Contacts of the helix formed by residues 300 - 313 (chain A) in PDB entry 5FSJ
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 SER 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A TYR* 3.3 24.0 - - - +
297A GLY 2.7 22.4 + - - -
298A SER 3.3 1.0 - - - +
299A THR* 1.3 82.8 + - - +
301A GLN* 1.3 64.5 + - - +
302A GLU* 3.2 15.8 + - - -
303A VAL* 3.1 20.4 + - - +
304A ALA* 3.2 19.5 + - - +
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Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A VAL* 3.7 30.0 - - + +
258A ILE* 4.3 11.0 - - + -
299A THR 3.9 0.4 + - - -
300A SER* 1.3 74.3 - - - +
302A GLU* 1.3 65.4 + - - +
304A ALA* 3.1 14.5 + - - +
305A SER* 2.8 53.2 + - - +
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ILE* 3.8 33.8 - - + +
262A LYS* 2.6 38.3 + - + -
266A ILE* 4.6 2.5 - - + -
292A ALA* 4.4 1.1 - - - -
296A TYR* 3.5 41.6 - - + +
300A SER* 3.1 18.5 - - - +
301A GLN* 1.3 81.2 + - - +
303A VAL* 1.3 62.6 + - - +
305A SER* 3.3 1.7 + - - -
306A VAL* 3.0 28.6 + - - +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A VAL* 4.2 8.1 - - + +
292A ALA* 3.5 10.5 - - + -
293A THR* 3.4 39.0 - - - +
297A GLY 3.3 22.4 - - - +
298A SER* 3.9 15.7 - - - +
300A SER* 3.1 11.9 + - - +
302A GLU* 1.3 76.9 - - - +
304A ALA* 1.3 64.9 + - - +
306A VAL* 3.2 5.2 + - - +
307A LYS* 3.1 48.7 + - - +
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A SER 3.2 10.6 + - - +
301A GLN* 3.1 20.7 + - - +
303A VAL* 1.3 79.5 - - - +
305A SER* 1.3 57.2 + - - +
307A LYS* 3.3 10.9 + - - +
308A GLN* 3.0 32.8 + - + +
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 4.2 6.5 - - - +
255A VAL* 3.8 8.2 - - - +
256A VAL* 2.6 30.7 + - - +
258A ILE* 3.8 16.1 - - - +
301A GLN* 2.8 31.8 + - - +
302A GLU 3.8 3.1 - - - -
304A ALA* 1.3 74.7 - - - +
306A VAL* 1.3 66.3 + - - +
308A GLN* 3.3 6.2 + - - +
309A ALA* 2.9 26.6 + - - +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 4.2 21.3 - - + -
266A ILE* 4.1 25.8 - - + -
288A ALA* 3.8 28.0 - - + +
289A VAL* 3.8 20.9 - - + +
292A ALA* 4.1 9.2 - - + -
302A GLU 3.0 15.3 + - - +
303A VAL* 3.2 8.5 + - - +
305A SER* 1.3 75.7 - - - +
307A LYS* 1.3 63.9 + - - +
309A ALA* 3.3 1.0 + - - +
310A PHE* 3.1 35.5 + - + -
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Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ARG* 3.6 26.2 + - - +
289A VAL* 3.9 26.8 - - + +
298A SER 5.3 2.2 + - - -
303A VAL* 3.1 36.2 + - + +
304A ALA* 3.6 9.9 - - - +
306A VAL* 1.3 77.4 - - - +
308A GLN* 1.3 57.9 + - - +
310A PHE 3.4 0.2 + - - -
311A ASP* 2.9 36.8 + - - +
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A VAL* 3.6 19.5 - - - +
254A SER* 2.7 35.5 + - - +
255A VAL* 3.8 10.5 - - + -
256A VAL 5.6 0.9 - - - +
304A ALA* 3.0 20.9 + - + +
305A SER* 3.3 5.8 + - - +
307A LYS* 1.3 78.2 - - + +
309A ALA* 1.3 58.8 + - - +
311A ASP* 3.3 18.1 + - - +
312A ALA* 2.8 29.3 + - - +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ALA* 3.6 17.1 - - + +
243A LEU* 4.1 11.2 - - + +
244A ILE* 3.4 34.3 - - + -
255A VAL* 3.8 12.0 - - + +
305A SER 2.9 10.7 + - - +
306A VAL 3.7 1.8 - - - +
308A GLN* 1.3 78.3 - - - +
310A PHE* 1.3 62.9 + - - +
312A ALA* 3.2 12.2 + - - +
313A VAL* 3.3 18.0 + - - +
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Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ILE* 4.2 13.5 - - + -
240A ALA* 4.4 12.6 - - + -
244A ILE* 4.3 14.6 - - + -
267A PHE* 4.3 11.7 - + - -
281A PHE 4.7 0.4 - - - -
284A LEU* 4.0 33.9 - - + -
285A ARG* 3.6 32.8 - - + +
288A ALA* 4.0 11.2 - - + -
306A VAL* 3.1 45.4 + - + +
309A ALA* 1.3 73.4 - - - +
311A ASP* 1.3 66.7 + - - +
313A VAL* 3.3 6.7 + - + +
314A GLY 3.1 4.2 + - - -
315A VAL* 2.9 59.9 + - + +
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Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A HIS* 4.8 1.4 + - - -
253A VAL* 4.3 15.8 - - + +
285A ARG* 2.7 23.9 + - - +
307A LYS* 2.9 18.0 + - - +
308A GLN* 3.4 23.6 - - - +
310A PHE* 1.3 76.0 - - - +
312A ALA* 1.3 62.9 + - - +
314A GLY* 3.0 14.8 + - - +
315A VAL 4.5 0.9 - - - -
316A LYS* 2.5 38.5 + - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A HIS* 3.3 16.6 + - - -
243A LEU* 3.9 21.5 - - + -
250A HIS* 3.5 24.4 - - + +
251A TYR* 4.1 2.9 - - - +
253A VAL* 3.8 29.5 - - + +
255A VAL* 4.3 2.2 - - + -
308A GLN 2.8 17.0 + - - +
309A ALA 3.2 7.6 + - - +
311A ASP* 1.3 77.0 - - - +
313A VAL* 1.3 57.8 + - - +
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ASP 3.7 18.6 - - - +
216A HIS* 3.6 9.2 - - - -
217A TYR* 2.8 27.7 + - - +
236A ILE* 3.7 37.0 - - + +
237A ILE* 5.7 0.2 - - + -
239A LYS* 3.8 18.8 - - + -
240A ALA* 3.9 15.7 - - + +
243A LEU* 4.5 2.0 - - + -
250A HIS* 4.1 3.1 - - + -
309A ALA 3.3 13.6 + - - +
310A PHE* 3.5 14.8 - - + +
312A ALA* 1.3 76.4 - - - +
314A GLY* 1.3 57.2 + - - +
315A VAL* 4.1 8.7 - - + -
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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