Contacts of the helix formed by residues 277 - 291 (chain A) in PDB entry 1O5K
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 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A GLU* 2.9 17.1 + - - -
275A PRO 3.6 1.6 + - - -
276A ALA* 1.3 77.8 - - - +
278A GLU* 1.3 64.3 + - - +
279A LYS* 3.5 10.3 + - - +
280A THR* 3.1 24.4 + - - -
281A VAL* 3.0 19.7 + - - +
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Residues in contact with GLU 278 (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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276A ALA 3.9 0.4 + - - -
277A SER* 1.3 73.2 - - - +
279A LYS* 1.3 57.0 + - + +
281A VAL* 3.4 9.0 + - - +
282A GLU* 2.9 36.7 + - - +
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Residues in contact with LYS 279 (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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277A SER* 3.3 9.3 - - - +
278A GLU* 1.3 80.1 - - + +
280A THR* 1.3 61.3 - - - +
282A GLU* 3.4 18.6 + - - +
283A LEU* 3.1 22.9 + - - +
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Residues in contact with THR 280 (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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248A VAL* 3.6 28.7 - - + +
249A GLU* 2.7 36.2 + - - +
254A PRO* 4.2 11.4 - - + -
276A ALA* 4.0 10.5 - - + -
277A SER* 3.1 11.7 + - - -
279A LYS* 1.3 72.6 - - - +
281A VAL* 1.3 61.4 + - - +
283A LEU* 3.3 6.0 + - - +
284A LEU* 2.8 51.6 + - + +
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Residues in contact with VAL 281 (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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257A ALA* 4.3 10.1 - - + -
261A LEU* 3.8 16.9 - - + +
267A ASN* 5.2 4.0 - - - +
276A ALA* 4.0 19.3 - - + +
277A SER 3.0 17.3 + - - +
278A GLU* 3.7 9.9 - - - +
279A LYS 3.3 0.2 - - - -
280A THR* 1.3 76.8 - - - +
282A GLU* 1.3 53.2 + - - +
284A LEU* 3.4 9.3 + - - +
285A ARG* 2.8 57.1 + - - +
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Residues in contact with GLU 282 (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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278A GLU* 2.9 22.0 + - - +
279A LYS* 3.5 18.1 - - - +
281A VAL* 1.3 76.5 - - - +
283A LEU* 1.3 62.1 + - - +
285A ARG* 3.4 18.7 + - - +
286A ASN* 3.2 35.8 + - - +
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Residues in contact with LEU 283 (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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245A ALA* 3.9 23.3 - - + -
248A VAL* 3.9 31.0 - - + -
279A LYS 3.1 14.1 + - - +
280A THR* 3.3 8.0 + - - +
282A GLU* 1.3 73.0 - - - +
284A LEU* 1.3 67.9 + - + +
286A ASN* 3.2 11.2 + - + +
287A VAL* 2.9 38.1 + - + +
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Residues in contact with LEU 284 (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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242A LEU* 4.9 6.1 - - + -
245A ALA* 3.9 26.9 - - + +
246A LEU* 3.8 27.6 - - + -
254A PRO* 3.4 23.1 - - + +
257A ALA* 3.9 15.7 - - + -
258A ALA* 4.0 7.9 - - + +
261A LEU* 4.1 7.9 - - + -
280A THR* 2.8 42.2 + - + +
281A VAL* 3.7 4.5 - - - +
283A LEU* 1.3 74.8 - - + +
285A ARG* 1.3 53.6 + - - +
287A VAL* 4.5 2.9 - - - -
288A LEU* 2.7 46.2 + - + +
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Residues in contact with ARG 285 (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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261A LEU* 3.7 34.2 - - + +
281A VAL* 2.8 32.8 + - - +
282A GLU* 3.6 23.6 - - - +
283A LEU 3.2 0.4 - - - -
284A LEU* 1.3 70.6 - - - +
286A ASN* 1.3 59.7 + - - +
288A LEU* 3.9 1.6 - - - +
289A LYS* 3.0 51.1 + - + +
294A LEU* 3.8 21.2 - - + +
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Residues in contact with ASN 286 (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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282A GLU* 3.2 23.5 + - - +
283A LEU* 3.2 11.9 + - + +
285A ARG* 1.3 75.7 - - - +
287A VAL* 1.3 61.4 + - + +
289A LYS* 3.1 31.4 + - - +
290A GLU* 2.9 37.8 + - + +
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Residues in contact with VAL 287 (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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241A PRO* 3.9 23.1 - - + +
242A LEU* 3.6 46.4 - - + +
245A ALA* 4.4 4.5 - - + -
283A LEU* 2.9 37.3 + - + +
284A LEU* 3.9 4.7 - - - +
286A ASN* 1.3 75.0 - - + +
288A LEU* 1.3 62.8 + - - +
290A GLU* 3.4 7.6 + - + +
291A SER* 2.6 36.9 + - - +
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Residues in contact with LEU 288 (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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212A VAL* 4.5 6.3 - - + -
242A LEU* 3.9 24.9 - - + -
258A ALA* 4.0 35.9 - - + +
261A LEU* 4.2 14.4 - - + -
262A MET* 4.2 15.9 - - + -
284A LEU* 2.7 26.7 + - - +
285A ARG 3.9 1.6 - - - +
287A VAL* 1.3 71.8 - - - +
289A LYS* 1.3 58.7 + - - +
291A SER* 3.2 8.7 + - - -
293A LEU* 2.9 52.2 + - + -
294A LEU* 3.9 23.1 - - + -
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Residues in contact with LYS 289 (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* 3.0 37.5 + - + +
286A ASN* 3.1 32.1 + - - +
288A LEU* 1.3 73.5 - - - +
290A GLU* 1.3 67.2 + - + +
292A GLY* 3.1 13.5 + - - -
294A LEU* 3.6 33.3 - - + +
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Residues in contact with GLU 290 (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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286A ASN* 2.9 28.5 + - + +
287A VAL* 3.8 7.9 - - - +
289A LYS* 1.3 74.6 - - + +
291A SER* 1.3 59.6 + - - +
292A GLY 3.3 1.1 + - - -
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Residues in contact with SER 291 (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 GLN* 5.7 4.7 + - - +
238A LYS 5.1 7.2 + - - -
239A LEU* 5.8 5.4 - - - +
241A PRO* 5.8 1.0 - - - +
242A LEU* 4.5 10.5 + - - +
287A VAL* 2.6 31.9 + - - +
288A LEU* 3.6 4.9 - - - -
289A LYS 3.1 0.4 - - - -
290A GLU* 1.3 74.7 - - - +
292A GLY* 1.3 60.2 + - - +
293A LEU* 3.5 22.6 + - - +
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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