Contacts of the helix formed by residues 245 - 254 (chain B) in PDB entry 4LLB
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B LYS 3.8 2.6 + - - -
244B PHE* 1.3 73.8 - - - +
246B PRO* 1.3 63.7 - - - +
247B GLU* 2.7 26.7 + - - +
248B LEU* 3.0 26.1 + - - +
249B THR* 2.8 31.5 + - - -
282B ASP 5.2 1.6 + - - -
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Residues in contact with PRO 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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246A PRO* 4.7 4.5 - - + +
250A VAL* 4.2 20.9 - - + -
244B PHE 4.5 1.6 - - - +
245B SER* 1.3 84.6 - - - +
247B GLU* 1.3 70.4 + - - +
249B THR* 3.6 8.1 - - - +
250B VAL* 3.2 30.9 + - + +
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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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246A PRO* 4.1 11.4 - - - +
247A GLU* 3.9 43.1 - - + +
250A VAL* 3.3 32.2 - - - +
245B SER* 2.7 25.5 + - - +
246B PRO* 1.3 78.6 - - - +
248B LEU* 1.3 60.6 + - - +
250B VAL* 3.4 5.4 + - - +
251B ARG* 3.4 28.9 + - - +
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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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243B LYS 5.6 0.2 - - - +
244B PHE* 3.7 33.0 - - + -
245B SER* 3.0 20.9 + - - +
247B GLU* 1.3 73.8 - - - +
249B THR* 1.3 65.5 + - - +
251B ARG* 3.3 1.0 + - - -
252B VAL* 2.9 41.5 + - + +
281B CYS 4.1 0.7 - - - +
282B ASP* 4.0 14.1 + - - +
283B SER 3.4 34.3 - - - +
284B CYS 3.6 4.3 - - - +
285B ASP* 3.6 13.2 - - + +
2D ARG* 3.4 26.7 - - - +
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Residues in contact with THR 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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228B ILE* 4.3 9.5 - - + +
239B PRO* 3.3 39.7 - - + +
244B PHE* 3.5 7.4 + - - +
245B SER 2.8 23.7 + - - -
246B PRO* 3.6 9.7 - - - +
248B LEU* 1.3 77.3 - - - +
250B VAL* 1.3 64.2 - - + +
252B VAL* 3.8 1.8 - - - +
253B LYS* 3.1 46.2 + - + +
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Residues in contact with VAL 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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246A PRO* 3.8 29.6 - - + -
246B PRO 3.2 16.2 + - - +
247B GLU 3.7 6.5 - - - +
248B LEU 3.3 0.2 - - - -
249B THR* 1.3 82.8 - - + +
251B ARG* 1.3 67.3 + - + +
253B LYS* 3.5 15.0 + - + +
254B ALA* 3.6 11.8 + - - +
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Residues in contact with ARG 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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247A GLU* 5.4 9.2 + - - +
190B HIS 5.7 1.4 + - - -
191B MET* 4.6 25.8 - - + +
247B GLU* 3.4 15.6 + - - +
248B LEU 3.3 4.2 + - - +
250B VAL* 1.3 77.9 - - + +
252B VAL* 1.3 66.3 + - - +
254B ALA* 3.1 15.6 + - - +
255B LEU* 3.1 24.5 + - + +
283B SER* 3.0 49.9 + - - +
284B CYS* 4.9 4.7 - - - +
310B CYS* 3.9 19.4 + - - +
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Residues in contact with VAL 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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228B ILE* 3.7 27.4 - - + -
244B PHE* 4.1 6.1 - - + -
248B LEU* 2.9 43.2 + - + +
249B THR 3.8 4.5 - - - +
251B ARG* 1.3 75.0 - - - +
253B LYS* 1.3 58.3 + - - +
255B LEU* 3.0 34.0 + - - +
257B TRP* 3.4 32.2 - - + +
284B CYS 3.8 14.4 - - - +
285B ASP* 3.9 10.3 - - + -
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Residues in contact with LYS 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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223A LYS* 5.9 2.4 - - - +
226B GLU* 4.5 22.2 + - - +
227B LEU 4.7 9.6 - - - +
228B ILE* 4.5 20.9 - - + -
239B PRO* 5.0 2.0 - - - +
249B THR* 3.1 39.9 + - + +
250B VAL* 3.7 9.6 - - + +
251B ARG 3.3 0.4 - - - -
252B VAL* 1.3 75.9 - - - +
254B ALA* 1.3 59.7 + - - +
255B LEU 3.6 3.3 + - - +
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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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191B MET* 5.9 5.8 - - + -
193B GLU* 4.1 9.4 - - - +
250B VAL 3.6 8.8 + - - +
251B ARG* 3.1 11.8 + - - +
252B VAL 3.1 1.0 - - - -
253B LYS* 1.3 77.7 - - - +
255B LEU* 1.3 67.3 + - + +
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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