Contacts of the helix formed by residues 242 - 254 (chain B) in PDB entry 5FV7
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 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B LEU* 5.1 0.4 - - - -
240B GLY 3.3 7.3 + - - -
241B ILE* 1.3 75.8 - - - +
243B PRO* 1.3 70.8 - - - +
244B LYS 3.3 2.0 - - - -
245B ARG* 3.1 11.5 + - - +
246B ALA* 2.8 28.1 + - - +
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Residues in contact with PRO 243 (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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4B GLN 5.9 0.4 - - - +
5B GLY* 4.8 11.4 - - - +
9B LEU* 3.7 27.1 - - + +
230B LEU* 3.4 18.4 - - + -
241B ILE 4.5 0.9 - - - +
242B GLY* 1.3 82.9 - - - +
244B LYS* 1.3 62.1 + - + +
246B ALA* 3.2 13.5 + - - +
247B VAL* 3.3 16.8 + - - +
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Residues in contact with LYS 244 (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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9B LEU* 4.8 6.2 - - + +
13B VAL* 5.8 5.6 - - + -
242B GLY 3.3 0.4 - - - -
243B PRO* 1.3 78.4 - - + +
245B ARG* 1.3 64.2 + - - +
247B VAL* 3.5 10.5 + - - +
248B ASP* 3.3 20.8 + - - +
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Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLY 4.3 8.3 + - - -
241B ILE* 3.8 26.7 - - + -
242B GLY* 3.1 21.5 + - - +
244B LYS* 1.3 78.3 - - - +
246B ALA* 1.3 57.1 + - - +
248B ASP* 3.4 7.9 + - - +
249B LEU* 3.1 46.0 + - + +
268B TYR* 3.6 25.9 + - - -
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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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226B LEU* 3.6 14.8 - - + +
229B LEU* 3.9 29.3 - - + +
230B LEU* 3.9 8.1 - - + -
241B ILE* 4.0 9.8 - - + +
242B GLY 2.8 12.4 + - - +
243B PRO 3.2 10.3 + - - +
245B ARG* 1.3 76.2 - - - +
247B VAL* 1.3 63.3 + - - +
249B LEU* 4.7 1.8 - - - +
250B ILE* 3.3 31.2 + - - +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.8 24.5 - - + -
13B VAL* 5.4 5.6 - - + -
216B LEU* 3.9 31.0 - - + -
218B LEU* 5.3 2.8 - - + +
226B LEU* 3.6 22.9 - - + -
243B PRO 3.3 15.7 + - - +
244B LYS* 3.5 9.2 + - - +
246B ALA* 1.3 75.2 - - - +
248B ASP* 1.3 63.2 + - - +
250B ILE* 4.3 3.1 - - - +
251B GLN* 3.4 38.8 + - + +
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Residues in contact with ASP 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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244B LYS 3.3 10.9 + - - +
245B ARG* 3.6 12.8 - - - +
246B ALA 3.3 0.4 - - - -
247B VAL* 1.3 80.4 - - - +
249B LEU* 1.3 69.4 + - + +
251B GLN* 3.4 21.0 + - - +
252B LYS* 3.6 13.0 + - - +
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Residues in contact with LEU 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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229B LEU* 5.5 2.7 - - + -
241B ILE* 3.8 30.1 - - + -
245B ARG* 3.1 35.3 + - - +
246B ALA* 4.3 4.3 - - - +
248B ASP* 1.3 87.3 - - + +
250B ILE* 1.3 62.7 + - - +
252B LYS* 3.4 1.8 + - - +
253B HIS* 3.1 41.1 + - + +
259B ILE* 3.7 35.9 - - + -
263B LEU* 5.2 8.1 - - + -
268B TYR* 6.4 0.2 - - + -
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Residues in contact with ILE 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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218B LEU* 3.8 25.1 - - + -
222B GLN* 3.8 24.5 - - + +
225B ASP* 3.7 28.3 - - + -
226B LEU* 4.1 11.0 - - + -
229B LEU* 3.8 17.5 - - + -
246B ALA 3.3 19.1 + - - +
247B VAL* 4.3 3.6 - - - +
248B ASP 3.4 0.2 - - - -
249B LEU* 1.3 76.4 - - - +
251B GLN* 1.3 56.9 + - - +
254B LYS* 2.6 36.3 + - - +
255B SER* 4.1 11.7 - - - -
256B ILE* 4.2 0.7 - - + +
259B ILE* 3.6 19.5 - - + -
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Residues in contact with GLN 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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214A GLN* 5.4 2.2 - - - +
216B LEU* 2.8 28.2 + - - +
217B GLY 4.8 2.7 - - - +
218B LEU* 3.8 19.9 - - + +
247B VAL* 3.4 31.2 + - - +
248B ASP* 3.4 16.2 + - - +
249B LEU 3.3 0.4 - - - -
250B ILE* 1.3 78.7 - - - +
252B LYS* 1.3 59.5 + - - +
254B LYS* 3.8 17.5 - - - +
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Residues in contact with LYS 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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248B ASP* 3.6 10.8 + - - +
249B LEU* 3.4 1.8 + - - -
250B ILE 3.4 0.4 - - - -
251B GLN* 1.3 78.1 - - - +
253B HIS* 1.3 81.3 + - + +
254B LYS* 3.8 2.3 - - - +
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Residues in contact with HIS 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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249B LEU* 3.1 32.5 + - + +
252B LYS* 1.3 92.9 + - + +
254B LYS* 1.3 62.4 + - - +
255B SER* 2.8 15.6 + - - -
258B GLU* 3.3 30.4 + - + +
259B ILE* 3.7 25.1 - - + -
262B ARG* 3.3 31.6 - - + +
263B LEU 5.6 0.2 + - - -
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Residues in contact with LYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 6.2 0.4 - - + -
222B GLN* 3.1 46.9 - - + +
225B ASP* 4.3 2.8 - - - +
250B ILE* 2.6 28.0 + - - +
251B GLN* 3.8 18.8 - - - +
252B LYS 5.1 1.3 - - - +
253B HIS* 1.3 72.6 - - - +
255B SER* 1.3 59.0 + - - +
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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