Contacts of the helix formed by residues 306 - 316 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232F ARG 5.2 0.9 - - - +
233F ILE* 3.7 17.9 - - + +
236F GLY* 3.4 44.4 - - - +
237F THR 3.7 1.6 - - - -
240F VAL* 3.8 18.2 - - + -
259F LEU* 5.6 0.7 - - + -
262F VAL* 4.0 12.8 - - + -
302F PHE* 3.8 16.2 - - + -
303F PRO* 3.0 27.0 + - + +
305F ASP* 1.3 78.0 - - - +
307F GLN* 1.3 64.7 + - - +
309F GLN* 3.3 34.7 + - + +
310F PHE* 3.1 33.9 + - + -
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Residues in contact with GLN 307 (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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296F THR* 3.9 14.4 - - + -
302F PHE* 4.1 6.5 - - + -
303F PRO 3.6 2.4 + - - -
304F THR 2.9 14.3 + - - +
305F ASP 3.4 0.2 - - - -
306F MET* 1.3 77.2 - - - +
308F ALA* 1.3 60.5 + - - +
310F PHE* 3.3 3.1 + - - -
311F THR* 2.8 35.9 + - - -
323F ILE* 3.6 25.6 - - + +
325F GLU* 3.0 28.3 + - + +
331F ARG* 3.0 31.7 + - - +
332F PHE* 3.7 17.2 - - + -
334F HIS* 2.9 28.9 + - - -
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Residues in contact with ALA 308 (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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304F THR 4.6 1.2 + - - -
307F GLN* 1.3 77.6 + - - +
309F GLN* 1.3 65.3 + - - +
311F THR* 3.3 3.3 + - - -
312F LEU* 3.1 17.8 + - - +
334F HIS* 3.4 41.5 - - + +
338F LEU* 5.1 0.3 - - - +
372F ALA* 3.4 38.5 - - + +
375F SER* 3.5 12.0 + - - +
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Residues in contact with GLN 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F ILE* 4.2 0.8 - - - +
237F THR* 3.1 36.8 + - + +
240F VAL* 3.8 22.2 - - + +
305F ASP 3.1 27.9 + - - +
306F MET* 3.4 32.8 - - + +
307F GLN 3.2 0.4 - - - -
308F ALA* 1.3 85.1 + - - +
310F PHE* 1.3 58.7 + - - +
312F LEU* 3.2 7.3 + - - +
313F LEU 3.1 20.3 + - - -
371F ARG 4.3 8.3 + - - -
372F ALA* 4.6 2.3 - - - -
374F ALA* 5.3 0.7 - - + -
375F SER* 4.2 16.8 - - - +
378F LEU* 4.8 4.5 - - + -
399F TYR* 3.6 12.1 + - - -
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Residues in contact with PHE 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F VAL* 3.7 17.9 - - + -
262F VAL* 4.0 14.8 - - + -
265F LYS* 3.6 23.6 - - + -
266F LEU* 3.6 36.1 - - + -
269F ALA* 5.8 0.2 - - + -
292F VAL* 4.3 19.7 - - + -
294F VAL* 4.5 3.8 - - + -
302F PHE* 3.3 40.2 - + + -
306F MET* 3.1 25.8 + - + +
307F GLN 4.1 0.9 - - - +
309F GLN* 1.3 73.0 - - - +
311F THR* 1.3 66.0 + - - +
313F LEU* 3.3 16.8 + - + +
314F ASN* 3.0 23.0 + - - +
323F ILE* 3.5 18.5 - - + +
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Residues in contact with THR 311 (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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307F GLN* 2.8 31.2 + - - -
308F ALA 3.4 8.5 - - - -
309F GLN 3.2 0.2 - - - -
310F PHE* 1.3 75.8 - - - +
312F LEU* 1.3 63.2 + - - +
314F ASN* 3.3 4.9 + - - +
315F LEU* 2.9 45.3 + - + +
323F ILE* 3.3 14.9 - - - +
334F HIS* 4.0 15.7 - - + +
