Contacts of the helix formed by residues 306 - 316 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232J ARG 5.3 0.7 - - - +
233J ILE* 3.5 44.2 - - + +
236J GLY* 3.3 34.8 - - - +
237J THR 3.6 1.3 - - - +
240J VAL* 3.7 15.7 - - + -
259J LEU* 5.4 0.9 - - + -
262J VAL* 4.4 12.1 - - + -
302J PHE* 3.8 17.5 - - + -
303J PRO* 3.0 18.6 + - + +
304J THR 3.0 1.2 - - - -
305J ASP* 1.3 75.7 - - - +
307J GLN* 1.3 65.4 + - - +
309J GLN* 3.2 32.4 + - + +
310J PHE* 3.1 28.3 + - + -
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Residues in contact with GLN 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296J THR* 3.6 14.6 - - + -
302J PHE* 4.0 6.7 - - + -
303J PRO 3.5 2.6 + - - -
304J THR* 2.7 18.0 + - - +
305J ASP 3.4 0.2 - - - -
306J MET* 1.3 78.3 - - - +
308J ALA* 1.3 60.1 + - - +
310J PHE* 3.4 3.8 + - - +
311J THR* 3.0 38.3 + - - -
323J ILE* 3.5 24.5 - - + +
325J GLU* 2.7 33.4 + - + +
331J ARG* 3.0 31.5 + - - +
332J PHE* 4.0 12.0 - - - -
334J HIS* 3.3 12.6 + - - -
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Residues in contact with ALA 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304J THR 4.4 1.4 + - - -
307J GLN* 1.3 81.5 + - - +
309J GLN* 1.3 68.5 + - - +
311J THR* 3.0 3.9 + - - -
312J LEU* 2.9 27.5 + - - +
334J HIS* 3.5 39.5 + - + -
338J LEU* 5.0 0.9 - - - +
372J ALA* 3.7 26.2 - - + +
375J SER* 3.7 6.9 + - - +
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Residues in contact with GLN 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233J ILE* 4.2 0.6 - - - +
237J THR* 3.8 26.1 + - + -
240J VAL* 3.6 25.6 - - + +
305J ASP 2.8 25.0 + - - +
306J MET* 3.2 45.2 - - + +
308J ALA* 1.3 84.8 + - - +
310J PHE* 1.3 56.6 + - - +
312J LEU* 3.3 6.7 + - - +
313J LEU 3.0 21.7 + - - -
371J ARG 4.2 7.7 + - - +
372J ALA* 4.7 2.1 - - - -
375J SER* 4.3 19.7 - - - +
378J LEU* 5.0 2.7 - - + -
399J TYR* 4.0 11.7 + - - -
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Residues in contact with PHE 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240J VAL* 3.5 21.5 - - + -
262J VAL* 4.0 15.5 - - + -
265J LYS* 4.1 19.1 - - + -
266J LEU* 3.6 42.0 - - + -
269J ALA* 5.8 0.4 - - + -
292J VAL* 5.0 8.3 - - + -
294J VAL* 4.7 5.4 - - + -
302J PHE* 3.3 39.7 - + + -
306J MET* 3.1 23.3 + - + +
307J GLN 3.4 1.1 + - - +
309J GLN* 1.3 73.5 - - - +
311J THR* 1.3 60.2 + - - +
313J LEU* 3.5 19.8 - - + +
314J ASN* 3.1 32.4 + - - +
323J ILE* 4.0 16.4 - - + -
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Residues in contact with THR 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307J GLN* 3.0 29.7 + - - -
308J ALA* 3.0 13.1 + - - -
310J PHE* 1.3 77.1 - - - +
312J LEU* 1.3 62.5 + - - +
314J ASN* 3.6 3.7 + - - +
315J LEU* 2.9 49.0 + - + +
323J ILE* 3.8 16.1 - - - +
334J HIS* 3.7 16.5 - - + +
335J VAL* 4.6 4.0 - - + -
