Contacts of the helix formed by residues 181 - 196 (chain D) in PDB entry 1JXQ
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 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D THR* 1.3 74.4 - - - +
182D SER* 1.3 63.2 + - - +
183D ASN* 3.1 8.6 - - - +
184D ILE* 3.1 27.0 + - - +
185D ASP* 3.3 11.0 + - - +
343D PRO 4.4 1.1 - - - -
344D LYS* 3.7 26.4 - - - +
346D GLY* 3.9 6.1 - - - -
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Residues in contact with SER 182 (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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169D ASN* 2.6 27.9 + - - -
171D VAL* 3.9 5.8 - - - -
179D ARG* 2.9 48.8 + - - -
180D THR 3.3 3.0 + - - -
181D GLY* 1.3 76.5 - - - +
183D ASN* 1.3 53.7 + - - +
184D ILE 3.2 0.2 - - - -
185D ASP* 3.1 12.5 + - - +
186D CYS* 2.7 33.3 + - - +
235D LEU* 3.7 5.5 - - - +
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Residues in contact with ASN 183 (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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169D ASN* 3.4 20.7 + - - +
171D VAL* 3.8 20.7 - - - +
180D THR* 5.8 1.2 - - - +
181D GLY 3.1 7.1 - - - +
182D SER* 1.3 74.7 - - - +
184D ILE* 1.3 67.8 + - + +
186D CYS* 3.6 2.1 - - - +
187D GLU* 2.8 26.9 + - - +
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Residues in contact with ILE 184 (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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339B SER* 5.7 0.7 - - - +
181D GLY* 3.2 16.4 - - - +
183D ASN* 1.3 80.7 - - + +
185D ASP* 1.3 64.4 + - - +
187D GLU* 3.2 6.0 + - - +
188D LYS* 3.0 49.4 + - + +
344D LYS 3.8 19.1 - - - +
345D SER* 4.0 12.3 - - - +
346D GLY* 4.4 3.4 - - - -
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Residues in contact with ASP 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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179D ARG* 4.9 4.9 + - - -
181D GLY 3.6 8.4 - - - +
182D SER* 3.1 19.3 + - - +
184D ILE* 1.3 77.9 - - - +
186D CYS* 1.3 61.2 + - - +
188D LYS* 3.3 4.3 + - - +
189D LEU* 3.1 27.7 + - - +
235D LEU* 4.1 13.1 - - + +
283D GLN* 5.3 3.8 - - - +
285D CYS* 5.5 2.6 - - - -
346D GLY* 3.7 2.4 - - - -
347D SER* 2.8 39.8 + - - -
350D VAL* 3.1 31.5 - - + +
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Residues in contact with CYS 186 (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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167D ILE* 3.7 16.6 - - - +
169D ASN* 3.4 31.2 - - - +
182D SER 2.7 12.5 + - - +
183D ASN* 3.6 4.3 - - - +
185D ASP* 1.3 72.0 - - - +
187D GLU* 1.3 59.7 + - - +
189D LEU* 3.2 4.8 + - - +
190D ARG* 2.8 32.4 + - - +
202D VAL* 3.3 39.5 - - - -
235D LEU* 3.8 8.7 - - + +
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Residues in contact with GLU 187 (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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183D ASN 2.8 17.8 + - - +
184D ILE* 3.7 5.6 - - - +
186D CYS* 1.3 77.8 - - - +
188D LYS* 1.3 63.9 + - + +
190D ARG* 2.8 41.9 + - - -
191D ARG* 3.0 40.1 + - + +
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Residues in contact with LYS 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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339B SER* 3.8 17.6 + - - -
341B ARG* 4.5 13.6 + - - +
184D ILE* 3.0 37.1 + - + +
185D ASP* 3.5 8.2 + - - +
187D GLU* 1.3 77.7 - - + +
189D LEU* 1.3 60.5 + - + +
191D ARG* 3.5 5.0 - - - +
192D ARG* 2.8 29.5 + - - +
338D VAL* 3.8 16.8 - - - +
345D SER 4.7 0.8 + - - -
350D VAL* 4.0 22.3 - - + +
351D GLU* 3.0 44.8 + - - +
354D ASP* 3.7 22.7 - - + +
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Residues in contact with LEU 189 (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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167D ILE* 4.0 12.1 - - + -
