Contacts of the helix formed by residues 284 - 302 (chain B) in PDB entry 6S6A
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 ALA 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B SER* 1.3 73.2 - - - +
285B ALA* 1.3 54.3 + - - +
286B THR* 3.3 4.5 + - - -
287B LEU* 3.2 22.6 + - - +
288B ILE* 2.8 47.9 + - + +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 4.9 13.2 - - + -
282B PRO* 4.3 15.7 - - + -
283B SER 2.3 25.4 + - - +
284B ALA* 1.3 64.1 - - - +
286B THR* 1.3 52.4 + - - +
288B ILE* 4.3 6.0 - - - +
289B ASN* 2.9 43.5 + - - +
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Residues in contact with THR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ILE* 3.5 12.2 - - + +
262B PHE* 3.8 26.2 - - + -
274B VAL* 5.1 1.3 - - + -
276B MET* 3.8 42.2 - - + -
281B ILE* 5.7 6.7 - - + +
283B SER* 3.6 24.8 + - - +
284B ALA 3.9 0.5 + - - -
285B ALA* 1.3 73.3 - - - +
287B LEU* 1.3 59.9 + - - +
289B ASN* 3.4 9.1 - - - +
290B ILE* 2.9 35.9 + - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B SER* 6.3 1.6 - - - -
253B GLU* 5.7 3.1 - - - +
262B PHE* 3.9 32.1 - - + -
263B ILE 6.1 1.1 - - - +
264B ASP* 4.3 15.3 - - + +
283B SER* 5.6 1.3 - - - +
284B ALA* 3.2 28.1 + - - +
286B THR* 1.3 73.3 - - - +
288B ILE* 1.3 66.1 + - + +
290B ILE* 3.4 14.3 + - + +
291B ARG* 2.8 47.1 + - - +
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Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ALA* 2.8 37.8 + - + +
285B ALA* 4.3 4.9 - - - +
287B LEU* 1.3 74.5 - - + +
289B ASN* 1.3 58.4 + - - +
291B ARG* 2.9 20.1 + - - +
292B ASN* 2.8 56.1 + - - +
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Residues in contact with ASN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 3.9 4.9 - - + -
197B ILE* 5.6 5.4 - - - +
198B ILE* 3.2 44.2 + - + +
281B ILE* 6.2 2.0 - - - +
285B ALA* 2.9 26.0 + - - +
286B THR* 3.4 2.1 - - - +
287B LEU 3.2 0.4 - - - -
288B ILE* 1.3 78.4 - - - +
290B ILE* 1.3 64.4 + - - +
292B ASN* 3.3 11.0 + - - +
293B ALA* 3.0 24.6 + - - +
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 4.1 15.5 - - + -
198B ILE* 4.0 11.2 - - + +
262B PHE* 4.2 25.4 - - + -
264B ASP* 4.5 11.0 - - + +
266B PHE* 3.9 22.5 - - + -
272B VAL* 4.1 11.9 - - + -
274B VAL* 4.3 12.6 - - + -
286B THR* 2.9 26.8 + - - +
287B LEU* 3.5 21.3 - - + +
289B ASN* 1.3 68.0 - - - +
291B ARG* 1.3 65.1 + - - +
293B ALA* 3.0 14.7 + - - +
294B ARG* 3.2 29.9 + - - +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B SER* 6.0 0.8 - - - -
264B ASP* 3.5 28.3 + - - -
287B LEU* 2.8 47.7 + - - +
288B ILE* 3.1 21.8 - - - +
290B ILE* 1.3 74.5 - - - +
292B ASN* 1.3 63.1 + - - +
293B ALA 3.5 0.2 + - - -
294B ARG* 3.6 42.3 + - - +
295B LYS* 3.4 20.6 - - - +
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Residues in contact with ASN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 2.8 45.8 + - - +
289B ASN* 3.8 11.1 + - - +
291B ARG* 1.3 77.6 - - - +
293B ALA* 1.3 58.1 + - - +
294B ARG 3.5 0.2 - - - -
295B LYS* 3.2 26.3 - - - +
296B HIS* 3.8 10.9 + - - +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 3.3 40.6 - - + -
266B PHE* 3.9 9.0 - - + -
289B ASN 3.0 6.1 + - - +
290B ILE 3.0 6.2 + - - +
292B ASN* 1.3 73.5 - - - +
294B ARG* 1.3 67.6 + - - +
295B LYS 3.0 2.9 - - - -
296B HIS* 2.8 26.3 + - + +
297B PHE* 3.4 17.2 + - + -
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Residues in contact with ARG 294 (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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264B ASP* 3.4 26.9 + - - -
