Contacts of the helix formed by residues 247 - 259 (chain B) in PDB entry 3E6G
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 GLY 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A ASP* 4.6 12.8 - - - -
63B ASN* 4.0 2.0 - - - -
245B VAL* 3.6 7.9 + - - -
246B GLN* 1.3 74.4 - - - +
248B PRO* 1.4 75.0 - - - +
249B PHE* 3.7 1.8 - - - -
250B ASP* 3.6 11.2 + - - -
251B SER* 2.9 27.1 + - - -
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Residues in contact with PRO 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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217A ASP 5.5 6.3 - - - +
219A VAL* 6.5 2.0 - - + -
250A ASP* 4.3 13.2 - - - +
63B ASN* 3.1 26.4 - - - +
65B THR* 3.8 16.2 - - - +
247B GLY* 1.4 82.0 - - - +
249B PHE* 1.3 63.6 + - + +
251B SER* 3.0 7.0 + - - -
252B PHE* 2.7 36.1 + - - +
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Residues in contact with PHE 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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217A ASP 5.5 4.5 - - - -
249A PHE* 3.4 54.3 - + + -
250A ASP* 3.2 33.0 - - - -
253A LEU* 3.1 33.7 - - + -
248B PRO* 1.3 87.0 - - + +
250B ASP* 1.3 59.5 + - - +
252B PHE* 3.2 11.2 - - + +
253B LEU* 2.9 33.3 + - + +
249C PHE* 5.9 1.1 - + - -
249D PHE* 5.0 19.7 - + + -
252D PHE* 5.2 10.3 - + - -
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Residues in contact with ASP 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLY* 4.4 11.5 - - - -
248A PRO* 4.5 10.7 - - - +
249A PHE* 4.0 20.4 - - - -
250A ASP* 4.3 13.1 - - - +
217B ASP 5.3 0.2 - - - +
218B MET* 4.1 24.0 - - - +
219B VAL 4.9 3.3 - - - +
246B GLN* 3.5 28.5 + - + +
247B GLY* 3.6 8.9 + - - +
248B PRO 3.2 0.6 - - - -
249B PHE* 1.3 75.1 - - - +
251B SER* 1.3 67.1 + - - +
253B LEU* 3.1 6.8 + - - +
254B ALA* 2.8 27.1 + - - +
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Residues in contact with SER 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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65B THR* 4.1 5.4 - - - -
66B ARG* 3.4 43.4 - - - +
69B TYR* 3.9 17.3 - - - +
246B GLN* 3.4 14.3 - - - +
247B GLY 2.9 19.7 + - - -
248B PRO* 3.0 8.6 + - - -
250B ASP* 1.3 75.3 - - - +
252B PHE* 1.3 64.4 + - - +
254B ALA* 3.3 1.6 + - - +
255B LEU* 2.9 25.5 + - - +
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Residues in contact with PHE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B THR* 3.7 17.6 - - + +
248B PRO 2.7 16.6 + - - +
249B PHE* 3.2 13.2 - - - +
251B SER* 1.3 74.5 - - - +
253B LEU* 1.3 79.1 + - + +
255B LEU* 3.4 8.0 + - + +
256B ARG* 3.2 28.6 + - + +
217C ASP* 3.3 40.8 - - + -
253C LEU* 4.3 21.3 - - + -
249D PHE* 4.6 15.0 - + - -
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Residues in contact with LEU 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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249A PHE* 4.1 26.7 - - + -
213B ASN* 3.2 10.0 + - - +
217B ASP* 4.0 24.7 - - - +
218B MET* 4.2 9.2 - - + -
249B PHE* 2.9 19.8 + - + +
250B ASP* 3.6 7.0 - - - +
252B PHE* 1.3 89.7 - - + +
254B ALA* 1.3 55.7 + - - +
256B ARG* 3.3 7.7 + - - +
257B GLY 2.8 28.9 + - - -
252C PHE* 4.7 9.0 - - + -
253C LEU* 4.3 19.5 - - + -
256C ARG* 3.3 26.0 + - - +
249D PHE* 6.5 0.2 - - + -
