Contacts of the helix formed by residues 184 - 200 (chain D) in PDB entry 1O1F
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 GLY 184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D ASN* 4.8 6.7 - - - -
180D GLU 4.4 0.2 + - - -
181D SER 4.6 2.8 + - - -
182D GLY* 3.1 6.1 + - - -
183D ALA* 1.3 78.7 - - - +
185D LYS* 1.3 65.6 + - - +
186D THR* 5.8 0.2 - - - -
187D VAL* 3.3 27.9 - - - +
188D ASN* 3.1 19.6 + - - -
240D ASN* 4.9 10.5 - - - -
674D CYS* 4.8 0.2 - - - -
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Residues in contact with LYS 185 (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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177D ILE* 3.6 19.7 - - + +
178D THR* 4.3 2.9 - - - -
179D GLY* 2.9 46.2 - - - +
180D GLU 3.9 10.9 + - - +
181D SER* 4.9 8.0 + - - +
184D GLY* 1.3 74.6 - - - +
186D THR* 1.4 55.2 + - - +
187D VAL 3.0 2.2 - - - -
188D ASN* 2.6 29.3 + - - +
189D THR* 2.5 24.7 + - - +
243D SER* 5.8 1.0 + - - -
244D SER* 4.6 19.2 + - - +
463D ASP* 4.4 17.1 + - - +
464D ILE 3.8 19.2 + - - +
465D ALA* 4.6 6.7 - - - +
674D CYS* 4.2 6.7 - - + -
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Residues in contact with THR 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D GLY* 3.7 0.4 - - - -
185D LYS* 1.4 76.3 + - - +
187D VAL* 1.3 57.3 - - - +
189D THR* 3.1 6.6 + - - -
190D MLY 2.6 46.5 + - + +
230D GLU* 3.6 23.1 - - + +
234D ASN* 4.6 4.7 + - - +
240D ASN* 5.5 2.6 + - - -
242D ASN* 4.5 8.6 + - - -
244D SER* 3.7 28.9 + - - +
248D MLY 3.3 31.9 - - - -
463D ASP* 3.8 6.0 + - - -
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Residues in contact with VAL 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D TYR* 5.5 6.7 - - + +
184D GLY* 3.3 32.5 - - - +
186D THR* 1.3 78.7 - - - +
188D ASN* 1.3 62.6 + - - +
190D MLY 3.6 15.9 + - - +
191D ARG* 3.0 48.6 + - - +
240D ASN* 5.5 5.2 - - - +
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Residues in contact with ASN 188 (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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116D TYR* 4.4 0.9 + - - -
125D THR* 4.2 14.7 - - - +
135D TYR* 3.9 16.8 + - - -
155D ILE* 3.3 31.1 - - + +
177D ILE* 4.8 8.1 - - + -
184D GLY 3.1 15.4 + - - -
185D LYS* 2.6 11.4 + - - +
187D VAL* 1.3 75.6 - - - +
189D THR* 1.3 55.3 + - - +
191D ARG* 2.8 7.1 + - - +
192D VAL* 2.6 41.9 + - + +
674D CYS* 2.9 35.7 - - - +
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Residues in contact with THR 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D ILE* 4.4 9.8 - - + +
185D LYS* 2.5 25.7 + - - +
186D THR* 3.3 5.6 - - - -
188D ASN* 1.3 70.8 - - - +
190D MLY 1.3 66.1 + - - +
192D VAL* 3.0 10.0 + - - +
193D ILE* 2.9 30.6 + - + +
248D MLY 4.8 15.9 - - - -
250D ILE* 5.0 2.0 - - + -
461D VAL* 3.7 26.7 - - + +
463D ASP* 3.1 36.9 + - + +
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Residues in contact with MLY 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D THR* 2.6 39.0 + - + +
187D VAL* 3.7 15.0 - - - +
189D THR* 1.3 71.3 - - - +
191D ARG* 1.3 102.1 + - - +
193D ILE* 2.8 25.4 + - - +
194D GLN* 2.9 21.4 + - - +
226D ASN* 4.1 30.1 - - + +
227D PRO* 6.1 2.0 - - - -
230D GLU* 2.8 43.7 - - - +
242D ASN* 4.0 8.3 - - - -
248D MLY 4.8 5.8 - - - -
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Residues in contact with ARG 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D TYR* 3.1 48.9 - - + -
155D ILE* 5.8 4.5 - - + -
156D PHE* 4.4 15.1 - - + -
187D VAL* 3.0 36.9 + - - +
188D ASN* 2.8 6.7 + - - +
190D MLY 1.3 113.8 + - - +
192D VAL* 1.3 61.2 + - - +
194D GLN* 3.6 28.9 + - + +
195D TYR* 3.3 17.8 + - - +
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Residues in contact with VAL 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D ILE* 4.4 26.7 - - + -
156D PHE* 5.9 0.2 - - - -
158D ILE* 6.5 0.7 - - + -
159D SER* 4.0 13.5 - - - -
175D ILE* 4.7 11.4 - - + -
177D ILE* 4.4 14.6 - - + -
188D ASN 2.6 24.8 + - - +
189D THR* 3.0 10.3 + - - +
191D ARG* 1.3 73.1 - - - +
193D ILE* 1.3 62.5 + - + +
