Contacts of the helix formed by residues 240 - 249 (chain R) in PDB entry 6CNC
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 THR 240 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238R ARG* 4.8 25.4 - - + +
239R ARG* 1.3 77.0 - - - +
241R HIS* 1.3 67.5 + - - +
242R THR* 2.9 23.0 + - - -
243R GLU* 3.2 20.7 + - - +
244R ILE* 3.1 19.8 + - - +
402S PHE* 5.3 0.9 - - - -
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Residues in contact with HIS 241 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229R LEU* 3.7 23.5 - - + +
239R ARG 5.8 0.7 - - - -
240R THR* 1.3 71.4 - - - +
242R THR* 1.3 66.9 + - + +
244R ILE* 2.9 20.4 + - - +
245R VAL* 2.9 19.1 + - - +
252R GLU* 4.4 19.3 - - + -
255R LEU* 3.4 28.9 - - + -
256R GLN* 2.9 43.6 + - + +
259R LEU* 4.9 1.6 - - - +
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Residues in contact with THR 242 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240R THR* 2.9 14.9 + - - -
241R HIS* 1.3 75.4 - - + +
243R GLU* 1.3 70.9 + - - +
244R ILE 3.1 0.3 + - - -
245R VAL* 3.1 13.0 + - - +
246R ALA* 2.9 26.1 + - - +
252R GLU* 3.1 23.1 + - - +
402S PHE* 4.1 26.2 - - + -
405S LEU* 4.9 6.0 - - + +
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Residues in contact with GLU 243 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189R LEU* 4.9 14.1 - - + +
190R ASP* 5.6 1.2 - - - +
238R ARG 4.6 0.3 - - - +
239R ARG* 2.9 53.6 + - + -
240R THR* 3.2 30.9 + - - +
242R THR* 1.3 81.6 + - - +
244R ILE* 1.3 59.9 + - + +
246R ALA* 3.9 10.0 - - - +
247R VAL* 4.5 6.9 + - - +
402S PHE* 4.1 26.9 - - + -
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Residues in contact with ILE 244 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189R LEU* 5.3 8.7 - - + -
225R GLY* 4.0 29.6 - - - +
228R ILE* 5.3 10.8 - - + -
229R LEU* 3.5 49.1 - - + +
232R CYS* 6.2 1.6 - - + -
239R ARG* 4.0 14.1 - - + +
240R THR 3.1 13.7 + - - +
241R HIS* 2.9 13.0 + - - +
243R GLU* 1.3 76.3 - - - +
245R VAL* 1.3 60.8 + - - +
246R ALA 3.1 2.3 + - - -
247R VAL* 3.2 13.5 - - + +
248R SER* 2.9 24.8 + - - -
255R LEU* 4.4 11.0 - - + -
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Residues in contact with VAL 245 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241R HIS 2.9 17.4 + - - +
242R THR* 3.2 21.1 - - - +
244R ILE* 1.3 73.3 - - + +
246R ALA* 1.3 60.9 + - - +
247R VAL 3.3 0.2 - - - -
248R SER* 3.5 8.5 - - - -
249R HIS* 2.6 28.4 + - - -
250R VAL* 3.4 37.7 - - + +
251R ALA 4.2 0.4 - - - -
252R GLU* 4.1 19.5 - - + +
255R LEU* 4.3 14.8 - - + -
405S LEU* 3.6 30.1 - - + +
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Residues in contact with ALA 246 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242R THR 2.9 15.8 + - - +
243R GLU 3.9 9.4 - - - +
244R ILE 3.1 0.6 - - - -
245R VAL* 1.3 78.9 - - - +
247R VAL* 1.3 60.7 - - + +
249R HIS* 3.2 21.1 + - - -
401S PRO 5.8 0.7 - - - +
402S PHE* 4.0 27.1 - - + -
404S ASN* 6.1 0.7 - - - +
405S LEU* 3.8 13.2 - - + +
406S TYR* 5.5 1.2 - - - -
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Residues in contact with VAL 247 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184R HIS* 6.0 2.9 - - + +
185R PHE* 3.4 45.7 - - + +
188R LYS* 3.6 35.7 - - + +
189R LEU* 4.6 10.1 - - + -
228R ILE* 6.2 0.2 - - + -
243R GLU 4.5 6.1 - - - +
244R ILE* 3.2 13.2 - - + +
246R ALA* 1.3 76.2 - - + +
248R SER* 1.3 63.1 + - - +
249R HIS* 2.4 28.9 + - - -
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Residues in contact with SER 248 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144R ILE* 5.5 0.2 - - - +
185R PHE* 4.2 13.4 - - - -
221R ALA* 3.2 32.3 + - - +
225R GLY* 4.1 9.1 - - - -
244R ILE* 2.9 29.1 + - - -
245R VAL* 3.7 8.5 - - - -
247R VAL* 1.3 80.0 - - - +
249R HIS* 1.3 68.3 + - - +
250R VAL* 3.2 25.0 + - - +
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Residues in contact with HIS 249 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144R ILE* 4.2 18.0 - - + +
145R ASP* 4.8 22.4 + - + +
185R PHE* 5.2 0.4 - - - -
245R VAL 2.6 20.5 + - - -
246R ALA 3.2 17.7 + - - -
247R VAL* 2.4 33.4 + - - -
248R SER* 1.3 72.4 + - - +
250R VAL* 1.3 61.5 + - - +
405S LEU* 6.3 0.2 - - + -
406S TYR* 2.7 65.6 + + - +
407S ASN* 3.2 18.6 - - - +
408S TYR* 4.1 11.1 - - - -
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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