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Residues in contact with ALA 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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69B TYR* 3.4 36.3 - - + +
208B ALA* 5.3 0.2 - - + -
213B ASN* 3.4 18.3 - - + +
218B MET* 4.3 13.2 - - + -
246B GLN* 4.8 0.4 - - - +
250B ASP 2.8 17.1 + - - +
251B SER 3.7 1.3 - - - +
253B LEU* 1.3 75.1 - - - +
255B LEU* 1.3 59.1 + - - +
257B GLY* 3.1 1.9 + - - -
258B LEU* 2.8 34.0 + - - +
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Residues in contact with LEU 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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21B ALA 5.6 0.7 - - - +
65B THR* 4.9 6.5 - - + +
68B ALA* 3.9 28.5 - - + +
69B TYR* 3.9 18.5 - - + +
72B CYS* 3.7 37.7 - - + -
251B SER 2.9 17.6 + - - +
252B PHE* 3.7 9.4 - - + +
253B LEU 3.3 0.2 - - - -
254B ALA* 1.3 75.8 - - - +
256B ARG* 1.3 58.5 + - - +
258B LEU* 3.3 16.6 + - + +
259B LYS* 3.6 29.5 + - - +
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Residues in contact with ARG 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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215B HIS* 6.1 0.2 - - - -
252B PHE* 3.2 25.4 + - + +
253B LEU* 3.5 9.6 - - - +
254B ALA 3.2 0.4 - - - -
255B LEU* 1.3 72.0 - - - +
257B GLY* 1.3 66.2 + - - +
258B LEU 3.1 1.6 - - - -
259B LYS* 3.2 27.1 + - + +
260B THR* 4.2 0.7 + - - -
213C ASN* 2.7 40.8 + - - +
215C HIS* 3.5 37.8 + - + +
217C ASP* 2.7 39.8 + - - +
253C LEU* 3.2 26.4 + - - +
256C ARG* 3.5 36.0 - - - +
257C GLY* 4.1 4.8 - - - +
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Residues in contact with GLY 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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212B LEU 3.8 2.5 - - - -
213B ASN* 3.6 20.2 - - - -
215B HIS* 4.2 5.8 - - - -
253B LEU 2.8 15.8 + - - -
254B ALA 3.1 4.2 + - - -
256B ARG* 1.3 75.9 - - - +
258B LEU* 1.3 62.9 + - - +
259B LYS 3.1 1.0 + - - -
260B THR* 3.2 9.6 + - - -
264B ARG* 2.8 23.4 + - - -
256C ARG* 3.8 9.1 - - - +
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Residues in contact with LEU 258 (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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21B ALA* 3.6 20.4 - - - +
69B TYR* 3.9 14.8 - - + -
72B CYS* 3.6 22.2 - - + -
73B VAL* 3.3 31.2 - - + +
76B LEU* 4.1 15.3 - - + -
212B LEU* 3.5 49.8 - - + +
213B ASN 4.5 0.2 - - - +
254B ALA 2.8 11.3 + - - +
255B LEU* 3.3 12.6 - - + +
256B ARG 3.1 0.4 - - - -
257B GLY* 1.3 77.9 - - - +
259B LYS* 1.3 61.3 + - - +
261B LEU* 3.1 23.1 + - + +
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Residues in contact with LYS 259 (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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21B ALA 3.7 16.6 - - - +
22B ILE* 3.9 38.0 + - + +
255B LEU* 3.6 38.2 + - - +
256B ARG* 3.2 12.8 + - + +
257B GLY 3.1 1.0 + - - -
258B LEU* 1.3 76.9 - - - +
260B THR* 1.3 58.5 + - - +
261B LEU 3.4 0.4 + - - -
262B PRO* 4.2 6.5 - - - +
215C HIS* 4.3 23.3 - - + +
343C VAL* 4.1 19.1 - - + -
344C GLU* 6.1 2.0 - - - -
379C ILE* 3.5 21.5 - - - +
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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