Contacts of the helix formed by residues 246 - 252 (chain A) in PDB entry 4O14
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 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ALA* 1.3 74.7 - - - +
247A HIS* 1.3 67.3 + - - +
248A SER* 2.6 30.3 + - - +
249A THR* 3.2 18.7 + - + +
250A ILE* 3.5 9.0 + - - +
277A VAL* 3.5 7.4 - - - -
311A ARG* 4.3 4.3 - - - +
18B TYR* 3.7 20.3 + - - +
19B LYS* 2.5 31.5 + - - -
22B HIS* 3.0 28.1 + - + +
146B ASN* 2.8 23.6 + - - +
149B GLU* 3.8 3.9 - - - +
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Residues in contact with HIS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 1.3 74.4 - - - +
248A SER* 1.3 59.8 + - - +
250A ILE* 3.2 2.3 + - - +
251A THR* 2.7 39.6 + - + +
277A VAL* 3.3 20.1 - - + +
279A ASP* 2.7 26.0 + - - -
280A SER* 3.4 26.5 - - - +
311A ARG* 4.6 5.4 + - - -
313A ASP* 3.3 26.7 - - + -
400B LYS* 4.9 11.1 + - + -
415B LYS* 3.4 43.5 + - + +
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 2.6 30.2 + - - +
247A HIS* 1.3 78.5 - - - +
249A THR* 1.3 58.5 + - - +
251A THR* 3.6 7.1 + - - -
252A ALA* 3.0 33.8 + - - +
26B TYR* 2.8 23.1 + - - -
146B ASN* 3.5 14.4 - - - -
400B LYS* 6.3 0.2 - - - +
401B CYS* 3.7 22.1 - - - +
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Residues in contact with THR 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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245A ALA* 3.4 4.7 - - - +
246A GLU* 3.2 18.4 + - + -
248A SER* 1.3 82.8 + - - +
250A ILE* 1.3 60.2 + - - +
252A ALA* 4.8 0.2 - - - -
253A TRP* 3.0 28.2 + - - -
265A ILE* 4.0 2.1 - - - +
22B HIS* 3.7 34.3 - - + +
25B GLN* 3.0 39.0 + - + +
26B TYR* 3.7 28.8 - - + -
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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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245A ALA* 4.0 8.3 - - + -
246A GLU 3.6 13.2 - - - +
247A HIS 3.2 4.4 + - - +
249A THR* 1.3 76.1 - - - +
251A THR* 1.3 66.0 + - - +
252A ALA 3.2 1.6 - - - -
253A TRP* 3.2 21.3 + - - +
254A GLY 4.4 2.4 + - - +
258A GLU* 3.7 32.0 - - + +
261A ALA* 3.9 9.6 - - + +
262A PHE* 3.9 23.8 - - + -
265A ILE* 3.5 29.2 - - + -
276A VAL* 4.1 3.6 - - + -
277A VAL* 3.9 19.5 - - + +
280A SER* 3.8 17.9 - - - +
281A TYR* 4.7 2.6 + - + -
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Residues in contact with THR 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 HIS* 2.7 31.4 + - + +
248A SER* 3.6 9.2 - - - -
250A ILE* 1.3 71.9 - - - +
252A ALA* 1.3 57.7 + - - +
253A TRP 3.1 0.9 - - - -
254A GLY* 3.0 19.4 + - - -
280A SER* 3.9 22.0 - - - +
281A TYR* 3.5 15.6 + - - +
401B CYS* 4.7 4.9 + - - +
413B VAL* 3.3 20.5 - - - +
414B PHE 3.2 38.3 + - - +
415B LYS* 4.2 7.0 - - + -
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Residues in contact with ALA 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 SER 3.0 20.9 + - - +
250A ILE 3.2 0.4 - - - -
251A THR* 1.3 78.0 + - - +
253A TRP* 1.3 61.8 + - + +
254A GLY 3.1 1.4 + - - -
26B TYR* 3.8 20.4 - - + -
27B PRO* 3.6 17.7 - - + +
401B CYS* 5.2 0.9 - - - -
404B VAL* 3.5 38.4 - - + +
406B THR* 4.7 1.4 + - - -
411B ILE* 4.0 3.8 - - - +
413B VAL* 4.0 10.5 - - - -
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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