Contacts of the helix formed by residues 192 - 206 (chain D) in PDB entry 4TNR
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 SER 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D GLN 3.3 4.5 + - - -
191D ILE* 1.3 75.3 - - - +
193D GLU* 1.3 66.3 + - - +
194D ARG* 3.5 12.4 - - - +
195D ASP* 2.9 42.2 + - - +
196D VAL* 3.1 14.9 + - - +
294D LYS* 5.0 0.8 + - - -
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Residues in contact with GLU 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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129D HIS* 4.2 20.8 + - - -
192D SER* 1.3 73.0 - - - +
194D ARG* 1.3 57.2 + - - +
196D VAL* 3.3 11.7 + - + +
197D LEU* 3.0 46.2 + - + +
257D TYR* 4.8 8.8 - - - +
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Residues in contact with ARG 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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192D SER* 3.1 12.7 - - - +
193D GLU* 1.3 80.6 - - - +
195D ASP* 1.3 62.1 + - - +
197D LEU* 3.4 2.8 + - - +
198D CYS* 3.0 29.6 + - - -
257D TYR 5.8 0.4 - - - -
258D GLY 3.3 27.6 - - - +
259D LEU* 4.0 15.0 - - + -
260D ILE* 3.5 23.8 - - - +
263D GLU* 2.8 31.1 + - - +
264D ASP* 2.8 42.0 + - - +
290D ARG* 3.8 15.1 - - - +
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Residues in contact with ASP 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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179D VAL* 5.1 0.9 - - - -
191D ILE* 3.7 9.4 - - + -
192D SER* 2.9 31.7 + - - +
194D ARG* 1.3 73.1 - - - +
196D VAL* 1.3 65.9 + - - +
198D CYS* 3.3 3.1 + - - +
199D VAL* 3.0 29.5 + - - +
290D ARG* 2.8 39.0 + - - +
294D LYS* 2.7 31.1 + - - -
297D LEU* 3.9 20.2 - - + -
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Residues in contact with VAL 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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176D GLY* 5.0 0.7 - - - -
179D VAL* 3.9 27.3 - - + +
180D HIS* 3.9 35.2 - - + +
191D ILE* 4.2 13.2 - - + -
192D SER 3.1 17.0 + - - +
193D GLU* 3.5 13.9 - - - +
195D ASP* 1.3 75.9 - - - +
197D LEU* 1.3 59.6 + - + +
199D VAL* 3.2 3.1 + - - +
200D GLN* 2.9 49.2 + - - +
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Residues in contact with LEU 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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129D HIS* 3.6 51.1 - - + +
131D LEU* 4.5 7.0 - - + -
132D LEU* 4.4 11.4 - - + -
193D GLU* 3.0 39.5 + - + +
194D ARG 3.9 3.6 - - - +
196D VAL* 1.3 77.8 - - + +
198D CYS* 1.3 58.3 + - - +
200D GLN* 3.3 18.4 + - - +
201D ILE* 2.9 40.0 + - + +
257D TYR* 4.5 6.1 - - + +
259D LEU* 4.1 24.2 - - + -
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Residues in contact with CYS 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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194D ARG 3.0 22.9 + - - +
195D ASP 3.6 1.3 - - - +
197D LEU* 1.3 76.7 - - - +
199D VAL* 1.3 60.9 + - - +
201D ILE* 3.5 0.8 + - - -
202D ALA 3.1 17.5 + - - -
259D LEU* 3.8 12.1 - - - -
264D ASP* 3.5 38.6 - - - -
267D PHE* 3.4 26.2 - - + -
268D ILE* 3.5 18.0 - - + +
271D GLN* 3.3 10.7 + - - -
290D ARG* 3.7 7.4 - - - -
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Residues in contact with VAL 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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175D ALA* 3.6 33.8 - - + +
179D VAL* 4.5 7.0 - - + -
195D ASP 3.0 19.7 + - - +
196D VAL 3.7 3.6 - - - +
198D CYS* 1.3 75.6 - - - +
200D GLN* 1.3 64.6 + - - +
202D ALA 3.3 1.0 + - - -
203D GLY 3.0 17.7 + - - -
267D PHE* 4.3 8.7 - - + -
271D GLN* 3.5 23.1 - - - +
297D LEU* 4.3 28.5 - - + +
300D ILE* 3.8 17.9 - - + -
301D VAL* 3.5 5.7 - - + +
