Contacts of the helix formed by residues 245 - 257 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B GLY* 1.3 76.5 - - - -
246B GLU* 1.3 65.9 + - - +
247B GLU* 3.6 5.8 + - - +
248B LEU* 3.3 23.4 + - - +
249B TYR* 3.2 24.4 + - - -
355C SER* 3.9 9.6 - - - -
356C PRO* 4.9 2.0 - - - -
3293C FFO 3.3 40.0 - - - +
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Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B SER* 1.3 72.0 - - - +
247B GLU* 1.3 68.6 + - + +
249B TYR* 3.1 12.3 + - - +
250B LYS* 2.9 24.0 + - - +
355C SER* 5.3 0.2 + - - -
357C PHE* 6.0 4.0 - - + -
3293C FFO 3.2 15.6 + - - +
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B SER* 3.2 6.4 + - - +
246B GLU* 1.3 84.6 - - + +
248B LEU* 1.3 57.9 + - - +
250B LYS* 2.9 11.4 + - - +
251B LYS* 2.8 48.3 + - - +
133C VAL* 6.0 1.3 - - + -
3293C FFO 3.0 34.5 + - + +
250D LYS* 5.6 7.5 - - - +
254D SER* 4.3 19.0 + - - +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 3.5 33.0 - - + -
196B TYR* 5.3 7.4 - - + +
221B HIS* 4.2 26.5 - - + +
222B VAL* 4.5 6.7 - - + -
244B GLY* 4.2 19.7 - - - -
245B SER* 3.3 19.1 + - - +
247B GLU* 1.3 79.1 - - - +
249B TYR* 1.3 66.8 + - + +
251B LYS* 3.5 10.3 + - + +
252B LEU* 3.0 39.6 + - + +
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Residues in contact with TYR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ASP* 2.6 30.8 + - - -
90B TYR* 3.5 44.8 - + + -
241B ALA* 3.6 20.9 - - + -
242B LYS* 3.6 4.3 - - - -
243B GLY 3.4 2.3 + - - -
244B GLY* 2.8 45.3 + - - -
245B SER 3.2 10.5 + - - -
246B GLU* 3.1 11.9 + - - +
247B GLU 3.1 0.6 - - - -
248B LEU* 1.3 83.8 - - + +
250B LYS* 1.3 65.0 + - - +
252B LEU* 3.4 5.1 + - + +
253B ASN* 3.0 30.7 + - - +
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B GLU 2.9 13.8 + - - +
247B GLU* 3.4 15.7 - - - +
249B TYR* 1.3 75.3 - - - +
251B LYS* 1.3 66.1 + - + +
253B ASN* 3.0 9.7 + - - +
254B SER* 2.9 28.1 + - - +
247D GLU* 5.6 7.6 - - - +
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Residues in contact with LYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA* 3.7 30.8 + - + +
109B LEU* 5.4 4.9 - - + +
196B TYR* 5.7 2.4 + - - -
247B GLU* 2.8 31.1 + - + +
248B LEU* 3.7 13.9 - - + +
250B LYS* 1.3 77.1 - - + +
252B LEU* 1.3 56.7 + - - +
254B SER* 3.2 7.5 + - - -
255B ALA* 2.8 30.7 + - - +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TYR* 3.5 33.7 - - + +
104B ALA 4.9 0.9 - - - +
105B VAL* 4.4 17.7 - - + +
108B ALA* 4.0 19.1 - - + -
109B LEU* 5.2 2.0 - - + -
222B VAL* 4.0 40.4 - - + -
239B ILE* 4.3 10.2 - - + +
241B ALA* 4.8 2.7 - - + -
248B LEU* 3.0 33.1 + - + +
249B TYR* 3.7 8.3 - - + +
250B LYS 3.2 0.2 - - - -
251B LYS* 1.3 77.4 - - - +
253B ASN* 1.3 62.3 + - - +
255B ALA* 3.4 2.6 + - - +
256B VAL* 3.3 26.9 + - - +
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Residues in contact with ASN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 2.7 48.6 + - + +
90B TYR* 2.7 30.3 + - - -
91B ALA 5.3 0.5 - - - +
92B ASN* 3.0 13.6 + - - +
249B TYR* 3.0 22.5 + - - +
250B LYS* 3.0 7.1 + - - +
252B LEU* 1.3 75.7 - - - +
254B SER* 1.3 58.9 + - - +
256B VAL 3.5 0.7 + - - -
257B PHE 3.0 18.2 + - - +
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Residues in contact with SER 254 (chain B).
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 5.0 0.3 - - - +
1293A FFO 5.6 2.1 + - - -
250B LYS* 2.9 18.1 + - - +
251B LYS* 3.6 7.4 - - - -
253B ASN* 1.3 75.4 - - - +
255B ALA* 1.3 56.7 + - - +
257B PHE 3.2 11.3 - - - -
258B PRO* 3.5 5.9 - - - +
259B GLY* 2.7 33.4 + - - -
247D GLU* 4.2 21.7 + - - -
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 5.5 0.3 - - - -
104B ALA* 3.4 37.3 - - + +
107B THR* 4.0 11.1 + - - +
108B ALA* 3.4 13.7 - - + -
251B LYS 2.8 17.3 + - - +
252B LEU* 3.6 5.6 - - - +
253B ASN 3.4 0.2 - - - -
254B SER* 1.3 75.7 - - - +
256B VAL* 1.3 58.8 + - - +
259B GLY* 3.3 4.3 - - - -
260B GLY* 2.8 27.5 + - - -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 3.6 17.5 - - - +
92B ASN* 3.8 10.3 - - - +
94B GLN* 4.1 19.1 - - + +
95B PRO* 4.1 9.0 - - + -
104B ALA* 3.8 11.9 - - + -
239B ILE* 3.5 32.1 - - + -
252B LEU 3.3 9.4 + - - +
253B ASN 3.8 0.7 - - - +
254B SER 3.2 0.4 - - - -
255B ALA* 1.3 77.0 - - - +
257B PHE* 1.3 60.3 + - + +
260B GLY* 3.4 0.6 + - - -
261B GLN* 2.9 53.8 + - - +
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Residues in contact with PHE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.0 6.5 - - + -
1293A FFO 3.5 25.6 - + - -
57B GLU* 3.5 34.8 - - + -
58B GLY* 3.5 32.5 - - - -
59B TYR* 4.3 15.1 - + - +
64B TYR* 3.9 15.0 - + - -
94B GLN* 4.8 7.6 - - - +
253B ASN 3.0 18.9 + - - +
254B SER* 3.2 10.4 + - - +
256B VAL* 1.3 83.4 - - + +
258B PRO* 1.3 79.9 - - + +
259B GLY 3.4 0.2 - - - +
261B GLN* 3.2 23.6 - - + +
262B GLY* 3.5 13.2 - - - +
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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