185D ASP 3.1 17.3 + - - +
186D CYS* 3.8 3.6 - - - +
188D LYS* 1.3 78.0 - - + +
190D ARG* 1.3 60.9 + - - +
192D ARG* 3.3 8.9 - - + +
193D PHE* 2.8 51.1 + - + +
233D VAL* 3.9 26.0 - - + -
235D LEU* 4.1 17.3 - - + -
281D PHE* 6.1 0.7 - - + -
350D VAL* 4.4 27.8 - - + +
353D LEU* 4.7 20.2 - - + -
354D ASP* 5.2 2.2 - - + -
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Residues in contact with ARG 190 (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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167D ILE* 3.6 14.9 - - + +
186D CYS* 2.8 21.0 + - - +
187D GLU* 2.8 39.1 + - - +
189D LEU* 1.3 71.7 - - - +
191D ARG* 1.3 82.9 + - - +
193D PHE 3.7 0.2 + - - -
194D SER* 3.1 35.0 + - - -
200D VAL* 3.7 20.8 - - + +
202D VAL* 3.7 27.6 - - + -
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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
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341B ARG* 3.0 61.4 - - - +
187D GLU* 3.0 27.1 + - - +
188D LYS* 3.5 4.5 - - - +
190D ARG* 1.3 98.8 - - - +
192D ARG* 1.3 61.0 + - - +
194D SER* 3.4 7.0 - - - -
195D SER* 3.2 24.6 + - - +
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Residues in contact with ARG 192 (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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340B TRP* 4.4 0.2 - - - -
341B ARG* 4.4 7.9 - - - +
188D LYS 2.8 18.0 + - - +
189D LEU* 3.1 14.6 + - + +
191D ARG* 1.3 73.8 - - - +
193D PHE* 1.3 71.4 + - + +
194D SER 2.9 4.0 - - - -
195D SER* 2.8 42.6 + - - -
196D LEU* 3.2 24.1 + - + +
353D LEU* 5.1 2.9 - - + -
354D ASP* 2.5 60.1 + - - +
357D PHE* 3.6 32.6 - - + +
358D GLU* 2.9 41.6 + - - +
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Residues in contact with PHE 193 (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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165D CYS* 4.0 16.4 - - + -
167D ILE* 5.2 0.7 - - + -
189D LEU* 2.8 42.6 + - + +
192D ARG* 1.3 78.4 - - + +
194D SER* 1.3 61.5 + - - +
196D LEU* 3.3 32.0 + - + -
198D PHE* 3.2 32.6 + + + +
200D VAL* 3.9 16.6 - - + -
231D VAL* 4.0 20.0 - - + -
233D VAL* 3.8 21.8 - - + -
281D PHE* 3.3 42.4 - + - -
353D LEU* 6.1 2.2 - - + -
357D PHE* 5.1 6.1 - + - -
400D PHE* 4.6 6.5 - + - -
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Residues in contact with SER 194 (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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190D ARG* 3.1 30.2 + - - -
191D ARG* 3.4 10.3 - - - -
192D ARG 2.9 0.2 - - - -
193D PHE* 1.3 79.5 - - - +
195D SER* 1.3 57.8 + - - +
197D HIS* 2.9 21.3 + - - -
198D PHE 3.8 15.6 + - - +
200D VAL* 3.9 5.3 - - - +
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Residues in contact with SER 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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341B ARG* 5.4 1.9 + - - -
191D ARG* 3.2 14.9 + - - +
192D ARG* 2.8 29.4 + - - -
194D SER* 1.3 72.6 - - - +
196D LEU* 1.3 60.0 + - - +
197D HIS* 3.0 27.6 + - - -
358D GLU* 5.5 0.2 + - - -
401D LYS 3.7 2.3 - - - +
402D THR* 4.5 0.5 - - - +
403D SER* 3.9 19.8 + - - -
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Residues in contact with LEU 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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162D CYS* 4.0 3.6 - - - -
192D ARG* 3.2 20.8 + - + +
193D PHE* 3.6 36.6 - - + +
194D SER 3.1 1.2 - - - -
195D SER* 1.3 80.3 - - - +
197D HIS* 1.3 71.5 + - - +
198D PHE* 3.3 22.9 - - + -
357D PHE* 4.1 18.8 - - + -
361D ALA* 4.3 16.6 - - + -
400D PHE* 3.7 38.1 - - + -
401D LYS* 3.4 15.9 + - - +
402D THR* 5.1 6.3 - - + -
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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