Contacts of the strand formed by residues 220 - 228 (chain B) in PDB entry 1D0G
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 ILE 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B TYR* 3.6 3.1 - - - -
212B LYS* 2.8 53.5 + - + +
214B THR* 4.0 26.7 - - + -
216B TYR* 4.4 16.6 - - + -
218B ASP 3.8 7.6 - - - +
219B PRO* 1.3 76.9 - - - +
221B LEU* 1.3 64.7 + - - +
222B LEU* 3.5 1.4 + - - +
161D HIS* 3.5 33.2 - - + +
57T LEU* 4.8 9.0 - - + -
59T PHE* 5.6 6.3 - - + -
61T LEU* 4.7 22.0 - - + -
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Residues in contact with LEU 221 (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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147B LEU* 5.4 4.9 - - + -
209B TYR* 3.8 19.3 - - + -
210B ILE 3.6 8.3 - - - +
211B TYR* 3.4 39.2 - - + +
219B PRO 4.1 0.4 + - - -
220B ILE* 1.3 71.5 - - - +
222B LEU* 1.3 57.5 + - - +
223B MET 3.5 20.9 - - - +
224B LYS* 4.2 20.4 - - + +
161D HIS* 3.1 21.7 + - - -
270D HIS* 4.6 0.2 + - - -
271D GLU* 3.6 46.2 - - + +
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Residues in contact with LEU 222 (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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184B ILE* 3.7 30.3 - - + -
210B ILE* 2.8 21.0 + - + +
211B TYR 4.7 0.7 - - - -
212B LYS* 3.9 35.0 - - + +
220B ILE 3.9 12.8 - - - +
221B LEU* 1.3 74.2 - - - +
223B MET* 1.3 69.9 + - + +
248B PHE* 3.6 43.3 - - + -
250B LEU* 4.6 2.9 - - + -
256B ILE* 4.5 5.2 - - + -
161D HIS* 3.8 27.3 + - + +
270D HIS 4.5 1.2 - - - +
271D GLU* 3.5 19.2 - - - +
274D PHE* 5.0 0.3 - - - -
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Residues in contact with MET 223 (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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184B ILE* 3.6 31.4 - - + +
209B TYR* 3.5 0.3 - - - -
210B ILE* 2.8 60.0 + - + -
221B LEU* 3.5 6.4 - - - +
222B LEU* 1.3 87.8 - - + +
224B LYS* 1.3 62.7 + - - +
244B GLN* 3.5 16.1 + - - +
245B GLY* 3.3 34.5 - - - +
246B GLY* 3.3 3.1 - - - -
248B PHE* 3.6 27.6 - - + -
271D GLU* 3.4 7.4 - - - +
274D PHE* 3.8 15.9 - - + -
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Residues in contact with LYS 224 (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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147B LEU* 5.9 3.2 - - + +
207B VAL* 4.7 4.5 - - + -
208B GLN 3.3 5.2 - - - +
209B TYR* 3.8 34.0 - - + -
221B LEU* 4.2 16.9 - - + +
223B MET* 1.3 77.1 - - - +
225B SER* 1.3 61.0 + - - +
226B ALA* 5.4 0.7 - - + +
244B GLN* 3.1 3.8 - - - -
187D GLN* 3.1 17.0 + - - -
189D TYR* 4.1 8.8 - - + -
241D SER* 4.5 1.4 + - - -
267D ASP* 5.2 1.8 + - - -
269D ASP* 4.5 14.9 + - - +
271D GLU* 3.0 13.7 + - + +
272D ALA* 3.9 29.3 - - + +
98T GLU* 2.6 33.5 + - - +
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Residues in contact with SER 225 (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 MET 3.9 0.3 - - - +
207B VAL* 3.4 4.2 - - - +
208B GLN 2.9 32.0 + - - -
224B LYS* 1.3 74.1 - - - +
226B ALA* 1.3 60.6 + - - +
242B ILE* 3.6 29.6 - - - +
243B TYR 4.5 2.4 + - - -
244B GLN* 3.3 22.0 - - - -
187D GLN* 3.6 10.4 + - - -
241D SER* 3.1 25.4 + - - -
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Residues in contact with ALA 226 (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 MET 3.3 2.9 - - - -
207B VAL* 3.8 24.9 - - + -
224B LYS* 5.7 0.9 - - + -
225B SER* 1.3 77.7 + - - +
227B ARG* 1.3 68.8 + - - +
242B ILE* 4.6 2.2 - - - -
189D TYR* 3.6 26.4 - - + +
239D LEU* 3.5 13.8 - - + +
241D SER* 2.8 36.3 + - - -
98T GLU* 4.5 2.7 - - + -
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Residues in contact with ARG 227 (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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227A ARG* 2.8 40.2 - - - +
205B GLN* 3.8 1.7 - - - -
206B MET* 2.9 46.2 + - + +
226B ALA* 1.3 80.7 - - - +
228B ASN* 1.3 79.6 + - - +
229B SER 5.4 1.2 - - - -
230B CYS* 5.5 1.2 - - - +
240B TYR* 4.1 16.9 - - + -
242B ILE* 4.5 17.5 - - + -
227D ARG* 2.9 19.2 - - - +
230D CYS* 6.3 0.2 - - - +
239D LEU* 3.1 27.3 + - - +
240D TYR* 3.4 35.2 + - - +
241D SER 4.5 6.7 - - - +
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Residues in contact with ASN 228 (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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203B ASP* 6.6 0.2 - - + -
204B LYS 3.3 7.0 - - - +
206B MET* 3.8 1.8 - - - -
227B ARG* 1.3 94.1 + - - +
229B SER* 1.3 82.0 + - - +
230B CYS* 4.8 0.7 - - - -
231B TRP* 3.3 21.2 + - + +
240B TYR* 3.9 3.3 - - - -
230D CYS* 4.8 0.9 - - - +
237D TYR* 4.0 27.4 - - + -
238D GLY* 3.3 8.3 - - - -
239D LEU* 2.9 33.2 + - + +
240D TYR* 3.4 24.1 + - - -
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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