335F VAL* 4.3 15.0 - - + -
338F LEU* 4.8 0.7 - - + -
352F VAL* 4.3 10.0 - - + +
354F CYS* 4.2 13.9 - - - -
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Residues in contact with LEU 312 (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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240F VAL* 5.6 0.4 - - + -
244F ILE* 3.7 18.2 - - + -
308F ALA 3.1 13.5 + - - +
309F GLN 3.5 9.2 - - - +
310F PHE 3.2 0.2 - - - -
311F THR* 1.3 73.6 - - - +
313F LEU* 1.3 67.8 + - - +
315F LEU* 2.9 16.1 + - + +
316F VAL* 3.4 15.5 + - + +
338F LEU* 4.3 20.8 - - + +
360F LEU* 4.0 27.1 - - + -
375F SER* 3.4 28.9 - - - +
378F LEU* 3.6 17.3 - - + -
379F ALA* 3.6 20.4 - - + +
382F ILE* 4.8 2.5 - - + -
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Residues in contact with LEU 313 (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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240F VAL* 4.7 6.5 - - + -
243F ALA* 4.1 18.4 - - + -
244F ILE* 3.7 20.8 - - + +
266F LEU* 4.1 25.8 - - + -
269F ALA* 4.1 25.6 - - + -
289F PRO* 4.2 13.4 - - + +
290F LYS 4.2 6.5 - - - +
292F VAL* 4.5 8.5 - - + -
309F GLN 3.1 11.5 + - - +
310F PHE* 3.3 19.0 + - + +
312F LEU* 1.3 77.7 - - - +
314F ASN* 1.3 76.3 + - - +
316F VAL* 3.3 5.4 + - - +
317F ALA* 3.2 22.2 + - + +
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Residues in contact with ASN 314 (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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291F ALA* 3.4 7.1 - - - +
292F VAL* 2.8 53.7 + - - +
310F PHE 3.0 11.6 + - - +
311F THR 3.8 5.4 - - - +
312F LEU 3.2 0.2 - - - -
313F LEU* 1.3 78.5 - - - +
315F LEU* 1.3 63.2 + - - +
317F ALA* 3.1 16.9 + - - +
319F GLY 4.9 1.9 - - - +
321F GLY* 3.8 18.9 + - - +
323F ILE* 3.9 22.2 - - - +
354F CYS* 3.7 19.8 - - + +
356F GLY* 3.5 13.3 + - - -
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Residues in contact with LEU 315 (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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311F THR* 2.9 32.6 + - + +
312F LEU* 2.9 9.7 + - + +
314F ASN* 1.3 77.1 - - - +
316F VAL* 1.3 60.7 + - + +
317F ALA 3.5 0.2 - - - -
335F VAL* 5.6 3.6 - - - +
338F LEU* 3.6 30.5 - - + -
343F ALA* 3.9 26.9 - - + +
344F HIS 3.4 26.5 - - - +
345F ALA* 3.8 14.8 - - + -
354F CYS* 3.7 18.2 - - + -
355F HIS 4.3 3.5 - - - +
356F GLY* 3.4 3.1 - - - -
357F VAL* 3.0 29.8 + - - +
360F LEU* 4.9 1.2 - - + +
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Residues in contact with VAL 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F ILE* 4.2 29.4 - - + +
288F ARG* 3.2 22.3 + - - +
289F PRO* 4.2 6.9 - - + +
312F LEU* 3.7 11.2 - - + +
313F LEU 3.5 10.3 - - - +
315F LEU* 1.3 82.4 - - - +
317F ALA* 1.3 60.3 + - - +
357F VAL* 3.3 16.0 - - + +
358F GLU 5.0 6.8 - - - +
359F LYS* 5.5 0.4 - - - -
360F LEU* 3.8 36.8 - - + +
382F ILE* 4.1 13.9 - - + -
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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