1.3 78.2 + - - +
309L GLN* 1.3 64.3 + - - +
311L THR* 3.2 3.8 + - - -
312L LEU* 3.1 17.0 + - - +
334L HIS* 3.5 27.6 - - + +
338L LEU* 5.1 0.3 - - - +
372L ALA* 3.4 47.3 - - + +
375L SER* 3.6 15.5 + - - +
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Residues in contact with GLN 309 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233L ILE* 4.2 0.6 - - - +
237L THR* 3.2 36.5 + - + +
240L VAL* 3.8 22.1 - - + +
305L ASP 3.0 28.1 + - - +
306L MET* 3.4 34.7 - - + +
307L GLN 3.2 0.2 - - - -
308L ALA* 1.3 84.1 + - - +
310L PHE* 1.3 58.6 + - - +
312L LEU* 3.2 7.5 + - - +
313L LEU 3.1 20.1 + - - -
371L ARG 4.4 7.7 + - - -
372L ALA* 4.6 2.8 - - - -
374L ALA* 5.3 0.2 - - + -
375L SER* 4.3 16.2 - - - +
378L LEU* 4.9 5.6 - - + -
399L TYR* 3.6 11.5 + - - -
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Residues in contact with PHE 310 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240L VAL* 3.6 21.5 - - + -
262L VAL* 4.0 15.9 - - + -
265L LYS* 3.6 24.0 - - + -
266L LEU* 3.6 35.2 - - + -
269L ALA* 5.8 0.2 - - + -
292L VAL* 4.3 19.3 - - + -
294L VAL* 4.5 4.5 - - + -
302L PHE* 3.3 37.7 - + + -
306L MET* 3.1 24.8 + - + +
307L GLN 3.3 1.3 + - - +
309L GLN* 1.3 72.6 - - - +
311L THR* 1.3 65.9 + - - +
313L LEU* 3.2 16.0 + - + +
314L ASN* 2.9 22.3 + - - +
323L ILE* 3.5 18.5 - - + +
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Residues in contact with THR 311 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307L GLN* 2.9 30.5 + - - -
308L ALA 3.4 8.3 - - - -
310L PHE* 1.3 77.6 - - - +
312L LEU* 1.3 57.5 + - - +
314L ASN* 3.3 4.7 + - - +
315L LEU* 2.9 50.8 + - + +
323L ILE* 3.3 15.4 - - - +
334L HIS* 4.0 15.5 - - + +
335L VAL* 4.3 15.5 - - + -
338L LEU* 4.8 0.7 - - + -
352L VAL* 4.3 9.4 - - + +
354L CYS* 4.2 13.2 - - - -
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Residues in contact with LEU 312 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240L VAL* 5.6 0.2 - - + -
244L ILE* 3.7 18.2 - - + -
308L ALA 3.1 12.2 + - - +
309L GLN 3.5 9.0 - - - +
310L PHE 3.1 0.4 - - - -
311L THR* 1.3 74.2 - - - +
313L LEU* 1.3 67.3 + - - +
315L LEU* 3.0 14.3 + - + +
316L VAL* 3.4 15.5 + - + +
338L LEU* 4.3 21.2 - - + +
360L LEU* 4.0 27.1 - - + -
375L SER* 3.4 29.4 - - - +
378L LEU* 3.7 17.3 - - + -
379L ALA* 3.6 19.5 - - + +
382L ILE* 4.8 2.2 - - + -
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Residues in contact with LEU 313 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240L VAL* 4.7 5.8 - - + -
243L ALA* 4.1 17.7 - - + -
244L ILE* 3.8 20.1 - - + +
266L LEU* 4.1 26.2 - - + -
269L ALA* 4.2 25.1 - - + -
289L PRO* 4.2 13.8 - - + +
290L LYS 4.3 6.7 - - - +
292L VAL* 4.5 9.2 - - + -
309L GLN 3.1 12.0 + - - +
310L PHE* 3.2 19.0 + - + +
312L LEU* 1.3 78.7 - - - +
314L ASN* 1.3 76.0 + - - +
316L VAL* 3.3 4.5 + - - +
317L ALA* 3.1 23.3 + - + +
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Residues in contact with ASN 314 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291L ALA* 3.5 8.3 - - + +
292L VAL* 2.8 54.4 + - - +
310L PHE 2.9 12.8 + - - +
311L THR 3.7 2.7 - - - +
313L LEU* 1.3 78.3 - - - +
315L LEU* 1.3 63.9 + - - +
317L ALA* 3.1 16.5 + - - +
319L GLY 4.9 1.0 - - - +
321L GLY* 3.8 16.0 + - - +
323L ILE* 3.8 25.5 - - - +
354L CYS* 3.7 20.2 - - + +
356L GLY* 3.5 13.7 + - - -
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Residues in contact with LEU 315 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311L THR* 2.9 33.7 + - + +
312L LEU* 3.0 9.3 + - + +
314L ASN* 1.3 76.3 - - - +
316L VAL* 1.3 61.1 + - + +
317L ALA 3.5 0.4 - - - -
335L VAL* 5.6 3.4 - - - +
338L LEU* 3.6 31.0 - - + -
343L ALA* 3.9 26.9 - - + +
344L HIS 3.5 27.1 - - - +
345L ALA* 3.7 15.3 - - + -
354L CYS* 3.7 17.7 - - + -
355L HIS 4.2 2.9 - - - +
356L GLY* 3.4 3.1 - - - -
357L VAL* 3.0 29.3 + - - +
360L LEU* 5.0 1.5 - - + +
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Residues in contact with VAL 316 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244L ILE* 4.2 28.3 - - + +
288L ARG* 3.2 22.5 + - - +
289L PRO* 4.2 6.3 - - + +
312L LEU* 3.4 11.9 + - + +
313L LEU 3.5 11.2 - - - +
315L LEU* 1.3 79.3 - - + +
317L ALA* 1.3 59.8 + - - +
357L VAL* 3.3 17.4 - - + +
358L GLU 5.0 6.0 - - - +
359L LYS* 5.5 0.4 - - - -
360L LEU* 3.8 36.6 - - + +
382L ILE* 4.1 14.6 - - + -
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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