Contacts of the helix formed by residues 306 - 316 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232D ARG 5.2 0.9 - - - +
233D ILE* 3.7 30.5 - - + +
236D GLY* 3.4 33.9 - - - +
237D THR 3.8 0.2 - - - +
240D VAL* 3.8 10.1 - - + -
259D LEU* 5.7 0.9 - - + -
262D VAL* 4.1 13.0 - - + -
302D PHE* 3.6 15.7 - - + -
303D PRO* 3.0 26.4 + - + +
305D ASP* 1.3 78.0 - - - +
307D GLN* 1.3 64.3 + - - +
309D GLN* 3.3 47.4 + - + +
310D PHE* 3.1 34.9 + - + -
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Residues in contact with GLN 307 (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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296D THR* 3.9 15.3 - - + -
302D PHE* 4.1 5.6 - - + -
303D PRO 3.5 1.8 + - - -
304D THR 2.9 15.1 + - - +
305D ASP 3.5 0.2 - - - -
306D MET* 1.3 75.2 - - - +
308D ALA* 1.3 64.1 + - - +
310D PHE* 3.3 3.0 + - - -
311D THR* 2.8 36.0 + - - -
323D ILE* 3.5 25.3 - - + +
325D GLU* 2.9 28.0 + - + +
331D ARG* 2.9 31.7 + - - +
332D PHE* 3.7 17.5 - - + -
334D HIS* 3.0 29.0 + - - -
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Residues in contact with ALA 308 (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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304D THR 4.6 1.2 + - - -
305D ASP 5.4 0.2 - - - -
307D GLN* 1.3 74.1 + - - +
309D GLN* 1.3 68.6 + - - +
311D THR* 3.2 3.2 + - - -
312D LEU* 3.1 18.0 + - - +
334D HIS* 3.5 40.2 - - + +
338D LEU* 5.1 0.7 - - - +
372D ALA* 3.4 40.5 - - + +
375D SER* 3.6 12.5 + - - +
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Residues in contact with GLN 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D ILE* 4.2 0.6 - - - +
237D THR* 3.2 36.2 + - + +
240D VAL* 3.8 22.6 - - + +
305D ASP 3.1 22.5 + - - +
306D MET* 3.3 38.9 - - + +
308D ALA* 1.3 84.1 + - - +
310D PHE* 1.3 63.1 + - - +
312D LEU* 3.3 6.8 + - - +
313D LEU 3.1 16.6 + - - -
371D ARG 4.2 7.8 + - - -
372D ALA* 4.7 2.1 - - - -
374D ALA* 5.3 0.4 - - + -
375D SER* 4.3 16.8 - - - +
378D LEU* 4.8 4.5 - - + -
399D TYR* 3.6 11.7 + - - -
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Residues in contact with PHE 310 (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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240D VAL* 3.6 19.1 - - + -
262D VAL* 4.0 15.9 - - + -
265D LYS* 3.7 23.8 - - + -
266D LEU* 3.7 35.0 - - + -
269D ALA* 5.8 0.2 - - + -
292D VAL* 4.3 18.4 - - + -
294D VAL* 4.5 3.4 - - + -
302D PHE* 3.3 40.2 - + + -
306D MET* 3.1 25.2 + - + +
307D GLN 3.3 1.1 + - - +
308D ALA 3.3 0.2 - - - -
309D GLN* 1.3 74.0 - - - +
311D THR* 1.3 66.5 + - - +
313D LEU* 3.3 15.6 + - + +
314D ASN* 3.0 23.9 + - - +
323D ILE* 3.5 17.4 - - + +
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Residues in contact with THR 311 (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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307D GLN* 2.8 33.4 + - - -
308D ALA 3.2 8.5 + - - -
310D PHE* 1.3 75.4 - - - +
312D LEU* 1.3 58.2 + - - +
314D ASN* 3.4 4.3 + - - +
315D LEU* 3.0 50.9 + - + +
323D ILE* 3.3 15.1 - - - +
