Contacts of the helix formed by residues 241 - 254 (chain C) in PDB entry 2PCB
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 ASP 241 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C ALA* 3.6 23.4 - - + +
155C ARG* 3.5 34.6 + - - -
237C SER 2.8 13.8 + - - +
239C ILE 4.3 0.2 - - - -
240C GLN* 1.3 77.2 - - - +
242C PRO* 1.3 66.0 - - - +
243C LYS* 2.9 29.6 + - - +
244C TYR* 3.0 14.1 + - + -
245C LEU* 2.4 38.4 + - - +
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Residues in contact with PRO 242 (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 GLN 3.9 5.8 - - - +
241C ASP* 1.3 99.0 - - - +
243C LYS* 1.3 68.8 - - + +
245C LEU* 3.8 8.1 - - + +
246C SER* 3.5 19.6 + - - -
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Residues in contact with LYS 243 (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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155C ARG* 4.3 8.7 - - - +
165C ASP* 3.9 22.4 - - + +
241C ASP* 2.9 10.7 + - - +
242C PRO* 1.3 83.0 - - + +
244C TYR* 1.3 68.9 + - - +
246C SER* 3.6 7.7 + - - -
247C ILE* 3.3 25.7 + - + +
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Residues in contact with TYR 244 (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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151C ALA* 3.8 24.7 - - + -
154C VAL* 3.9 6.2 - - + +
155C ARG* 3.1 43.0 + - - +
165C ASP* 3.4 33.0 + - + -
168C VAL* 3.8 19.2 - - + +
169C VAL* 3.4 20.2 - - + -
237C SER* 3.8 7.0 - - - -
238C LEU* 2.9 43.1 - - + +
241C ASP* 3.0 25.3 + - + +
243C LYS* 1.3 79.3 - - - +
245C LEU* 1.3 56.9 + - - +
247C ILE* 2.8 14.0 + - - +
248C VAL* 2.7 21.4 + - - +
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Residues in contact with LEU 245 (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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207C LEU* 4.1 26.7 - - + -
238C LEU 2.8 7.9 + - - -
239C ILE* 3.9 25.4 - - + +
241C ASP 2.4 32.0 + - - +
242C PRO* 3.8 9.9 - - + +
244C TYR* 1.3 65.3 - - - +
246C SER* 1.3 57.1 + - - +
248C VAL* 3.2 5.7 - - + +
249C LYS* 2.9 43.1 + - + +
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Residues in contact with SER 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C PRO 3.5 12.4 + - - -
243C LYS* 3.6 9.9 + - - -
244C TYR 3.2 1.2 - - - -
245C LEU* 1.3 77.9 - - - +
247C ILE* 1.3 66.5 + - - +
249C LYS* 3.6 11.3 + - - +
250C GLU* 3.4 21.0 + - - +
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Residues in contact with ILE 247 (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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165C ASP* 3.6 17.3 - - + +
166C ARG* 3.2 60.1 - - + +
169C VAL* 3.8 14.8 - - + -
243C LYS* 3.3 15.7 + - + +
244C TYR 2.8 8.4 + - - +
246C SER* 1.3 74.5 - - - +
248C VAL* 1.3 61.9 + - - +
250C GLU* 3.7 6.4 - - - +
251C TYR* 2.9 60.3 + - + -
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Residues in contact with VAL 248 (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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169C VAL* 4.1 9.4 - - + -
203C TYR* 3.5 33.5 - - + +
206C LEU* 4.0 20.9 - - + -
207C LEU* 4.5 4.7 - - + -
238C LEU* 3.5 26.9 - - + +
239C ILE* 4.5 7.0 - - + -
244C TYR* 2.7 31.9 - - - +
245C LEU* 3.2 9.6 - - + +
247C ILE* 1.3 77.6 - - - +
249C LYS* 1.3 53.0 + - - +
252C ALA* 2.7 37.8 + - - +
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Residues in contact with LYS 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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207C LEU* 3.9 20.4 - - + +
245C LEU* 2.9 39.3 + - + +
246C SER* 3.9 9.9 - - - +
247C ILE 3.2 0.2 - - - -
248C VAL* 1.3 76.3 - - - +
250C GLU* 1.4 57.6 + - - +
252C ALA* 3.0 7.4 - - - +
253C ASN* 2.9 41.3 + - - +
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Residues in contact with GLU 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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166C ARG* 2.7 39.0 + - - -
246C SER 3.4 15.7 + - - +
247C ILE* 3.4 6.4 + - - +
248C VAL 3.2 0.2 - - - -
249C LYS* 1.4 76.2 - - - +
251C TYR* 1.3 75.5 + - + +
252C ALA 3.0 1.1 - - - -
253C ASN* 3.2 7.5 + - - +
254C ASP* 3.1 25.7 + - + +
257C LYS* 3.0 37.0 + - + +
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Residues in contact with TYR 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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166C ARG* 2.6 26.2 + - - +
169C VAL* 4.1 2.5 - - + -
170C ALA* 3.6 24.9 - - + +
200C ASN* 3.0 24.1 - - - +
203C TYR* 3.9 35.9 - + + -
247C ILE* 2.9 31.6 + - + +
250C GLU* 1.3 87.6 - - + +
252C ALA* 1.3 60.3 + - - +
253C ASN 3.4 0.2 + - - -
254C ASP 3.6 10.3 + - - -
255C GLN 4.0 0.2 + - - -
257C LYS* 3.4 24.7 - - + -
258C PHE* 3.6 31.9 - + + +
261C ASP* 2.6 36.2 + - + +
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Residues in contact with ALA 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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200C ASN* 3.7 6.1 - - - +
203C TYR* 3.7 16.8 - - + +
204C LEU* 3.4 27.3 - - + +
207C LEU* 3.4 24.9 - - + -
248C VAL 2.7 22.8 + - - +
249C LYS 3.0 10.3 - - - +
251C TYR* 1.3 79.2 - - - +
253C ASN* 1.3 56.1 + - - +
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Residues in contact with ASN 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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200C ASN* 5.3 0.2 - - - -
249C LYS* 2.9 24.3 + - - +
250C GLU* 3.6 8.0 - - - +
252C ALA* 1.3 78.5 - - - +
254C ASP* 1.3 56.1 + - + +
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Residues in contact with ASP 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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200C ASN* 4.8 0.2 + - - -
250C GLU* 3.1 14.0 + - + +
251C TYR 3.6 6.7 + - - +
252C ALA 3.7 0.2 - - - -
253C ASN* 1.3 77.4 - - + +
255C GLN* 1.3 68.2 + - - +
256C ASP* 3.0 27.1 + - - +
257C LYS* 2.9 30.7 + - + +
258C PHE* 3.1 9.7 + - - +
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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