Contacts of the helix formed by residues 256 - 276 (chain w) in PDB entry 6AH0
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 256 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254w GLU 3.8 3.0 + - - -
255w LEU* 1.3 66.7 - - - +
257w SER* 1.3 65.1 + - - +
258w LEU 3.3 2.5 - - - -
259w GLY* 3.3 7.2 + - - +
260w LEU* 3.3 16.6 + - - -
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Residues in contact with SER 257 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255w LEU 3.0 8.7 + - - -
256w ALA* 1.3 71.8 - - - +
258w LEU* 1.3 58.0 + - - +
260w LEU* 3.2 3.7 + - - +
261w ASP* 2.9 25.5 + - - -
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Residues in contact with LEU 258 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256w ALA 3.3 0.6 - - - -
257w SER* 1.3 75.5 - - - +
259w GLY* 1.3 63.1 + - - +
261w ASP* 3.3 2.0 + - - +
262w ARG* 2.9 22.5 + - - -
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Residues in contact with GLY 259 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256w ALA* 3.3 9.3 + - - +
257w SER 3.3 0.8 - - - -
258w LEU* 1.3 76.3 - - - +
260w LEU* 1.3 55.9 + - - +
262w ARG* 3.4 0.9 + - - -
263w LEU* 2.9 27.0 + - - -
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Residues in contact with LEU 260 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256w ALA 3.3 8.7 + - - -
257w SER* 3.2 6.7 + - - +
259w GLY* 1.3 70.8 - - - +
261w ASP* 1.3 66.4 + - - +
263w LEU* 3.2 2.4 + - - +
264w LYS* 2.9 21.1 + - - -
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Residues in contact with ASP 261 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257w SER 2.9 14.2 + - - -
258w LEU* 3.3 3.6 + - - +
260w LEU* 1.3 76.0 - - - +
262w ARG* 1.3 56.7 + - - +
264w LYS* 3.2 1.6 + - - -
265w SER* 2.9 25.3 + - - -
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Residues in contact with ARG 262 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258w LEU 2.9 15.8 + - - -
259w GLY 3.8 0.9 - - - -
261w ASP* 1.3 71.7 - - - +
263w LEU* 1.3 66.2 + - - +
265w SER* 3.3 2.3 + - - +
266w ALA* 2.9 22.7 + - - -
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Residues in contact with LEU 263 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259w GLY 2.9 15.1 + - - -
260w LEU* 3.6 3.6 - - - +
262w ARG* 1.3 75.3 - - - +
264w LYS* 1.3 62.0 + - - +
266w ALA* 3.2 1.2 + - - -
267w LEU* 2.9 20.1 + - - -
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Residues in contact with LYS 264 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260w LEU 2.9 12.7 + - - -
261w ASP 3.7 2.9 - - - -
263w LEU* 1.3 73.1 - - - +
265w SER* 1.3 57.1 + - - +
267w LEU* 3.1 3.4 + - - +
268w LEU* 2.9 26.9 + - - -
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Residues in contact with SER 265 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261w ASP 2.9 14.6 + - - -
262w ARG* 3.3 3.6 + - - +
264w LYS* 1.3 73.7 - - - +
266w ALA* 1.3 56.8 + - - +
268w LEU* 3.1 3.1 + - - +
269w ALA* 2.9 25.1 + - - -
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Residues in contact with ALA 266 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262w ARG 2.9 14.2 + - - -
263w LEU 3.7 2.5 - - - -
265w SER* 1.3 72.9 - - - +
267w LEU* 1.3 60.1 + - - +
269w ALA* 4.4 1.1 - - - +
270w LEU* 2.9 28.9 + - - -
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Residues in contact with LEU 267 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263w LEU 2.9 13.2 + - - -
264w LYS* 3.1 4.7 + - - +
266w ALA* 1.3 77.2 - - - +
268w LEU* 1.3 60.8 + - - +
271w GLY* 3.1 24.3 + - - +
272w LEU 4.4 0.3 + - - -
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Residues in contact with LEU 268 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264w LYS 2.9 13.5 + - - -
265w SER* 3.1 5.3 + - - +
267w LEU* 1.3 80.3 - - - +
269w ALA* 1.3 61.5 + - - +
272w LEU* 3.8 13.2 + - - -
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Residues in contact with ALA 269 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265w SER 2.9 14.9 + - - -
266w ALA* 3.9 1.1 - - - +
268w LEU* 1.3 77.5 - - - +
270w LEU* 1.3 61.8 + - - +
272w LEU* 4.5 0.3 - - - -
273w LYS* 3.7 21.7 + - - +
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Residues in contact with LEU 270 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266w ALA 2.9 15.3 + - - -
269w ALA* 1.3 76.6 - - - +
271w GLY* 1.3 64.7 + - - +
273w LYS* 3.8 10.5 + - - +
274w CYS 4.6 2.9 + - - -
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Residues in contact with GLY 271 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267w LEU* 3.1 18.0 + - - +
270w LEU* 1.3 77.9 - - - +
272w LEU* 1.3 61.9 - - - +
273w LYS 3.5 0.3 + - - -
274w CYS* 4.4 2.9 + - - -
275w GLY 4.4 1.7 + - - -
276w GLY 4.2 0.3 + - - -
277w THR* 3.3 25.2 + - - -
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Residues in contact with LEU 272 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267w LEU 4.4 0.2 + - - -
268w LEU 3.8 15.5 + - - -
269w ALA 4.5 0.2 - - - -
270w LEU 3.4 0.6 - - - -
271w GLY* 1.3 77.0 - - - +
273w LYS* 1.3 63.9 + - - +
274w CYS 3.4 0.2 - - - -
276w GLY* 2.6 40.4 + - - -
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Residues in contact with LYS 273 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269w ALA 3.7 17.9 + - - +
270w LEU* 3.8 5.5 + - - +
271w GLY 3.4 1.6 - - - -
272w LEU* 1.3 76.8 - - - +
274w CYS* 1.3 63.8 + - - +
302w ALA* 6.2 0.2 - - - -
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Residues in contact with CYS 274 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270w LEU 4.6 3.6 + - - -
271w GLY 4.4 2.2 + - - -
272w LEU 3.4 0.4 - - - -
273w LYS* 1.3 81.8 - - - +
275w GLY* 1.3 56.1 + - - +
298w THR* 5.2 10.4 - - - +
302w ALA* 6.0 0.9 + - - -
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Residues in contact with GLY 275 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271w GLY 4.4 1.8 + - - -
272w LEU 3.3 0.8 + - - -
274w CYS* 1.3 77.6 - - - +
276w GLY* 1.3 60.4 + - - +
277w THR* 3.0 9.2 + - - +
278w LEU 3.6 14.7 + - - +
279w GLU* 5.3 0.3 - - - -
285w LEU* 4.1 14.0 - - - -
286w PHE 4.2 0.7 - - - +
298w THR* 6.3 1.6 - - - -
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Residues in contact with GLY 276 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272w LEU* 2.6 32.0 + - - -
275w GLY* 1.3 70.1 - - - -
277w THR* 1.3 50.2 - - - +
278w LEU* 2.2 24.7 + - - -
286w PHE 3.7 17.5 - - - +
287w SER* 5.5 1.6 - - - -
288w THR 5.6 3.4 + - - -
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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