334D HIS* 4.0 15.9 - - + +
335D VAL* 4.3 15.0 - - + -
338D LEU* 4.8 0.4 - - + -
352D VAL* 4.3 8.6 - - + +
354D CYS* 4.2 14.1 - - - -
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Residues in contact with LEU 312 (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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240D VAL* 5.5 0.4 - - + -
244D ILE* 3.8 17.9 - - + -
308D ALA 3.1 11.6 + - - +
309D GLN* 3.5 9.6 - - - +
310D PHE 3.1 0.2 - - - -
311D THR* 1.3 74.2 - - - +
313D LEU* 1.3 67.3 + - - +
315D LEU* 2.9 17.7 + - + -
316D VAL* 3.3 15.4 + - + +
338D LEU* 4.2 19.0 - - + +
360D LEU* 4.0 27.1 - - + -
375D SER* 3.4 28.7 - - - +
378D LEU* 3.7 17.7 - - + -
379D ALA* 3.6 20.4 - - + +
382D ILE* 4.8 2.2 - - + -
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Residues in contact with LEU 313 (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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240D VAL* 4.6 6.1 - - + -
243D ALA* 4.1 26.2 - - + -
244D ILE* 3.8 21.3 - - + +
266D LEU* 4.1 17.3 - - + -
269D ALA* 4.1 24.7 - - + -
289D PRO* 4.1 13.8 - - + +
290D LYS 4.2 7.6 - - - +
292D VAL* 4.5 8.5 - - + -
309D GLN 3.1 12.6 + - - +
310D PHE* 3.3 18.8 + - + +
312D LEU* 1.3 78.5 - - - +
314D ASN* 1.3 76.7 + - - +
316D VAL* 3.3 4.7 + - - +
317D ALA* 3.2 22.3 + - + +
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Residues in contact with ASN 314 (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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291D ALA* 3.4 7.3 - - + +
292D VAL* 2.8 54.8 + - - +
310D PHE 3.0 14.3 + - - +
311D THR 3.8 2.7 - - - +
312D LEU 3.2 0.2 - - - -
313D LEU* 1.3 78.4 - - - +
315D LEU* 1.3 62.3 + - - +
317D ALA* 3.1 16.7 + - - +
319D GLY 4.9 1.9 - - - +
321D GLY* 3.9 16.6 + - - +
323D ILE* 3.8 24.5 - - - +
354D CYS* 3.7 21.0 - - + +
356D GLY* 3.5 13.9 + - - -
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Residues in contact with LEU 315 (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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311D THR* 3.0 35.7 + - + +
312D LEU* 2.9 10.9 + - + +
314D ASN* 1.3 76.2 - - - +
316D VAL* 1.3 60.5 + - + +
335D VAL* 5.6 3.4 - - - +
338D LEU* 3.6 31.2 - - + -
343D ALA* 3.9 27.7 - - + +
344D HIS 3.5 26.7 - - - +
345D ALA* 3.7 14.1 - - + -
354D CYS* 3.7 17.5 - - + -
355D HIS 4.3 3.5 - - - +
356D GLY* 3.5 3.5 - - - -
357D VAL* 3.0 29.1 + - - +
360D LEU* 4.9 2.1 - - + +
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Residues in contact with VAL 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ILE* 4.2 29.6 - - + +
288D ARG* 3.2 21.5 + - - +
289D PRO* 4.2 6.7 - - + +
312D LEU* 3.7 10.8 - - + +
313D LEU 3.6 10.1 - - - +
314D ASN 3.2 0.2 - - - -
315D LEU* 1.3 81.0 - - - +
317D ALA* 1.3 60.0 + - - +
357D VAL* 3.3 16.7 - - + +
358D GLU 5.0 6.8 - - - +
359D LYS* 5.5 0.4 - - - -
360D LEU* 3.8 37.0 - - + +
382D ILE* 4.1 14.4 - - + -
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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