Contacts of the helix formed by residues 243 - 252 (chain B) in PDB entry 4CRU
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 PRO 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B ASP 3.8 6.9 - - - +
242B ASN* 1.3 90.2 - - - +
244B ARG* 1.3 65.1 + - + +
246B ARG* 3.4 11.7 + - + +
247B GLU* 3.1 23.2 + - - +
250B ARG* 5.6 0.2 + - - -
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Residues in contact with ARG 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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1603A TRP* 3.0 80.4 - - + +
1604A ALA 6.3 0.4 - - - -
200B CYS 4.3 6.5 + - - -
201B GLN* 4.5 7.1 + - - +
242B ASN* 3.0 11.9 + - - +
243B PRO* 1.3 76.5 - - + +
245B ALA* 1.3 64.9 + - - +
247B GLU* 3.4 11.8 + - - +
248B ALA 3.1 17.2 + - - -
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Residues in contact with ALA 245 (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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1603A TRP* 4.1 4.3 - - - -
200B CYS* 3.9 14.1 - - - -
206B PHE* 3.7 28.3 - - + -
239B LEU* 3.1 26.0 - - + +
242B ASN* 2.8 13.9 + - - +
244B ARG* 1.3 77.0 - - - +
246B ARG* 1.3 51.7 + - - +
248B ALA* 3.1 2.4 + - - +
249B LEU* 2.7 40.9 + - - +
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Residues in contact with ARG 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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239B LEU 4.2 0.4 + - - -
240B SER* 2.8 31.0 + - - +
241B ASP* 4.5 8.4 + - - +
242B ASN 2.8 17.1 + - - +
243B PRO* 3.6 10.9 - - + +
245B ALA* 1.3 75.9 - - - +
247B GLU* 1.3 62.1 + - - +
249B LEU* 3.3 3.4 + - - +
250B ARG* 3.0 36.3 + - - +
282B ASN* 3.2 51.5 + - - +
283B LEU* 3.7 20.4 - - + +
285B GLU* 3.7 27.6 + - - +
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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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243B PRO 3.1 13.4 + - - +
244B ARG* 3.7 13.7 - - - +
245B ALA 3.2 0.2 - - - -
246B ARG* 1.3 78.1 - - - +
248B ALA* 1.3 62.2 + - - +
250B ARG* 3.3 31.5 + - - +
251B GLN* 3.2 30.4 + - - +
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Residues in contact with ALA 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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1603A TRP* 4.3 10.3 - - + -
203B TYR* 4.6 8.7 - - + -
206B PHE* 3.5 28.5 - - + -
244B ARG 3.1 14.3 + - - +
245B ALA 3.6 4.5 - - - +
247B GLU* 1.3 78.2 - - - +
249B LEU* 1.3 58.8 + - - +
251B GLN* 3.0 24.4 + - - +
252B CYS* 3.0 16.0 + - - +
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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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206B PHE* 4.1 13.5 - - + -
210B ALA* 5.0 1.3 - - + -
236B TYR* 3.7 53.6 - - + +
239B LEU* 4.0 17.0 - - + -
240B SER* 4.1 16.6 - - - +
245B ALA 2.7 24.4 + - - +
246B ARG 3.7 4.5 - - - +
248B ALA* 1.3 69.6 - - - +
250B ARG* 1.3 66.1 + - - +
251B GLN 3.0 1.6 - - - -
252B CYS* 3.9 17.7 - - - -
253B LEU* 2.9 35.2 + - + +
279B LEU* 4.7 3.6 - - + -
283B LEU* 3.8 15.5 - - + +
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Residues in contact with ARG 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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243B PRO 5.6 0.2 + - - -
246B ARG* 3.0 30.4 + - - +
247B GLU* 3.3 39.8 + - - +
248B ALA 3.2 0.2 - - - -
249B LEU* 1.3 77.6 - - - +
251B GLN* 1.3 73.3 + - - +
258B LYS* 4.7 10.9 + - - -
283B LEU* 3.1 46.9 + - + +
284B GLN* 5.2 0.4 - - - +
285B GLU 4.6 11.1 + - - -
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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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247B GLU* 3.2 30.3 + - - +
248B ALA* 3.0 12.2 + - - +
250B ARG* 1.3 93.0 - - - +
252B CYS* 1.3 59.9 + - + +
253B LEU 3.7 2.1 - - - +
258B LYS* 5.6 2.2 + - - -
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Residues in contact with CYS 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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206B PHE* 4.5 6.1 - - - -
210B ALA* 4.3 19.5 - - - -
236B TYR* 5.8 1.1 - - - -
248B ALA* 3.0 19.5 + - - +
249B LEU* 3.9 21.8 - - - -
251B GLN* 1.3 79.0 - - + +
253B LEU* 1.3 68.3 + - - +
254B PRO* 3.2 8.8 - - - +
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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