Contacts of the helix formed by residues 300 - 313 (chain B) in PDB entry 3SSB
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B TYR* 3.3 22.8 - - - +
297B GLY 2.7 22.1 + - - -
298B SER 3.3 0.9 - - - +
299B THR* 1.3 82.6 + - - +
301B GLN* 1.3 63.8 + - - +
302B GLU* 3.2 15.8 + - - -
303B VAL* 3.1 23.2 + - - +
304B ALA* 3.2 19.8 + - - +
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Residues in contact with GLN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B VAL* 3.7 30.3 - - + +
258B ILE* 4.1 11.9 - - + -
299B THR 3.9 0.6 + - - -
300B SER* 1.3 71.2 - - - +
302B GLU* 1.3 68.1 + - - +
304B ALA* 3.3 15.4 + - - +
305B SER* 2.8 54.5 + - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ILE* 3.8 32.4 - - + +
262B LYS* 2.7 35.7 + - + -
266B ILE* 4.5 2.5 - - + -
292B ALA* 4.4 1.1 - - + -
296B TYR* 3.4 47.4 - - + +
300B SER* 3.2 17.4 - - - +
301B GLN* 1.3 81.4 + - - +
303B VAL* 1.3 63.5 + - - +
305B SER* 3.2 2.1 + - - -
306B VAL* 3.1 29.5 + - - +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B VAL* 4.2 6.1 - - + +
292B ALA* 3.4 11.7 - - + -
293B THR* 3.4 40.2 - - - +
297B GLY 3.3 14.6 - - - +
298B SER* 3.9 15.3 - - - +
300B SER* 3.1 25.0 + - - +
302B GLU* 1.3 75.7 - - - +
304B ALA* 1.3 63.5 + - - +
306B VAL* 3.2 4.7 + - - +
307B LYS* 3.1 49.9 + - + +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B SER 3.2 12.0 + - - +
301B GLN* 3.7 19.3 - - - +
303B VAL* 1.3 80.3 - - - +
305B SER* 1.3 57.0 - - - +
307B LYS* 3.3 10.2 + - - +
308B GLN* 2.9 34.7 + - + +
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 4.0 5.5 - - - +
255B VAL* 3.8 7.3 - - - +
256B VAL* 2.6 31.1 + - - +
258B ILE* 3.8 17.3 - - - +
301B GLN* 2.8 38.8 + - - +
302B GLU 3.2 4.2 + - - -
304B ALA* 1.3 71.8 - - - +
306B VAL* 1.3 60.2 + - - +
308B GLN* 4.4 4.5 - - - +
309B ALA* 2.9 31.7 + - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 4.1 21.3 - - + -
266B ILE* 4.0 29.6 - - + -
288B ALA* 3.6 29.2 - - + +
289B VAL* 3.8 19.3 - - + +
292B ALA* 4.0 9.4 - - + -
302B GLU 3.1 18.7 + - - +
303B VAL* 3.7 7.4 - - - +
305B SER* 1.3 75.6 - - - +
307B LYS* 1.3 63.3 + - - +
309B ALA* 3.7 0.5 - - - +
310B PHE* 3.1 39.7 + - + -
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ARG* 3.6 24.0 + - - +
289B VAL* 3.6 38.3 - - + +
298B SER 5.5 1.2 + - - -
303B VAL* 3.1 28.5 + - + +
304B ALA* 3.6 11.0 - - - +
306B VAL* 1.3 76.6 - - - +
308B GLN* 1.3 56.6 + - - +
310B PHE 3.5 0.2 + - - -
311B ASP* 2.9 37.0 + - - +
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B VAL* 3.6 17.4 - - - +
254B SER 3.1 22.5 + - - +
255B VAL* 3.9 16.4 - - + +
256B VAL 5.7 0.2 - - - +
304B ALA* 2.9 23.3 + - + +
305B SER* 3.9 6.7 - - - +
307B LYS* 1.3 73.1 - - - +
309B ALA* 1.3 57.8 + - - +
311B ASP* 3.4 24.8 + - - +
312B ALA* 2.8 29.5 + - - +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ALA* 3.5 16.8 - - + +
243B LEU* 4.1 10.7 - - + +
244B ILE* 3.4 27.1 - - + -
255B VAL* 3.9 12.2 - - + +
305B SER 2.9 18.1 + - - +
306B VAL 3.7 2.5 - - - +
307B LYS 3.4 0.2 - - - -
308B GLN* 1.3 73.7 - - - +
310B PHE* 1.3 64.3 + - - +
312B ALA* 3.2 11.9 + - - +
313B VAL* 3.3 18.9 + - - +
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Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ILE* 3.9 24.5 - - + -
240B ALA* 4.3 13.7 - - + -
244B ILE* 4.4 7.0 - - + -
267B PHE* 4.2 16.4 - + - -
281B PHE 4.5 0.2 - - - -
284B LEU* 3.9 26.7 - - + -
285B ARG* 3.7 38.4 - - + +
288B ALA* 4.0 9.9 - - + -
306B VAL* 3.1 46.8 + - + +
309B ALA* 1.3 73.2 - - - +
311B ASP* 1.3 65.3 + - - +
313B VAL* 3.2 6.2 + - + +
314B GLY 3.1 4.9 + - - -
315B VAL* 3.0 53.0 + - + +
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Residues in contact with ASP 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B HIS* 4.7 1.7 + - - -
253B VAL* 5.1 5.1 - - + +
285B ARG* 2.8 29.6 + - - +
307B LYS* 2.9 23.2 + - - +
308B GLN* 3.4 30.5 + - - +
310B PHE* 1.3 75.9 - - - +
312B ALA* 1.3 57.9 + - - +
314B GLY* 3.0 20.1 + - - -
315B VAL 4.5 2.0 - - - +
316B LYS* 3.2 29.3 + - - +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B HIS* 3.4 15.9 + - - -
243B LEU* 3.9 20.9 - - + -
250B HIS* 3.5 23.2 - - + +
251B TYR* 4.4 1.9 - - - +
253B VAL* 3.9 31.4 - - + +
255B VAL* 4.3 3.8 - - + -
308B GLN 2.8 19.9 + - - +
309B ALA 3.2 7.3 + - - +
311B ASP* 1.3 72.2 - - - +
313B VAL* 1.3 59.5 + - - +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASP 3.7 18.4 - - - +
216B HIS* 3.6 9.0 - - - -
217B TYR* 2.7 31.4 + - - +
236B ILE* 3.6 37.8 - - + +
237B ILE* 5.6 0.2 - - + -
239B LYS* 3.8 20.0 - - + -
240B ALA* 3.9 12.8 - - + +
243B LEU* 4.5 2.0 - - + -
250B HIS* 4.1 2.5 - - + -
309B ALA 3.3 13.2 + - - +
310B PHE* 3.4 18.4 - - + +
311B ASP 3.2 0.2 - - - -
312B ALA* 1.3 77.4 - - - +
314B GLY* 1.3 54.4 - - - +
315B VAL* 3.6 8.2 + - + -
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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