Contacts of the helix formed by residues 248 - 258 (chain C) in PDB entry 4LCC
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 VAL 248 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C LEU* 5.2 1.3 - - + -
196C HIS* 4.1 33.4 - - + +
197C TYR* 3.2 49.8 - - + +
232C PHE* 4.8 4.5 - - + -
246C ASP* 3.1 4.3 + - - +
247C ASN* 1.3 77.7 - - + +
249C ALA* 1.3 61.8 + - - +
250C ASP 2.9 6.0 + - - -
251C ILE* 3.2 23.4 + - + +
252C ILE* 3.4 12.8 - - + +
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C PHE* 3.5 55.3 - - + +
233C LEU* 3.5 17.5 - - + +
244C ALA* 3.6 4.3 - - + +
246C ASP* 3.0 22.0 + - + +
248C VAL* 1.3 78.6 - - - +
250C ASP* 1.3 57.1 + - - +
251C ILE 3.3 0.2 - - - -
252C ILE* 3.7 4.4 + - - +
253C ARG 3.2 18.4 + - - -
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Residues in contact with ASP 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ALA* 3.6 12.2 - - + +
246C ASP 3.0 9.9 + - - +
247C ASN* 3.3 18.2 - - - +
248C VAL 2.9 0.6 - - - -
249C ALA* 1.3 77.1 - - - +
251C ILE* 1.3 64.8 + - - +
253C ARG* 3.1 35.7 + - - +
254C ARG* 3.1 22.3 + - - +
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Residues in contact with ILE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C HIS* 4.1 33.4 - - + +
247C ASN 4.0 8.5 - - - +
248C VAL* 3.2 24.0 + - + +
250C ASP* 1.3 77.4 + - - +
252C ILE* 1.3 65.0 + - + +
254C ARG* 3.1 16.9 + - - +
255C VAL* 3.2 23.1 + - + +
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Residues in contact with ILE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLN* 6.2 2.0 - - + -
193C LEU* 4.1 22.9 - - + -
196C HIS* 3.7 27.1 - - + +
232C PHE* 4.5 3.8 - - + -
233C LEU* 3.6 16.6 - - + -
248C VAL* 3.4 21.1 - - + +
249C ALA* 3.9 8.7 - - - +
250C ASP 3.3 0.2 - - - -
251C ILE* 1.3 76.9 - - + +
253C ARG* 1.3 66.7 + - - +
255C VAL* 3.1 10.6 + - + +
256C TRP* 3.0 59.5 + - + +
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Residues in contact with ARG 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C LEU* 4.8 4.0 - - + +
242C TRP* 3.8 27.6 + - + +
244C ALA* 4.1 13.7 - - + +
249C ALA 3.2 15.2 + - - +
250C ASP* 3.1 42.0 + - - +
252C ILE* 1.3 76.1 - - - +
254C ARG* 1.3 67.5 + - - +
255C VAL 3.1 0.7 + - - -
256C TRP* 3.1 4.0 + - - +
257C GLU* 2.9 68.6 + - + +
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Residues in contact with ARG 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ASP* 3.1 10.0 + - - +
251C ILE* 3.6 9.4 - - - +
253C ARG* 1.3 91.3 - - - +
255C VAL* 1.3 62.5 + - + +
257C GLU* 4.1 6.9 - - - +
258C ALA* 3.7 21.1 + - - +
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ILE* 3.2 24.7 - - + +
252C ILE* 3.4 11.0 - - + +
253C ARG 3.1 0.4 - - - -
254C ARG* 1.3 80.8 - - + +
256C TRP* 1.3 76.3 + - + +
258C ALA* 3.9 8.4 + - - +
259C ASN* 4.0 16.1 + - - +
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Residues in contact with TRP 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLU* 4.4 20.9 + - - -
205C TYR* 4.7 4.0 - - - -
225C TYR* 3.7 28.9 - + - -
233C LEU* 3.6 23.8 - - + -
242C TRP* 3.4 59.7 - + + +
252C ILE* 3.0 33.1 + - + +
253C ARG 3.9 2.0 - - - +
255C VAL* 1.3 90.0 - - + +
257C GLU* 1.3 62.1 + - - +
259C ASN* 3.0 28.6 + - - +
262C GLU* 6.5 0.2 - - + -
263C LEU* 3.1 14.5 - - + +
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Residues in contact with GLU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C LEU 5.5 0.2 - - - +
241C SER* 3.9 10.5 - - - -
242C TRP* 3.1 48.2 + - + +
253C ARG* 2.9 52.4 + - + +
254C ARG* 4.6 4.9 - - - +
255C VAL 3.4 0.2 - - - -
256C TRP* 1.3 74.1 - - - +
258C ALA* 1.3 57.5 + - - +
259C ASN 3.0 6.1 + - - -
260C GLN* 3.7 22.9 + - - +
263C LEU* 4.4 10.5 - - + -
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Residues in contact with ALA 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C ARG 3.7 17.1 + - - +
255C VAL* 4.3 5.6 - - - +
256C TRP 3.2 0.8 - - - -
257C GLU* 1.3 75.4 - - - +
259C ASN* 1.3 56.3 + - - +
260C GLN* 3.2 8.5 + - - +
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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