Contacts of the helix formed by residues 222 - 234 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D THR* 6.2 0.6 - - - +
51D PHE* 3.9 22.3 - - + -
85D ILE* 5.2 2.4 - - - +
100D ILE 2.9 24.5 + - - -
101D ASN* 3.3 17.7 - - - +
102D PRO* 3.5 10.4 - - - +
220D GLY 2.8 10.2 + - - +
221D ILE* 1.3 83.4 - - + +
223D PRO* 1.3 70.9 - - - +
224D ALA* 3.2 8.5 + - - +
225D ARG* 3.1 25.2 + - + +
226D SER* 3.0 23.6 + - - -
245D PHE 4.6 0.9 + - - -
249D PRO* 4.1 2.2 - - - +
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Residues in contact with PRO 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ASN* 3.6 12.3 - - - +
102D PRO* 4.2 4.9 - - + -
103D ALA* 3.9 13.7 - - + +
222D ASN* 1.3 86.1 - - - +
224D ALA* 1.3 55.8 + - - +
226D SER* 3.3 3.2 + - - -
227D PHE* 2.8 30.3 + - - +
245D PHE 3.4 21.8 - - - +
246D TRP* 3.5 40.4 - - + -
249D PRO* 4.0 9.6 - - + -
250D PHE* 3.8 24.2 - - + -
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Residues in contact with ALA 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D THR* 4.6 4.3 - - + -
100D ILE 5.5 0.2 - - - +
101D ASN* 5.4 0.4 - - - -
102D PRO* 3.5 27.6 - - + +
126D GLN* 3.7 30.7 - - + +
127D CYS* 3.9 13.4 - - - +
130D ALA* 3.1 12.8 - - + +
222D ASN* 3.2 4.2 + - - +
223D PRO* 1.3 73.9 - - - +
225D ARG* 1.4 61.5 + - - +
227D PHE* 3.9 1.2 - - - +
228D GLY 2.9 26.9 + - - -
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Residues in contact with ARG 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D THR* 5.6 0.4 - - - +
51D PHE* 4.0 22.4 - - + -
52D LEU* 3.7 29.0 - - + +
56D VAL* 4.9 3.0 - - - +
59D VAL* 5.5 2.6 - - - +
81D PHE* 3.6 32.1 - - + -
130D ALA* 4.5 0.2 - - - +
151D GLY* 3.1 23.0 + - - -
153D ASN* 2.8 31.4 + - - +
210D HIS* 6.0 0.2 - - - -
218D GLY* 4.5 4.4 + - - -
219D THR 3.5 13.9 + - - -
220D GLY* 4.2 22.2 - - - -
222D ASN* 3.1 25.6 + - + +
224D ALA* 1.4 80.2 - - - +
226D SER* 1.3 63.7 + - - +
228D GLY 3.9 0.2 + - - -
229D ALA* 3.8 18.6 + - - +
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Residues in contact with SER 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASN* 4.3 11.7 + - - +
220D GLY* 3.8 16.5 - - - -
222D ASN 3.0 12.1 + - - -
223D PRO 3.7 6.7 - - - -
225D ARG* 1.3 84.8 - - - +
227D PHE* 1.3 59.8 + - - +
229D ALA* 3.6 1.9 + - - +
230D ALA* 3.2 18.0 + - - +
238D VAL* 5.5 0.2 - - - +
242D GLN* 3.5 16.6 + - - -
245D PHE* 3.3 40.7 - - - +
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Residues in contact with PHE 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D CYS* 3.9 27.8 - - + -
131D ILE* 3.8 24.5 - - + -
223D PRO 2.8 21.4 + - - +
224D ALA* 3.9 3.1 - - - +
226D SER* 1.3 71.2 - - - +
228D GLY* 1.3 67.1 + - - +
230D ALA* 3.1 2.3 + - - +
231D VAL* 2.8 44.2 + - + +
239D TRP* 4.1 17.3 - + - -
242D GLN* 3.2 20.8 + - + +
246D TRP* 3.8 17.7 - + + -
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Residues in contact with GLY 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ALA* 4.0 4.9 - - - -
131D ILE* 3.9 29.6 - - - -
134D VAL* 3.8 6.2 - - - +
224D ALA 2.9 20.0 + - - -
225D ARG 4.4 0.7 - - - -
227D PHE* 1.3 76.2 - - - +
229D ALA* 1.3 56.8 + - - +
231D VAL* 3.6 1.9 + - - +
232D ILE* 3.1 32.7 + - - +
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Residues in contact with ALA 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 5.1 1.3 - - + -
56D VAL* 5.4 0.4 - - + -
134D VAL* 3.9 20.9 - - + +
145D TYR* 3.8 0.5 + - - -
150D GLY 4.0 7.6 - - - +
151D GLY* 3.9 22.7 - - - +
152D ALA* 4.0 11.2 - - - -
153D ASN 5.2 0.2 - - - +
225D ARG* 3.8 17.7 + - - +
226D SER 3.6 3.4 + - - +
227D PHE 3.3 0.6 - - - -
228D GLY* 1.3 72.7 - - - +
230D ALA* 1.3 56.9 + - - +
233D PHE* 2.7 39.4 + - - +
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Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ALA* 5.0 0.2 - - - +
226D SER 3.2 15.9 + - - +
227D PHE 3.1 8.2 + - - +
229D ALA* 1.3 73.2 - - - +
231D VAL* 1.3 59.2 + - - +
233D PHE 4.7 0.2 - - - +
234D ASN* 2.9 29.4 + - - +
235D SER 4.7 0.3 + - - -
238D VAL* 3.8 23.9 - - + +
239D TRP* 3.4 29.2 - - + -
242D GLN* 3.6 17.7 - - - +
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ILE* 4.1 30.7 - - + -
227D PHE* 2.8 48.8 + - + +
228D GLY 3.8 4.3 - - - +
230D ALA* 1.3 74.4 - - - +
232D ILE* 1.3 65.7 + - + +
234D ASN* 3.8 14.0 + - - +
239D TRP* 3.8 22.6 - - + -
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Residues in contact with ILE 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ILE* 3.6 35.2 - - + +
134D VAL* 3.1 28.0 - - + +
135D GLY* 4.6 5.4 - - - -
138D LYS* 3.1 52.4 + - + +
145D TYR* 3.4 17.7 - - + +
146D ASN* 5.4 0.9 - - - +
228D GLY 3.1 18.2 + - - +
231D VAL* 1.3 79.3 - - + +
233D PHE* 1.3 64.5 + - - +
234D ASN* 4.3 2.8 - - - +
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Residues in contact with PHE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D TYR* 3.5 31.8 + + - +
146D ASN* 3.5 42.1 - - - +
149D GLY* 3.9 19.1 - - - -
150D GLY* 3.9 8.5 - - - -
152D ALA* 3.5 25.4 - - + -
229D ALA 2.7 22.4 + - - +
230D ALA* 4.5 1.1 - - - +
232D ILE* 1.3 72.5 - - - +
234D ASN* 1.3 72.1 + - - +
235D SER* 3.5 34.7 + - - -
238D VAL* 4.0 7.9 - - + -
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Residues in contact with ASN 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D ALA* 2.9 17.4 + - - +
231D VAL 3.8 14.4 + - - +
232D ILE 4.3 2.7 - - - +
233D PHE* 1.3 81.1 - - - +
235D SER* 1.3 57.4 + - - +
236D ASN* 5.6 1.2 - - - +
239D TRP* 3.3 19.1 + - - +
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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