265B ILE* 3.1 27.6 + - - +
266B PHE* 3.1 37.5 - - + +
267B THR* 4.4 0.9 - - - +
290B ILE* 3.2 16.9 + - - +
291B ARG* 3.6 54.9 - - - +
292B ASN 3.5 0.4 - - - -
293B ALA* 1.3 75.2 - - - +
295B LYS* 1.3 71.1 + - - +
296B HIS 3.2 0.2 + - - -
297B PHE* 3.3 1.5 + - - +
298B GLU* 2.8 29.1 + - + +
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Residues in contact with LYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG 3.4 18.2 - - - +
292B ASN* 3.2 24.7 - - - +
293B ALA 3.0 0.2 - - - -
294B ARG* 1.3 86.0 - - - +
296B HIS* 1.3 72.4 - - + +
298B GLU* 3.5 6.9 + - - +
299B LYS* 3.4 19.0 + - - +
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Residues in contact with HIS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASN* 5.4 7.6 + - - +
292B ASN 3.8 18.9 + - - -
293B ALA* 2.8 14.9 + - + +
295B LYS* 1.3 83.7 - - + +
297B PHE* 1.3 66.7 + + + +
299B LYS* 3.1 31.8 - - - +
300B LEU* 3.9 8.8 + - - +
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Residues in contact with PHE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 4.0 23.5 - - + +
190B ASN* 3.5 42.6 - - + -
191B LEU* 3.6 29.6 - - + -
194B PHE* 4.1 13.9 - - + -
205B LEU* 5.3 1.8 - - + -
266B PHE* 3.3 37.9 - + + -
267B THR* 3.8 12.1 - - + -
293B ALA* 3.5 16.8 - - + -
294B ARG 3.3 3.0 + - - +
296B HIS* 1.3 80.7 - + + +
298B GLU* 1.3 65.5 + - - +
300B LEU* 3.0 27.6 + - + +
301B GLU* 3.6 8.1 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE 4.8 0.3 - - - +
267B THR* 3.3 17.0 - - + +
268B SER* 2.4 44.2 + - - -
294B ARG* 2.8 23.3 + - + +
295B LYS* 3.6 6.7 - - - +
297B PHE* 1.3 71.1 - - - +
299B LYS* 1.3 64.4 + - - +
301B GLU* 2.9 31.0 + - - +
302B ARG* 4.0 9.1 + - + +
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Residues in contact with LYS 299 (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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295B LYS 3.4 8.3 + - - +
296B HIS* 3.1 21.9 + - - +
298B GLU* 1.3 77.8 - - - +
300B LEU* 1.3 60.8 + - + +
301B GLU 3.4 1.0 + - - -
302B ARG* 3.5 17.5 + - - +
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Residues in contact with LEU 300 (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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55B ASN* 4.2 11.1 + - - -
183B ASN* 6.2 0.2 - - + -
186B GLN* 3.1 37.0 - - + +
187B LEU* 4.1 35.4 - - + +
190B ASN* 3.4 27.4 - - - +
296B HIS 4.2 5.6 - - - +
297B PHE* 3.0 25.3 + - + +
299B LYS* 1.3 75.7 - - + +
301B GLU* 1.3 66.2 - - - +
302B ARG 3.3 6.9 + - - +
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Residues in contact with GLU 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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53B LEU* 3.0 30.9 - - - +
54B GLY 3.6 9.5 - - - +
55B ASN* 3.5 26.8 - - - +
267B THR* 2.4 39.5 + - - +
268B SER* 4.5 0.4 - - - +
269B ASN* 2.9 32.0 + - - +
270B THR* 4.5 3.9 - - - +
297B PHE 3.6 9.6 + - - +
298B GLU* 2.9 26.3 + - - +
300B LEU* 1.3 79.5 - - - +
302B ARG* 1.3 65.2 + - - +
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Residues in contact with ARG 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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51B ARG* 5.9 3.6 - - - +
53B LEU 4.6 2.2 + - - -
54B GLY* 3.9 29.7 + - - -
55B ASN* 5.6 1.8 - - - +
268B SER* 5.4 4.4 + - - -
269B ASN* 4.8 7.9 + - - +
298B GLU* 4.0 8.9 + - + +
299B LYS 3.5 16.1 + - - +
300B LEU 3.3 6.1 - - - +
301B GLU* 1.3 93.2 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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