Contacts of the helix formed by residues 245 - 257 (chain B) in PDB entry 2FQ6
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B HIS* 3.7 0.4 - - - -
219B MET 5.4 0.2 - - - +
243B MET* 4.7 7.4 - - - +
244B VAL* 1.3 79.3 - - - +
246B ALA* 1.3 64.7 + - - +
247B ASP* 3.2 13.0 + - - +
248B THR* 2.7 44.0 + - - -
249B ALA* 3.1 19.4 + - - +
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Residues in contact with ALA 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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28B ILE* 4.5 6.7 - - + -
29B GLN 3.3 30.5 - - - +
30B ARG* 4.5 5.8 - - + -
31B ALA 5.6 0.4 - - - +
61B THR* 5.2 0.7 - - + -
63B THR* 3.3 20.7 - - + +
64B HIS* 3.5 23.1 + - - +
245B ASP* 1.3 73.0 - - - +
247B ASP* 1.3 58.9 + - - +
249B ALA* 3.2 3.4 + - - +
250B TYR* 3.0 23.6 + - - +
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Residues in contact with ASP 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 3.1 18.3 + - - +
28B ILE* 3.7 8.8 - - - +
30B ARG* 2.6 54.1 + - - +
245B ASP* 3.2 9.4 + - - +
246B ALA* 1.3 72.6 - - - +
248B THR* 1.3 65.0 + - - +
250B TYR* 3.3 9.7 - - - +
251B ILE* 3.0 27.8 + - + +
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Residues in contact with THR 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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218B ALA* 3.9 19.6 - - + +
219B MET 3.4 25.4 + - - +
220B ILE* 3.8 22.0 - - + -
244B VAL* 3.9 6.1 - - + -
245B ASP* 2.7 39.1 + - - -
247B ASP* 1.3 70.9 - - - +
249B ALA* 1.3 57.3 + - - +
251B ILE* 3.2 6.4 + - - +
252B THR* 2.9 33.1 + - - -
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 4.1 16.6 - - + +
64B HIS* 4.0 21.3 - - + +
67B LEU* 3.9 26.3 - - + +
82B LEU* 5.0 0.2 - - + -
220B ILE* 4.7 2.5 - - - -
244B VAL* 4.5 4.2 - - + +
245B ASP 3.1 12.4 + - - +
246B ALA 3.2 8.9 + - - +
248B THR* 1.3 74.8 - - - +
250B TYR* 1.3 64.0 + - - +
252B THR* 3.2 3.5 + - - -
253B SER* 3.0 26.3 + - - -
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Residues in contact with TYR 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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30A ARG* 3.7 44.9 + - + +
25B ASN* 3.3 34.9 + - + +
26B SER* 3.1 35.4 - - - -
27B VAL 4.6 0.4 - - - -
28B ILE* 3.4 30.7 - - + -
63B THR* 3.8 7.3 - - + +
246B ALA 3.0 12.1 + - - +
247B ASP 3.3 9.0 - - - +
249B ALA* 1.3 76.5 - - - +
251B ILE* 1.3 67.2 + - + +
253B SER* 3.3 8.5 + - - -
254B ARG* 2.9 53.8 + - + +
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Residues in contact with ILE 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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30A ARG* 5.1 6.7 - - - +
213B VAL* 4.5 15.9 - - + +
217B ASP* 4.5 10.1 - - - +
218B ALA* 4.1 23.8 - - + -
247B ASP* 3.0 16.8 + - + +
248B THR* 3.7 5.8 - - - +
250B TYR* 1.3 85.0 - - + +
252B THR* 1.3 61.9 + - - +
254B ARG* 3.4 31.1 - - - +
255B GLY* 2.9 25.3 + - - -
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Residues in contact with THR 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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67B LEU* 3.8 24.9 - - + -
71B MET* 5.4 0.2 - - - -
208B ALA* 4.1 14.1 - - + -
212B LEU* 4.0 28.3 - - + +
213B VAL* 3.6 11.1 - - + +
220B ILE* 3.4 23.1 - - + +
222B THR* 5.6 0.7 - - + -
248B THR* 2.9 17.2 + - - +
249B ALA 3.6 4.5 - - - -
251B ILE* 1.3 73.9 - - - +
253B SER* 1.3 66.6 + - - +
255B GLY* 3.0 12.5 + - - -
256B LEU* 3.1 13.4 + - + +
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Residues in contact with SER 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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26B SER* 4.9 9.5 + - - -
63B THR 4.9 0.9 + - - -
66B SER* 4.3 5.1 + - - -
67B LEU* 3.4 35.0 + - - +
70B ALA* 5.0 1.4 - - - +
249B ALA 3.0 12.6 + - - -
250B TYR* 3.6 10.5 - - - -
252B THR* 1.3 72.3 - - - +
254B ARG* 1.3 60.8 + - - +
256B LEU* 3.1 28.0 + - - +
257B ARG* 3.2 34.3 + - - -
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Residues in contact with ARG 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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25B ASN* 4.7 13.6 + - - +
215B HIS* 5.6 8.5 + - - -
250B TYR* 2.9 45.9 + - + +
251B ILE* 3.4 23.8 - - + +
253B SER* 1.3 75.0 - - - +
255B GLY* 1.3 62.9 + - - +
257B ARG* 3.2 28.6 + - + +
258B THR* 4.3 3.5 + - - +
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Residues in contact with GLY 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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212B LEU 3.0 23.8 - - - -
213B VAL 4.1 10.1 - - - -
215B HIS* 5.6 3.6 - - - -
251B ILE 2.9 15.0 + - - -
252B THR 3.0 2.0 + - - -
254B ARG* 1.3 69.9 - - - +
256B LEU* 1.3 64.8 + - - +
257B ARG 3.0 2.8 + - - -
258B THR* 3.3 10.5 + - - -
262B ARG* 2.9 21.7 + - - -
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Residues in contact with LEU 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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10B LEU* 3.5 29.1 - - + +
13B ALA* 4.8 0.2 - - + -
67B LEU* 4.5 5.8 - - + -
70B ALA* 3.7 30.3 - - + -
71B MET* 4.3 10.5 - - - -
74B LEU* 3.9 24.5 - - + -
212B LEU* 3.8 32.3 - - + -
252B THR* 3.1 12.1 + - + +
253B SER* 3.1 23.5 + - - +
255B GLY* 1.3 74.8 - - - +
257B ARG* 1.3 68.4 + - - +
259B LEU* 3.0 23.8 + - + +
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Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 2.9 37.4 + - - +
11B VAL* 3.3 35.5 + - + +
13B ALA* 2.7 34.1 + - - +
14B GLY* 4.9 1.2 - - - -
15B ARG* 3.4 28.7 - - - +
25B ASN* 4.9 11.6 + - - +
26B SER* 5.7 3.6 - - - +
66B SER* 5.3 2.0 + - - -
253B SER* 3.2 34.3 + - - +
254B ARG* 3.2 22.6 - - + +
255B GLY 3.0 1.2 + - - -
256B LEU* 1.3 80.6 - - - +
258B THR* 1.3 64.7 + - + +
260B GLY 5.1 0.9 + - - -
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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