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Residues in contact with GLN 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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127D GLU 4.9 9.1 + - - -
128D LEU* 5.7 1.4 - - - +
129D HIS* 5.0 2.2 - - - +
132D LEU* 3.7 29.8 - - + +
172D GLY* 3.7 27.5 + - - +
173D TYR* 5.2 3.8 - - - +
175D ALA* 4.5 1.3 - - - -
176D GLY* 3.8 19.1 - - - -
196D VAL* 2.9 36.5 + - - +
197D LEU* 3.6 22.1 - - - +
199D VAL* 1.3 76.7 - - - +
201D ILE* 1.3 56.0 + - - +
203D GLY* 3.2 1.7 + - - -
204D LEU* 2.8 31.6 + - + +
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Residues in contact with ILE 201 (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 LEU* 4.0 23.8 - - + -
132D LEU* 3.4 21.3 - - + -
135D ILE* 3.7 30.1 - - + -
197D LEU* 2.9 25.5 + - + +
198D CYS 3.9 4.0 - - - +
200D GLN* 1.3 73.1 - - - +
202D ALA* 1.3 65.5 + - - +
204D LEU* 3.3 4.7 + - - +
205D CYS* 2.9 27.1 + - - +
241D PHE* 3.9 19.1 - - + -
254D MET* 5.4 2.9 - - + -
259D LEU* 4.3 13.2 - - + -
268D ILE* 3.8 20.9 - - + -
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Residues in contact with ALA 202 (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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198D CYS 3.1 10.3 + - - +
199D VAL 3.7 0.7 - - - +
201D ILE* 1.3 76.2 - - - +
203D GLY* 1.3 63.9 + - - +
205D CYS 3.7 0.3 - - - -
206D ARG* 3.0 28.1 + - - +
268D ILE* 4.0 18.1 - - + +
271D GLN* 3.4 48.5 - - + +
272D ILE* 4.0 5.5 - - + +
301D VAL* 3.7 5.9 - - + +
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Residues in contact with GLY 203 (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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168D SER* 4.0 1.7 - - - +
171D VAL* 3.5 28.1 - - - +
172D GLY* 3.9 13.0 - - - -
175D ALA* 4.6 0.4 - - - -
199D VAL 3.0 12.9 + - - -
200D GLN 3.2 3.8 + - - -
202D ALA* 1.3 78.7 - - - +
204D LEU* 1.3 61.0 + - - +
205D CYS 3.3 0.7 + - - -
206D ARG* 3.6 9.4 - - - +
207D ASN* 4.8 0.5 + - - -
301D VAL* 3.5 20.7 - - - +
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Residues in contact with LEU 204 (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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128D LEU* 5.5 4.7 - - + -
132D LEU* 3.7 43.7 - - + +
135D ILE* 4.9 8.3 - - + -
136D ILE* 4.1 15.7 - - + -
141D PHE* 3.2 26.4 - - + -
144D LEU* 5.2 0.9 - - - +
168D SER* 3.4 36.1 + - - +
169D LEU* 3.8 29.6 - - + +
172D GLY* 3.8 8.1 - - - -
200D GLN* 2.8 13.5 + - + +
201D ILE* 3.3 9.4 + - + +
203D GLY* 1.3 74.0 - - - +
205D CYS* 1.3 65.0 + - - +
206D ARG 3.5 0.6 + - - -
207D ASN 4.6 0.2 + - - -
208D LEU* 5.1 0.3 - - - +
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Residues in contact with CYS 205 (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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135D ILE* 4.0 25.8 - - - -
141D PHE* 4.7 3.6 - - - -
201D ILE* 2.9 20.7 + - - +
202D ALA* 3.7 2.2 - - - +
203D GLY 3.2 0.2 - - - -
204D LEU* 1.3 84.3 - - - +
206D ARG* 1.3 64.0 + - - +
207D ASN 3.1 4.3 + - - -
208D LEU* 3.3 43.2 + - + +
237D SER* 3.7 6.9 - - - +
241D PHE* 3.9 24.7 - - + -
244D LEU* 5.2 0.2 - - - -
268D ILE* 5.5 0.2 - - + -
272D ILE* 4.0 11.3 - - + +
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Residues in contact with ARG 206 (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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171D VAL* 4.4 2.9 - - + -
202D ALA 3.0 13.6 + - - +
203D GLY 3.6 15.3 - - - +
204D LEU 3.5 0.6 - - - -
205D CYS* 1.3 78.2 - - - +
207D ASN* 1.3 70.7 + - - +
233D HIS* 4.5 24.6 + - - -
234D GLU* 5.3 6.4 + - - +
237D SER* 2.8 16.0 + - - -
272D ILE* 4.1 24.8 - - + +
301D VAL* 3.0 38.6 + - + -
302D SER* 3.6 22.1 + - - +
309D ASP* 4.0 5.1 + - - -
311D ASP* 3.3 42.5 + - - +
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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