195D TYR* 2.8 27.7 + - - +
196D PHE* 3.1 31.3 + - + -
461D VAL* 4.8 9.6 - - + -
672D VAL* 6.4 0.9 - - + -
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Residues in contact with ILE 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D THR* 3.0 20.0 - - + +
190D MLY 2.8 14.4 + - - +
192D VAL* 1.3 78.2 - - + +
194D GLN* 1.3 65.0 + - - +
196D PHE* 3.0 18.1 + - - +
197D ALA* 3.0 12.0 + - - +
222D ILE* 4.0 29.2 - - + +
223D ILE* 5.3 6.1 - - + -
226D ASN* 5.6 7.6 - - - +
248D MLY 5.6 3.1 - - - -
250D ILE* 3.1 37.5 - - + -
252D ILE* 3.9 24.0 - - + -
461D VAL* 4.7 7.6 - - + -
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Residues in contact with GLN 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D MLY 2.9 18.3 + - - +
191D ARG* 3.8 37.3 + - + +
192D VAL 3.3 0.2 - - - -
193D ILE* 1.3 73.6 - - - +
195D TYR* 1.3 54.9 + - - +
197D ALA* 2.9 5.0 + - - +
198D THR* 2.5 43.2 + - + +
223D ILE* 3.2 40.1 - - + +
226D ASN* 6.0 0.2 + - - -
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Residues in contact with TYR 195 (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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140D VAL* 3.4 36.0 + - + -
143D TYR* 3.9 5.4 + - - +
144D ARG* 4.0 0.9 + - - -
156D PHE* 2.9 41.1 - + + -
159D SER* 2.8 34.8 - - - +
160D ASP* 2.4 32.5 + - + +
191D ARG 3.3 10.5 + - - +
192D VAL* 2.8 15.9 + - - +
194D GLN* 1.3 78.4 - - - +
196D PHE* 1.3 64.3 + + - +
198D THR* 3.0 13.5 + - - -
199D ILE* 2.9 55.1 + - + +
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Residues in contact with PHE 196 (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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159D SER* 3.1 34.3 - - - -
162D ALA* 4.3 5.2 - - + -
163D TYR* 4.0 14.8 - + + -
175D ILE* 4.2 5.6 - - + -
192D VAL* 3.1 38.4 + - + -
193D ILE* 3.0 8.0 + - - +
195D TYR* 1.3 81.3 - + - +
197D ALA* 1.3 68.6 + - - +
199D ILE* 3.6 11.5 + - + -
200D ALA* 3.3 23.2 + - - +
252D ILE* 4.6 17.7 - - + -
254D PHE* 3.6 28.2 - + + -
260D LEU* 4.7 2.6 - - + +
459D ILE* 3.7 42.4 - - + -
461D VAL* 4.9 1.6 - - + -
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Residues in contact with ALA 197 (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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193D ILE 3.0 10.7 + - - +
194D GLN* 2.9 11.9 + - - +
196D PHE* 1.3 79.5 - - - +
198D THR* 1.3 64.0 + - + +
201D ALA* 3.0 27.5 + - - +
219D GLU* 4.3 23.8 - - + +
222D ILE* 5.2 6.1 - - + -
223D ILE* 4.9 6.5 - - + -
260D LEU* 3.9 19.7 - - + -
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Residues in contact with THR 198 (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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140D VAL* 5.1 12.5 - - + +
194D GLN* 2.5 32.5 + - + +
195D TYR* 3.0 12.5 + - - -
197D ALA* 1.3 75.8 - - + +
199D ILE* 1.3 61.3 + - - +
200D ALA 2.8 7.3 + - - -
201D ALA* 3.7 8.7 + - - +
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Residues in contact with ILE 199 (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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140D VAL* 4.8 8.7 - - + +
144D ARG* 4.5 16.9 + - + -
160D ASP* 4.1 7.0 - - - +
163D TYR* 4.3 22.0 + - + -
195D TYR* 2.9 68.7 + - + +
196D PHE* 4.1 19.3 - - + +
198D THR* 1.3 75.3 - - - +
200D ALA* 1.3 64.6 + - + +
259D LYS* 4.5 4.7 + - - -
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Residues in contact with ALA 200 (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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163D TYR* 3.1 35.4 - - + +
196D PHE 3.3 12.2 + - - +
197D ALA 3.8 3.1 - - - -
198D THR 2.8 9.3 + - - -
199D ILE* 1.3 78.9 - - + +
201D ALA* 1.3 59.0 + - - +
254D PHE* 4.3 5.6 - - + -
258D GLY 3.6 6.7 - - - +
259D LYS* 3.7 12.9 - - - +
260D LEU* 3.1 28.8 + - - +
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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
------------------------------------------------------------
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