Contacts of the helix formed by residues 247 - 258 (chain A) in PDB entry 6MOL
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 HIS 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ALA 3.4 23.3 - - - +
211A ARG 3.6 0.8 + - - -
212A ALA 3.3 28.8 + - - -
213A GLY* 3.4 15.7 + - - -
242A ALA* 3.3 9.7 + - - +
245A ALA* 3.3 29.8 - - + +
246A GLY* 1.3 75.5 + - - +
248A LEU* 1.3 66.0 + - - +
249A GLU* 3.1 9.2 - - + +
250A ILE* 3.0 20.9 + - + +
251A VAL* 3.0 24.5 + - - +
283A ILE* 4.5 0.2 - - - +
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Residues in contact with LEU 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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246A GLY 3.7 4.9 + - - -
247A HIS* 1.3 73.2 - - - +
249A GLU* 1.3 75.5 + - - +
251A VAL* 3.3 3.6 + - + +
252A GLU* 3.0 49.7 + - + +
282A GLU* 3.7 44.2 - - + +
283A ILE* 4.1 20.6 - - + +
286A VAL* 3.8 11.4 - - + -
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Residues in contact with GLU 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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215A LEU* 3.6 32.8 - - + -
247A HIS* 4.0 5.5 - - - +
248A LEU* 1.3 93.3 + - + +
250A ILE* 1.3 61.1 + - + +
252A GLU* 3.6 7.2 + - - +
253A VAL* 3.2 28.6 + - - +
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Residues in contact with ILE 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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210A ALA* 3.7 30.3 - - + -
213A GLY* 3.6 32.1 - - - +
214A HIS 3.7 10.8 - - - +
215A LEU* 3.8 25.6 - - + -
218A VAL* 3.7 23.3 - - + -
242A ALA* 4.0 4.7 - - + -
247A HIS* 3.0 17.7 + - + +
249A GLU* 1.3 75.0 - - + +
251A VAL* 1.3 61.0 + - - +
253A VAL* 3.2 2.3 + - - +
254A LEU* 2.9 44.7 + - + +
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Residues in contact with VAL 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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239A LEU* 3.9 13.4 - - + +
242A ALA* 3.6 22.7 - - + -
243A ALA* 4.0 10.8 - - + +
247A HIS 3.0 17.3 + - - +
248A LEU* 3.7 8.7 - - + +
250A ILE* 1.3 76.0 - - - +
252A GLU* 1.3 62.5 + - + +
254A LEU* 4.1 0.9 - - - +
255A LEU* 3.1 31.3 + - + +
283A ILE* 4.0 23.1 - - + -
286A VAL* 4.8 7.6 - - + -
287A LEU* 3.8 29.6 - - + -
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Residues in contact with GLU 252 (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 LEU* 3.0 48.8 + - + +
249A GLU* 4.1 6.6 - - - +
251A VAL* 1.3 76.5 - - - +
253A VAL* 1.3 62.9 + - + +
255A LEU* 4.1 5.8 - - - +
256A LYS* 3.2 50.1 + - - +
286A VAL* 4.0 25.8 - - + +
290A TYR* 4.6 2.4 + - + +
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Residues in contact with VAL 253 (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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215A LEU* 3.7 17.7 - - + -
218A VAL* 4.5 6.7 - - + -
219A GLU* 3.9 28.0 - - + +
222A LEU* 3.9 23.1 - - + -
249A GLU 3.2 17.6 + - - +
250A ILE* 3.2 5.5 + - - +
252A GLU* 1.3 76.2 - - + +
254A LEU* 1.3 65.7 + - - +
256A LYS* 3.4 7.5 + - + +
257A TYR* 3.0 32.4 + - + +
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Residues in contact with LEU 254 (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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206A LEU* 4.3 13.2 - - + -
210A ALA* 4.4 1.3 - - + -
218A VAL* 4.0 12.1 - - + -
222A LEU* 4.0 17.7 - - + -
228A VAL* 3.6 22.6 - - + +
238A PRO* 3.6 38.1 - - + +
239A LEU* 3.7 11.9 - - + +
242A ALA* 4.3 2.7 - - + -
250A ILE* 2.9 35.6 + - + +
251A VAL 4.1 2.7 - - - +
253A VAL* 1.3 76.2 - - - +
255A LEU* 1.3 60.1 + - - +
257A TYR* 3.3 1.5 + - - -
258A GLY 3.1 6.6 + - - -
259A ALA* 2.9 35.1 + - + +
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Residues in contact with LEU 255 (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 LEU* 3.7 29.4 - - + -
251A VAL* 3.1 22.4 + - + +
252A GLU* 4.1 3.1 - - - +
254A LEU* 1.3 76.9 - - - +
256A LYS* 1.3 61.9 + - - +
258A GLY* 3.0 14.4 + - - -
259A ALA 3.9 12.8 + - - +
261A VAL* 4.1 18.8 - - + -
286A VAL* 3.9 17.3 - - + +
287A LEU* 3.8 22.2 - - + -
290A TYR* 3.8 48.6 - - + -
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Residues in contact with LYS 256 (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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252A GLU* 3.2 38.6 + - - +
253A VAL* 3.9 6.7 - - + +
255A LEU* 1.3 76.4 - - - +
257A TYR* 1.3 63.6 + - + +
258A GLY* 3.3 1.2 + - - -
290A TYR* 3.3 26.7 - - + +
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Residues in contact with TYR 257 (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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219A GLU* 4.9 4.5 + - + -
222A LEU* 3.7 51.0 + - + +
223A LYS* 4.2 20.4 - - - +
228A VAL* 4.2 20.1 - - + +
253A VAL* 3.0 31.6 + - + +
254A LEU 3.7 4.5 - - - +
255A LEU 3.2 0.2 - - - -
256A LYS* 1.3 78.5 - - + +
258A GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 258 (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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228A VAL* 3.6 8.5 - - - +
229A ASN* 3.1 16.1 + - - -
254A LEU 3.1 0.4 + - - -
255A LEU 3.0 11.5 + - - -
256A LYS 3.2 1.7 - - - -
257A TYR* 1.3 78.8 - - - +
259A ALA* 1.3 67.5 + - - +
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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