Contacts of the helix formed by residues 245 - 254 (chain A) in PDB entry 3EAX
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 ASP 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A GLU* 5.5 1.5 - - - +
238A ARG* 4.5 2.2 - - - +
243A SER 3.2 8.2 + - - +
244A VAL* 1.3 71.4 - - - +
246A ILE* 1.3 67.5 + - - +
247A LYS* 2.9 28.7 + - - +
248A LYS* 2.9 53.2 + - + +
249A VAL* 2.9 17.3 + - - +
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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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3A MET* 3.4 55.0 - - + -
6A GLU* 5.3 3.6 - - - +
227A LEU* 3.8 31.1 - - + +
231A CYS* 4.1 18.2 - - - -
244A VAL* 3.7 9.9 + - + +
245A ASP* 1.3 72.7 + - - +
247A LYS* 1.3 57.1 + - - +
249A VAL* 3.1 1.7 + - - +
250A LEU* 2.8 29.6 + - - +
267A LEU* 5.2 2.2 - - + -
270A SER* 5.0 2.2 - - - -
271A TYR* 3.8 36.6 - - + +
274A VAL* 5.0 7.4 - - + -
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Residues in contact with LYS 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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6A GLU* 3.0 32.5 + - - -
19A ILE* 3.9 23.6 - - + +
23A ILE* 4.3 24.7 - - + -
245A ASP* 2.9 19.6 + - - +
246A ILE* 1.3 75.7 - - - +
248A LYS* 1.3 69.6 + - - +
250A LEU* 3.4 5.4 + - - +
251A LEU* 3.0 36.6 + - + +
267A LEU* 6.0 0.7 - - - -
271A TYR* 3.1 19.9 + - + +
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Residues in contact with LYS 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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26A GLU* 5.3 7.9 + - - -
245A ASP* 2.9 39.5 + - + +
247A LYS* 1.3 89.5 - - - +
249A VAL* 1.3 67.9 + - + +
251A LEU* 3.3 16.3 + - - +
252A GLU* 3.0 23.1 + - - +
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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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74A MET* 3.9 9.9 - - + -
227A LEU* 3.8 14.4 - - + -
230A THR* 3.7 28.7 - - + -
231A CYS* 3.9 18.6 - - - -
234A LEU* 4.0 21.5 - - + -
238A ARG* 6.4 0.4 - - - +
244A VAL* 4.6 4.0 - - + -
245A ASP 2.9 16.2 + - - +
246A ILE 3.6 5.6 - - - +
248A LYS* 1.3 78.1 - - + +
250A LEU* 1.3 58.3 + - - +
252A GLU* 3.0 9.3 + - - +
253A MET* 2.9 28.4 + - + +
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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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20A TYR* 5.8 0.7 - - + -
23A ILE* 3.8 39.0 - - + -
223A GLY 5.8 0.4 - - - +
227A LEU* 3.8 19.5 - - + +
246A ILE 2.8 16.5 + - - +
247A LYS* 3.7 5.4 - - - +
249A VAL* 1.3 77.3 - - - +
251A LEU* 1.3 57.9 + - - +
253A MET* 3.1 5.6 + - + +
254A ARG* 2.8 38.0 + - + +
260A LEU* 4.0 24.9 - - + +
261A ILE* 3.7 32.1 - - + -
267A LEU* 3.9 18.6 - - + -
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Residues in contact with LEU 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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23A ILE* 3.7 38.1 - - + +
26A GLU* 3.9 26.5 - - + +
27A ALA* 3.8 34.5 - - + +
28A SER* 4.4 3.3 + - - +
247A LYS* 3.0 28.2 + - + +
248A LYS* 3.7 18.2 - - - +
250A LEU* 1.3 75.4 - - - +
252A GLU* 1.3 64.3 + - - +
254A ARG* 3.2 14.6 + - + +
255A LYS* 3.4 18.7 + - - +
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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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73A LYS 5.0 1.4 - - - +
74A MET* 3.7 22.4 - - + -
75A GLU 6.3 0.2 - - - +
248A LYS 3.0 12.9 + - - +
249A VAL* 3.0 12.1 + - - +
251A LEU* 1.3 76.9 - - - +
253A MET* 1.3 61.7 + - - +
255A LYS* 2.8 55.5 + - - +
256A PHE* 3.3 28.6 - - - -
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Residues in contact with MET 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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72A ILE* 4.5 9.7 - - + +
74A MET* 3.5 25.6 - - + -
81A TYR* 4.1 2.9 - - + -
223A GLY* 4.8 2.0 - - - +
226A CYS* 3.2 40.4 - - + +
227A LEU* 3.8 26.5 - - - +
230A THR* 3.3 23.3 - - + +
249A VAL* 2.9 19.0 + - + +
250A LEU* 3.6 7.9 - - - +
252A GLU* 1.3 73.0 - - - +
254A ARG* 1.3 56.4 + - - +
255A LYS 2.9 5.4 - - - -
256A PHE* 2.8 33.8 + - - +
257A ARG 3.5 3.5 + - - -
260A LEU* 3.4 22.9 - - + +
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Residues in contact with ARG 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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20A TYR* 3.5 19.4 + - - -
23A ILE* 4.2 17.9 - - - +
24A ARG* 4.1 14.3 - - - +
27A ALA* 3.8 32.6 - - + +
28A SER* 3.9 12.0 + - - +
52A PHE* 3.5 12.8 - - - -
250A LEU* 2.8 30.6 + - + +
251A LEU* 3.2 10.5 + - - +
253A MET* 1.3 75.6 - - - +
255A LYS* 1.3 58.6 + - - +
256A PHE 3.1 2.8 + - - -
257A ARG 3.5 16.0 - - - +
258A MET* 4.9 1.8 - - - +
259A GLY* 3.9 21.7 + - - +
260A LEU* 2.7 37.0 + - + +
261A ILE* 2.8 18.0 + - - +
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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