338J LEU* 4.5 1.6 - - + -
352J VAL* 4.2 15.2 - - + +
354J CYS* 4.3 11.4 - - - -
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Residues in contact with LEU 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240J VAL* 5.8 0.2 - - + -
244J ILE* 3.8 24.5 - - + -
308J ALA 2.9 11.8 + - - +
309J GLN* 3.5 9.9 - - - +
311J THR* 1.3 74.0 - - - +
313J LEU* 1.3 70.9 + - - +
315J LEU* 2.9 23.6 + - + +
316J VAL* 3.3 7.7 + - + +
338J LEU* 3.8 21.3 - - + +
360J LEU* 3.9 17.9 - - + -
375J SER* 3.2 28.9 - - - +
378J LEU* 4.0 5.8 - - + -
379J ALA* 3.5 34.8 - - + +
382J ILE* 4.9 6.1 - - + -
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Residues in contact with LEU 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240J VAL* 4.7 5.8 - - + -
243J ALA* 4.5 10.5 - - + -
244J ILE* 3.4 27.1 - - + +
266J LEU* 4.2 15.7 - - + -
269J ALA* 4.7 11.4 - - + -
289J PRO* 4.1 14.8 - - + -
290J LYS 4.3 6.1 - - - +
292J VAL* 5.5 2.9 - - + -
309J GLN 3.0 13.0 + - - +
310J PHE* 3.5 37.0 - - + +
311J THR 3.3 0.2 - - - -
312J LEU* 1.3 78.2 - - - +
314J ASN* 1.3 80.7 + - - +
316J VAL* 2.8 15.2 + - - +
317J ALA* 3.1 21.7 + - + +
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Residues in contact with ASN 314 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291J ALA* 3.2 11.4 - - + -
292J VAL* 2.9 49.7 + - - +
310J PHE 3.1 16.7 + - - +
311J THR 3.9 3.6 - - - +
313J LEU* 1.3 85.0 - - - +
315J LEU* 1.3 58.8 + - - +
317J ALA* 3.0 23.1 + - - +
319J GLY 4.5 2.6 - - - +
321J GLY 3.9 14.6 + - - +
322J PHE 4.1 5.9 + - - -
323J ILE* 4.1 12.1 - - - +
354J CYS* 3.9 17.0 - - + +
355J HIS 4.3 0.3 - - - -
356J GLY* 3.4 13.9 + - - -
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Residues in contact with LEU 315 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311J THR* 2.9 33.8 + - + +
312J LEU* 2.9 12.9 + - + +
313J LEU 2.8 0.8 + - - -
314J ASN* 1.3 76.1 - - - +
316J VAL* 1.3 61.4 + - + +
335J VAL* 5.7 2.0 - - + -
338J LEU* 3.2 40.4 - - + -
343J ALA* 3.6 24.1 - - + +
344J HIS 3.8 13.7 - - - +
345J ALA* 3.7 27.8 - - + -
354J CYS* 3.9 11.9 - - + -
355J HIS 3.7 4.4 - - - +
356J GLY* 3.3 4.4 - - - -
357J VAL* 3.1 24.4 + - - +
360J LEU* 4.4 3.3 - - + +
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Residues in contact with VAL 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244J ILE* 3.9 29.4 - - + +
246J ARG* 5.2 1.2 + - - -
288J ARG* 3.3 21.9 + - - +
289J PRO* 4.5 5.4 - - + +
312J LEU* 3.6 8.5 - - + +
313J LEU 2.8 17.0 + - - +
315J LEU* 1.3 77.4 - - - +
317J ALA* 1.3 58.4 - - - +
356J GLY* 4.4 0.2 - - - -
357J VAL* 3.3 19.4 - - + +
358J GLU 4.7 8.7 - - - +
359J LYS* 5.2 0.7 - - + -
360J LEU* 3.9 34.1 - - + +
382J ILE* 4.3 14.8 - - + -
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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