Contacts of the helix formed by residues 222 - 234 (chain C) in PDB entry 2B5F
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 ASN 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C THR* 6.2 0.4 - - - +
51C PHE* 3.9 22.3 - - + -
85C ILE* 5.2 3.0 - - - +
100C ILE 2.9 24.5 + - - -
101C ASN* 3.3 16.4 - - - +
102C PRO* 3.5 10.2 - - - +
220C GLY 4.1 6.3 - - - +
221C ILE* 1.3 83.7 - - + +
223C PRO* 1.3 72.0 - - - +
224C ALA* 3.2 8.0 + - - +
225C ARG* 3.1 27.6 + - + +
226C SER* 3.0 23.7 + - - -
245C PHE 4.6 0.4 - - - -
249C PRO* 4.1 2.4 - - - +
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Residues in contact with PRO 223 (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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101C ASN* 3.6 12.3 - - - +
102C PRO* 4.2 4.7 - - + -
103C ALA* 3.9 13.0 - - + +
222C ASN* 1.3 87.5 - - - +
224C ALA* 1.3 55.9 + - - +
226C SER* 3.3 3.5 + - - -
227C PHE* 2.8 30.7 + - - +
245C PHE 3.4 21.1 - - - +
246C TRP* 3.5 40.7 - - + -
249C PRO* 4.0 9.6 - - + -
250C PHE* 3.8 24.5 - - + -
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Residues in contact with ALA 224 (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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48C THR* 4.6 4.3 - - + -
100C ILE 5.5 0.4 - - - +
102C PRO* 3.5 26.8 - - + +
126C GLN* 3.7 31.4 - - + +
127C CYS* 3.9 13.6 - - - +
130C ALA* 3.1 13.5 - - + +
222C ASN* 3.2 4.0 + - - +
223C PRO* 1.3 75.0 - - - +
225C ARG* 1.4 61.8 + - - +
227C PHE* 3.9 1.2 - - - +
228C GLY 2.9 26.0 + - - -
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Residues in contact with ARG 225 (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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48C THR* 5.6 0.6 - - - +
51C PHE* 4.0 22.2 - - + -
52C LEU* 3.7 29.0 - - + +
56C VAL* 4.9 3.8 - - - +
59C VAL* 5.5 2.6 - - - +
81C PHE* 3.6 33.5 - - + -
130C ALA* 4.5 0.2 - - - +
151C GLY* 2.8 27.7 + - - -
153C ASN* 2.8 31.4 + - - +
210C HIS* 5.3 0.4 - - - -
218C GLY 4.4 9.7 + - - -
219C THR 3.9 10.8 + - - -
220C GLY 4.6 9.2 - - - -
222C ASN* 3.1 27.3 + - + +
224C ALA* 1.4 80.3 - - - +
226C SER* 1.3 64.7 + - - +
229C ALA* 3.8 22.5 + - - +
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Residues in contact with SER 226 (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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153C ASN* 3.1 36.2 + - - -
220C GLY* 4.3 4.0 - - - -
222C ASN 3.0 12.7 + - - -
223C PRO 3.7 7.6 - - - -
225C ARG* 1.3 79.5 - - - +
227C PHE* 1.3 61.1 + - - +
229C ALA* 3.6 2.4 + - - +
230C ALA* 3.2 17.2 + - - +
242C GLN* 3.5 16.1 + - - -
245C PHE* 3.3 35.5 - - - +
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Residues in contact with PHE 227 (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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127C CYS* 3.9 27.1 - - + -
131C ILE* 3.8 24.5 - - + -
223C PRO 2.8 21.6 + - - +
224C ALA* 3.9 3.4 - - - +
226C SER* 1.3 70.7 - - - +
228C GLY* 1.3 68.5 + - - +
230C ALA* 3.1 2.6 + - - +
231C VAL* 2.8 43.4 + - + +
239C TRP* 4.1 18.6 - + - -
242C GLN* 3.2 21.4 + - + +
246C TRP* 3.8 18.6 - + + -
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Residues in contact with GLY 228 (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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130C ALA* 4.0 0.9 - - - -
131C ILE* 3.9 24.8 - - - -
134C VAL* 3.2 15.7 - - - +
224C ALA 2.9 19.9 + - - -
225C ARG 4.4 0.4 - - - -
226C SER 3.5 0.2 - - - -
227C PHE* 1.3 75.8 - - - +
229C ALA* 1.3 56.4 + - - +
231C VAL* 3.6 1.9 + - - +
232C ILE* 3.1 32.9 + - - +
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Residues in contact with ALA 229 (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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52C LEU* 5.1 1.3 - - + -
56C VAL* 5.4 1.1 - - + -
134C VAL* 3.3 23.9 - - + +
150C GLY 3.9 4.3 - - - +
151C GLY 4.3 0.4 - - - -
152C ALA* 3.4 33.7 - - + +
225C ARG* 3.8 19.7 + - - +
226C SER 3.6 1.9 + - - +
227C PHE 3.3 0.4 - - - -
228C GLY* 1.3 72.9 - - - +
230C ALA* 1.3 57.7 + - - +
232C ILE* 4.2 0.2 - - - +
233C PHE* 2.7 38.8 + - - +
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Residues in contact with ALA 230 (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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152C ALA* 3.9 1.2 - - - +
226C SER 3.2 14.8 + - - +
227C PHE 3.1 8.0 + - - +
229C ALA* 1.3 73.0 - - - +
231C VAL* 1.3 60.2 + - - +
234C ASN* 2.9 28.7 + - - +
235C SER 4.7 0.5 + - - -
238C VAL* 3.8 23.3 - - + -
239C TRP* 3.4 29.1 - - + -
242C GLN* 3.6 18.4 - - - +
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Residues in contact with VAL 231 (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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131C ILE* 4.1 30.5 - - + -
227C PHE* 2.8 49.2 + - + +
228C GLY 3.8 4.0 - - - +
230C ALA* 1.3 74.6 - - - +
232C ILE* 1.3 65.9 + - + +
234C ASN* 3.8 14.4 + - - +
239C TRP* 3.8 22.2 - - + -
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Residues in contact with ILE 232 (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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131C ILE* 3.6 22.7 - - + +
134C VAL* 3.3 13.0 - - + -
135C GLY* 3.4 40.2 - - - +
138C LYS* 3.6 40.0 + - + +
145C TYR* 3.2 15.3 + - - +
146C ASN* 5.5 0.2 - - - +
228C GLY 3.1 15.3 + - - +
231C VAL* 1.3 80.1 - - + +
233C PHE* 1.3 65.5 + - - +
234C ASN* 4.3 2.9 - - - +
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Residues in contact with PHE 233 (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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145C TYR* 3.8 15.0 + + - +
146C ASN* 3.6 33.9 - - - +
149C GLY* 3.0 33.2 - - - -
150C GLY* 3.3 26.5 - - - -
152C ALA* 4.3 3.4 - - + -
229C ALA 2.7 23.3 + - - +
230C ALA* 4.5 0.9 - - - +
232C ILE* 1.3 72.0 - - - +
234C ASN* 1.3 71.7 + - - +
235C SER* 3.6 34.3 - - - -
238C VAL* 4.0 16.8 - - + -
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Residues in contact with ASN 234 (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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230C ALA* 2.9 17.4 + - - +
231C VAL 3.8 13.8 + - - +
232C ILE 4.3 3.1 - - - +
233C PHE* 1.3 82.0 - - - +
235C SER* 1.3 56.6 + - - +
236C ASN* 5.6 1.0 - - - +
239C TRP* 3.3 21.5 + - - +
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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