Contacts of the helix formed by residues 245 - 257 (chain D) in PDB entry 1EQB
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 SER 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A SER* 3.9 11.2 - - - -
356A PRO* 4.8 2.2 - - - -
1293A FFO 3.4 39.5 - - - +
244D GLY* 1.3 75.4 - - - -
246D GLU* 1.3 65.7 + - - +
247D GLU* 3.6 5.8 + - - +
248D LEU* 3.3 23.4 + - - +
249D TYR* 3.2 23.8 + - - -
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Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A PHE* 6.0 4.3 - - + -
1293A FFO 3.2 17.2 + - - +
245D SER* 1.3 73.4 - - - +
247D GLU* 1.3 69.9 + - + +
249D TYR* 3.2 12.0 + - - +
250D LYS* 2.9 23.0 + - - +
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Residues in contact with GLU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL* 6.0 1.3 - - + -
1293A FFO 3.0 33.0 - - + +
250B LYS* 5.6 6.6 - - - +
254B SER* 4.2 19.0 + - - +
245D SER* 3.2 6.8 + - - +
246D GLU* 1.3 83.8 - - + +
248D LEU* 1.3 57.5 + - - +
250D LYS* 2.9 11.2 + - - +
251D LYS* 2.8 48.1 + - - +
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Residues in contact with LEU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LEU* 3.5 32.1 - - + -
196D TYR* 5.4 7.0 - - + +
221D HIS* 4.2 26.2 - - + +
222D VAL* 4.5 6.3 - - + -
244D GLY* 4.2 20.6 - - - -
245D SER* 3.3 18.9 + - - +
247D GLU* 1.3 79.1 - - - +
249D TYR* 1.3 65.3 + - + +
251D LYS* 3.5 9.8 + - + +
252D LEU* 3.0 37.0 + - + +
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Residues in contact with TYR 249 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D ASP* 2.5 32.1 + - - -
90D TYR* 3.5 41.0 - + + -
241D ALA* 3.6 21.5 - - + -
242D LYS* 3.6 4.2 - - - -
243D GLY 3.4 1.9 + - - -
244D GLY* 2.8 44.2 + - - -
245D SER 3.5 10.8 - - - -
246D GLU* 3.2 12.2 + - - +
247D GLU 3.1 0.8 - - - -
248D LEU* 1.3 84.7 - - + +
250D LYS* 1.3 64.5 + - - +
252D LEU* 3.8 5.5 - - + +
253D ASN* 3.0 30.6 + - - +
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Residues in contact with LYS 250 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B GLU* 5.6 7.2 - - - +
246D GLU 2.9 12.9 + - - +
247D GLU* 2.9 16.7 + - - +
249D TYR* 1.3 76.6 - - - +
251D LYS* 1.3 66.3 + - + +
253D ASN* 3.1 9.2 + - - +
254D SER* 3.0 26.9 + - - +
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Residues in contact with LYS 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ALA* 3.7 31.0 + - + +
109D LEU* 5.4 4.5 - - + +
196D TYR* 5.8 2.4 + - - -
247D GLU* 2.8 33.8 + - - +
248D LEU* 3.6 10.3 - - + +
250D LYS* 1.3 76.9 - - + +
252D LEU* 1.3 58.0 + - - +
254D SER* 3.1 8.1 + - - -
255D ALA* 2.8 29.5 + - - +
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Residues in contact with LEU 252 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D TYR* 3.5 35.3 + - + +
104D ALA 5.0 0.9 - - - +
105D VAL* 4.4 17.0 - - + +
108D ALA* 4.0 20.6 - - + -
109D LEU* 5.3 2.0 - - + -
222D VAL* 4.0 39.9 - - + -
239D ILE* 4.3 10.6 - - + +
241D ALA* 4.8 3.1 - - + -
248D LEU* 3.0 33.6 + - + +
249D TYR* 3.8 8.1 - - + +
250D LYS 3.2 0.2 - - - -
251D LYS* 1.3 77.4 - - - +
253D ASN* 1.3 61.7 + - - +
255D ALA* 3.4 2.4 + - - +
256D VAL* 3.3 26.2 + - - +
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Residues in contact with ASN 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D TYR* 2.6 48.4 + - + +
90D TYR* 2.7 30.7 + - - -
91D ALA 5.3 0.7 - - - +
92D ASN* 3.0 14.2 + - - +
249D TYR* 3.0 22.9 + - - +
250D LYS* 3.1 7.3 + - - +
252D LEU* 1.3 76.1 - - - +
254D SER* 1.3 57.9 + - - +
256D VAL 3.5 0.3 + - - -
257D PHE 2.9 18.4 + - - +
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Residues in contact with SER 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLU* 4.3 20.5 + - - +
133C VAL 5.0 0.2 - - - +
3293C FFO 5.7 1.4 + - - -
250D LYS* 3.0 14.1 + - - +
251D LYS* 3.6 9.6 - - - -
253D ASN* 1.3 75.2 - - - +
255D ALA* 1.3 58.6 + - - +
257D PHE 3.2 11.4 - - - -
258D PRO* 3.5 6.6 - - - +
259D GLY* 2.7 33.8 + - - -
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Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D PHE* 5.5 0.7 - - - -
104D ALA* 3.3 38.0 - - + +
107D THR* 4.0 10.0 + - - +
108D ALA* 3.4 22.7 - - + -
251D LYS 2.8 7.6 + - - +
252D LEU 3.6 5.8 - - - +
254D SER* 1.3 78.2 - - - +
256D VAL* 1.3 57.3 + - - +
259D GLY* 3.3 4.4 - - - -
260D GLY* 2.8 26.2 + - - -
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Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D TYR* 3.6 17.3 - - - +
92D ASN* 3.8 17.7 - - - +
94D GLN* 4.1 11.0 - - + +
95D PRO* 4.1 9.0 - - + -
104D ALA* 3.8 11.0 - - + -
239D ILE* 3.5 32.5 - - + -
252D LEU 3.3 8.7 + - - +
253D ASN 3.8 0.9 - - - +
254D SER 3.2 0.2 - - - -
255D ALA* 1.3 78.0 - - - +
257D PHE* 1.3 60.7 + - + +
260D GLY* 3.8 0.8 - - - -
261D GLN* 3.0 55.1 + - - +
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Residues in contact with PHE 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LEU* 4.0 6.7 - - + -
3293C FFO 3.5 24.5 - + - -
57D GLU* 3.5 36.6 - - + -
58D GLY* 3.5 29.6 - - - -
59D TYR* 4.3 16.0 - + + +
64D TYR* 3.9 17.7 - + - -
94D GLN* 4.8 7.2 - - - +
253D ASN 2.9 18.0 + - - +
254D SER* 3.2 10.9 + - - +
256D VAL* 1.3 82.9 - - + +
258D PRO* 1.3 80.4 - - + +
259D GLY 3.4 0.2 - - - +
261D GLN* 3.2 24.0 - - + +
262D GLY 3.6 12.8 - - - +
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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