Contacts of the helix formed by residues 239 - 251 (chain A) in PDB entry 3K8G
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 ASN 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A LYS* 4.0 2.6 + - - +
238A ILE* 1.3 77.3 - - - +
240A PHE* 1.3 64.6 + - - +
241A PRO* 3.9 15.8 - - + +
242A ILE* 3.2 32.6 + - - +
243A GLN* 3.3 18.6 + - - +
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Residues in contact with PHE 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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238A ILE 5.5 0.9 - - - -
239A ASN* 1.3 75.1 - - - +
241A PRO* 1.4 62.4 - - + +
243A GLN* 3.2 24.8 - - + +
244A PHE* 2.8 46.7 + + + +
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Residues in contact with PRO 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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239A ASN* 3.7 17.7 - - + +
240A PHE* 1.4 91.2 - - + +
242A ILE* 1.3 66.2 + - + +
244A PHE* 3.8 3.8 - - + +
245A LEU* 3.2 38.0 + - + +
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Residues in contact with ILE 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 ILE* 3.8 18.2 - - + -
239A ASN* 3.2 24.2 + - - +
241A PRO* 1.3 77.7 - - + +
243A GLN* 1.3 62.8 + - - +
245A LEU* 4.0 11.4 - - + +
246A ILE* 3.1 45.2 + - + +
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Residues in contact with GLN 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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238A ILE* 3.5 30.7 - - + +
239A ASN 3.3 8.0 + - - +
240A PHE* 3.2 32.2 - - + +
242A ILE* 1.3 79.6 - - - +
244A PHE* 1.3 63.4 + - - +
246A ILE* 3.9 3.7 - - - +
247A SER* 3.0 24.9 + - - -
254A ILE* 3.8 26.5 + - + +
255A HIS* 3.9 24.5 - - - +
256A VAL* 3.8 20.5 - - - +
261A LEU* 4.8 3.4 - - + -
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Residues in contact with PHE 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 PHE* 2.8 29.7 + + + +
241A PRO* 3.8 6.1 - - + +
243A GLN* 1.3 72.2 - - - +
245A LEU* 1.3 61.8 + - + +
247A SER* 3.1 8.6 - - - -
248A ARG* 2.8 81.6 + - - +
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Residues in contact with LEU 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 PRO* 3.2 25.6 + - + +
242A ILE* 4.0 12.6 - - + +
244A PHE* 1.3 89.3 - - + +
246A ILE* 1.3 56.5 + - + +
248A ARG* 3.5 4.3 + - - +
249A VAL* 2.9 36.1 + - + +
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Residues in contact with ILE 246 (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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202A LEU* 4.2 11.7 - - + -
204A PHE* 4.6 18.2 - - + -
238A ILE* 4.4 10.5 - - + -
242A ILE* 3.1 42.1 + - + +
243A GLN* 3.9 3.1 - - - +
245A LEU* 1.3 74.1 - - + +
247A SER* 1.3 54.2 + - - +
249A VAL* 3.2 8.6 + - - +
250A LEU* 2.8 49.2 + - + +
254A ILE* 3.5 18.8 - - + -
261A LEU* 5.7 7.2 - - + -
263A ILE* 4.7 4.5 - - + -
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Residues in contact with SER 247 (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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243A GLN 3.0 20.8 + - - -
244A PHE* 3.1 11.2 - - - -
246A ILE* 1.3 76.4 - - - +
248A ARG* 1.3 56.4 + - - +
250A LEU* 3.2 1.8 + - - -
251A ASN* 2.7 31.2 + - - -
252A ALA 2.9 30.2 + - - +
253A HIS* 4.8 0.2 - - - -
254A ILE* 3.5 24.1 + - - +
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Residues in contact with ARG 248 (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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244A PHE* 2.8 57.5 + - - +
245A LEU* 4.1 4.7 - - - +
247A SER* 1.3 72.5 - - - +
249A VAL* 1.3 66.7 + - - +
250A LEU 3.4 0.2 + - - -
251A ASN* 3.4 13.4 + - - +
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Residues in contact with VAL 249 (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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202A LEU 4.8 2.5 - - - +
204A PHE* 3.7 35.0 - - + -
245A LEU* 2.9 21.8 + - + +
246A ILE* 3.3 11.4 - - - +
248A ARG* 1.3 76.7 - - - +
250A LEU* 1.3 69.5 - - + +
251A ASN* 5.1 0.7 - - - +
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Residues in contact with LEU 250 (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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202A LEU* 3.6 59.5 - - + +
227A TYR* 4.0 11.2 - - - +
246A ILE* 2.8 29.0 + - + +
247A SER* 4.0 2.9 - - - +
249A VAL* 1.3 85.4 - - + +
251A ASN* 1.3 69.0 + - - +
252A ALA* 3.4 13.0 + - + +
254A ILE* 4.5 1.6 - - + -
263A ILE* 3.9 26.0 - - + -
266A GLY* 4.5 7.0 - - - -
267A THR* 4.6 11.8 + - - +
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Residues in contact with ASN 251 (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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247A SER 2.7 14.4 + - - -
248A ARG* 3.4 12.4 + - - +
249A VAL 5.1 0.7 - - - +
250A LEU* 1.3 77.5 - - - +
252A ALA* 1.3 55.5 + - - +
253A HIS* 5.6 1.0 - - - -
265A ASP* 3.7 10.4 - - - +
267A THR* 6.0 0.9 - - - +
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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