Contacts of the helix formed by residues 236 - 245 (chain A) in PDB entry 1O6K
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 GLU 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A GLY* 1.3 72.9 - - - -
237A LEU* 1.3 64.6 + - - +
238A PHE* 3.5 24.0 - - + +
239A PHE* 3.1 17.6 + - + +
240A HIS* 3.1 17.7 - - - -
278A LEU 3.8 5.8 - - - +
279A GLU* 3.7 16.1 - - - +
281A LEU 3.6 6.1 - - - -
282A MET* 3.8 7.0 - - + -
283A LEU* 5.6 0.2 - - - -
438A TYR 4.2 4.4 + - - +
439A PHE* 5.0 3.5 - - + -
440A ASP* 4.5 5.9 - - - +
443A PHE* 5.6 0.5 - - - -
1480A ANP 2.6 40.7 + - - +
6C ARG* 3.0 33.6 + - - -
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Residues in contact with LEU 237 (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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235A GLY 4.0 0.2 + - - -
236A GLU* 1.3 72.3 - - - +
238A PHE* 1.3 56.2 + - - +
240A HIS* 3.3 6.6 + - + +
241A LEU* 2.9 32.7 + - - +
247A PHE* 4.3 13.2 - - + -
255A TYR* 3.9 29.6 - - + -
259A ILE* 4.9 0.4 - - + -
278A LEU* 3.4 24.8 + - + +
281A LEU* 2.8 34.1 + - + +
283A LEU* 4.1 25.6 - - + -
289A ILE* 4.0 18.6 - - + -
343A MET* 4.0 24.5 - - + -
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Residues in contact with PHE 238 (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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236A GLU* 3.5 24.2 - - - +
237A LEU* 1.3 75.0 - - - +
239A PHE* 1.3 59.2 + - - +
241A LEU* 4.8 0.4 - - + -
242A SER* 2.7 54.1 + - - -
278A LEU* 3.4 35.9 + - + +
279A GLU* 4.0 6.5 - - + +
440A ASP* 5.1 5.8 - - - -
3C GLY 5.1 0.7 - - - -
4C ARG* 3.1 61.5 - - - -
5C PRO 4.1 6.1 - - - -
6C ARG* 3.8 31.0 - - + -
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Residues in contact with PHE 239 (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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236A GLU* 3.1 18.9 + - + +
238A PHE* 1.3 82.9 - - - +
240A HIS* 1.3 64.1 - - + +
242A SER* 3.8 4.6 - - - -
243A ARG* 3.2 50.7 + - + +
437A ARG 3.6 24.2 - - - -
438A TYR* 3.4 32.8 - + + +
439A PHE* 3.9 14.4 - - - -
440A ASP* 3.6 35.2 - - - +
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Residues in contact with HIS 240 (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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234A GLY 2.7 24.4 + - - -
235A GLY 4.7 0.2 - - - -
236A GLU 3.1 24.7 - - - -
237A LEU* 3.3 7.9 + - + +
239A PHE* 1.3 78.2 - + + +
241A LEU* 1.3 59.2 + - - +
243A ARG* 3.1 33.5 + - - +
244A GLU* 2.9 34.5 + - - +
247A PHE* 4.0 16.6 - - + -
251A ARG* 4.4 6.1 - - - +
283A LEU* 3.9 22.1 - - + +
426A PHE* 3.5 21.0 - + - -
438A TYR* 3.5 31.5 - + + +
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Residues in contact with LEU 241 (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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237A LEU 2.9 17.9 + - - +
238A PHE 4.3 2.0 - - - +
240A HIS* 1.3 74.2 - - - +
242A SER* 1.3 58.0 + - - +
244A GLU 4.5 0.2 - - - +
245A ARG* 2.8 38.3 + - - +
246A VAL* 3.9 25.8 - - - -
247A PHE* 3.8 29.3 - - + -
278A LEU* 3.6 33.7 - - + -
342A GLU* 3.5 28.5 - - + +
343A MET* 3.9 13.0 - - + +
346A GLY* 5.8 0.9 - - - -
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Residues in contact with SER 242 (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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238A PHE* 2.7 50.0 + - - -
239A PHE* 3.8 5.2 - - - -
241A LEU* 1.3 76.2 - - - +
243A ARG* 1.3 53.9 + - - +
245A ARG* 2.7 33.3 + - - -
3C GLY 4.9 7.5 + - - -
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Residues in contact with ARG 243 (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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239A PHE* 3.2 40.2 + - + +
240A HIS* 3.1 40.9 + - - +
241A LEU 3.2 0.4 - - - -
242A SER* 1.3 79.4 - - - +
244A GLU* 1.3 93.9 + - + +
245A ARG* 3.3 21.7 + - - +
426A PHE* 3.9 17.1 - - - -
438A TYR* 4.1 9.9 - - - -
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Residues in contact with GLU 244 (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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240A HIS 2.9 15.0 + - - +
243A ARG* 1.3 110.0 + - + +
245A ARG* 1.3 58.7 + - - +
246A VAL* 2.8 31.3 + - - +
247A PHE* 4.1 13.8 - - + -
251A ARG* 2.8 37.0 + - - -
426A PHE* 4.9 3.1 - - - -
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Residues in contact with ARG 245 (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 LEU* 2.8 24.8 + - - +
242A SER 2.7 32.1 + - - -
243A ARG* 3.3 17.3 + - - +
244A GLU* 1.3 76.9 - - - +
246A VAL* 1.3 59.3 + - + +
346A GLY* 3.3 26.3 - - - +
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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