Contacts of the helix formed by residues 255 - 267 (chain B) in PDB entry 3C6M
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 ASP 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B ILE* 3.8 21.5 - - + +
254B GLU* 1.3 73.7 - - - +
256B CYS* 1.3 73.7 + - - +
257B ILE* 3.1 16.2 + - - +
258B PRO* 3.3 35.1 - - + +
259B VAL* 3.3 12.6 - - - +
282B ILE 4.5 5.0 - - - +
283B SER* 4.9 1.0 - - - -
284B THR* 4.5 17.7 + - - -
294B PHE* 6.2 0.2 - - - -
401B MTA 3.0 25.6 + - - -
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Residues in contact with CYS 256 (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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197B LEU* 4.0 20.9 - - + -
219B VAL* 3.7 22.9 - - + +
254B GLU 3.6 1.0 + - - -
255B ASP* 1.3 75.0 + - - +
257B ILE* 1.3 66.1 + - - +
259B VAL* 3.2 1.6 + - + +
260B LEU* 2.7 51.4 + - - +
277B LEU* 4.3 21.1 - - - -
298B ILE* 5.1 2.0 - - - -
401B MTA 3.1 32.9 + - + +
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Residues in contact with ILE 257 (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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255B ASP* 3.1 13.7 + - - +
256B CYS* 1.3 84.3 - - - +
258B PRO* 1.4 73.5 - - + +
260B LEU* 3.0 9.4 + - + +
261B LYS* 3.0 47.7 + - - +
285B SER* 5.9 2.7 - - - +
294B PHE* 4.0 24.2 - - + -
297B LEU* 4.5 10.8 - - + -
298B ILE* 3.9 26.9 - - + -
301B LEU* 3.8 21.8 - - + -
401B MTA 5.0 0.4 - - - +
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Residues in contact with PRO 258 (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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254B GLU* 5.0 5.6 - - + +
255B ASP* 3.3 35.9 - - + +
257B ILE* 1.4 97.2 - - + +
259B VAL* 1.3 59.7 + - - +
261B LYS* 3.2 10.8 + - + +
262B ARG* 3.0 37.8 + - - +
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Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LEU* 5.4 0.2 - - + -
219B VAL* 3.6 28.3 - - + -
252B LEU* 4.4 6.5 - - + -
254B GLU* 3.5 34.8 - - + +
255B ASP 3.3 15.9 - - - +
256B CYS* 3.2 6.7 + - - +
257B ILE 3.1 0.8 - - - -
258B PRO* 1.3 76.2 - - - +
260B LEU* 1.3 64.7 + - + +
261B LYS 3.3 0.2 + - - -
262B ARG* 3.5 12.4 - - - +
263B TYR* 3.0 56.8 + - + +
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Residues in contact with LEU 260 (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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195B LEU* 3.7 29.8 - - + -
197B LEU* 3.8 27.6 - - + -
256B CYS* 2.7 36.0 + - - +
257B ILE* 3.4 10.1 - - + +
259B VAL* 1.3 73.1 - - + +
261B LYS* 1.3 56.0 + - - +
263B TYR* 3.4 5.0 + - + +
264B ALA* 3.0 29.0 + - - +
298B ILE* 4.5 7.0 - - + -
301B LEU* 3.8 36.1 - - + +
302B SER* 4.3 7.0 - - - +
305B VAL* 3.9 23.1 - - + +
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Residues in contact with LYS 261 (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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257B ILE* 3.0 37.7 + - + +
258B PRO* 3.2 11.2 + - + +
260B LEU* 1.3 72.4 - - - +
262B ARG* 1.3 56.0 + - - +
264B ALA* 3.2 6.3 + - - +
265B LYS* 2.7 38.6 + - - +
297B LEU* 5.6 6.4 - - - +
301B LEU* 4.0 24.0 - - + -
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Residues in contact with ARG 262 (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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252B LEU* 5.3 4.8 - - - +
254B GLU* 3.3 35.7 + - - -
258B PRO* 3.0 27.2 + - - +
259B VAL* 3.5 17.6 - - - +
261B LYS* 1.3 74.8 - - - +
263B TYR* 1.3 77.6 + - + +
265B LYS* 3.2 6.8 + - - +
266B GLU* 3.0 41.7 + - - +
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Residues in contact with TYR 263 (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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195B LEU* 3.8 19.7 - - + -
217B THR* 3.6 19.3 - - + +
250B GLN* 4.4 3.3 + - - -
252B LEU* 3.7 14.9 - - + +
259B VAL* 3.0 41.4 + - + +
260B LEU* 3.8 4.9 - - - +
261B LYS 3.3 0.2 - - - -
262B ARG* 1.3 86.8 - - + +
264B ALA* 1.3 58.6 + - - +
266B GLU* 3.3 19.6 + - - +
267B GLY 2.9 8.5 + - - -
268B ARG* 2.8 60.5 + - + +
270B PHE* 3.6 31.9 - + + -
305B VAL* 3.9 12.6 - - + -
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Residues in contact with ALA 264 (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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260B LEU 3.0 18.2 + - - +
261B LYS* 3.6 5.6 - - - +
263B TYR* 1.3 75.0 - - - +
265B LYS* 1.3 57.8 + - - +
267B GLY* 2.7 26.6 + - - +
268B ARG 4.8 0.4 - - - -
301B LEU* 5.4 5.6 - - + +
304B LYS* 4.3 24.2 - - + +
305B VAL* 3.5 15.5 - - + +
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Residues in contact with LYS 265 (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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261B LYS 2.7 22.5 + - - +
262B ARG* 3.7 5.8 - - - +
264B ALA* 1.3 75.0 - - - +
266B GLU* 1.3 58.5 + - - +
267B GLY 3.4 0.5 + - - -
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Residues in contact with GLU 266 (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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262B ARG* 3.0 33.9 + - - +
263B TYR* 3.5 28.5 - - - +
265B LYS* 1.3 73.9 - - - +
267B GLY* 1.3 62.7 + - - +
268B ARG* 3.4 21.0 + - + +
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Residues in contact with GLY 267 (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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263B TYR 2.9 0.2 + - - -
264B ALA* 2.7 24.9 + - - -
265B LYS 3.1 1.2 + - - -
266B GLU* 1.3 74.2 - - - +
268B ARG* 1.3 62.8 + - - +
269B GLU* 3.9 9.8 + - - +
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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