Contacts of the helix formed by residues 190 - 205 (chain D) in PDB entry 6CP3
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 ARG 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C ARG* 4.7 4.0 - - - +
309C GLU* 4.5 5.6 - - - -
345C ILE 3.8 0.4 + - - -
346C SER* 2.6 41.9 + - - +
347C ILE 3.5 19.6 + - - +
348C THR 3.7 7.1 + - - -
349C ASP* 3.3 22.4 - - - +
375C ARG* 3.5 26.2 - - - +
159D ALA* 5.7 0.2 - - - +
160D GLY 5.2 0.2 - - - +
189D GLU* 1.3 92.8 + - - +
191D THR* 1.3 58.9 + - - +
192D ARG* 3.3 2.5 - - - +
193D GLU* 2.9 48.8 + - + +
194D GLY 3.2 7.8 + - - -
221D GLN* 3.7 0.4 - - - +
222D MET* 4.6 3.1 - - + +
600D ADP 2.4 37.1 + - - -
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Residues in contact with THR 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PRO 4.1 1.8 - - - +
137C GLY* 3.3 31.5 - - - +
138C ILE* 4.6 3.8 - - + +
141C ARG* 3.4 17.6 + - - +
166C ARG* 5.2 0.4 - - - +
309C GLU* 3.2 25.6 + - - +
189D GLU 3.9 1.2 + - - -
190D ARG* 1.3 72.1 - - - +
192D ARG* 1.3 57.9 + - - +
194D GLY* 2.8 18.4 + - - -
195D ASN* 3.0 10.6 + - - +
221D GLN* 3.0 41.5 + - + +
222D MET 4.8 1.0 + - - -
223D ASN* 4.9 5.6 - - - +
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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
----------------------------------------------------------
141C ARG* 3.5 17.6 - - + +
142C ARG 5.8 3.1 - - - +
143C SER* 5.9 4.7 - - - +
144C VAL* 5.4 12.3 - - + +
164C GLY 5.8 4.0 - - - +
165C GLN* 5.3 0.9 - - - +
166C ARG* 4.3 14.1 - - - +
309C GLU* 4.8 0.6 + - - -
312C ALA* 5.3 3.8 - - + -
349C ASP* 3.1 44.5 + - - +
375C ARG* 3.4 30.7 + - - +
376C VAL* 3.6 29.2 - - - +
190D ARG* 5.1 1.1 - - - +
191D THR* 1.3 78.8 - - - +
193D GLU* 1.3 80.9 + - - +
195D ASN* 3.2 13.7 + - + +
196D ASP* 2.8 48.9 + - - -
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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
----------------------------------------------------------
375C ARG* 4.3 7.6 - - - +
164D THR* 3.8 26.7 - - + +
189D GLU* 4.5 5.1 - - + +
190D ARG* 2.9 42.4 + - + +
192D ARG* 1.3 111.8 + - - +
194D GLY* 1.3 60.4 + - - +
196D ASP* 3.7 8.7 - - + +
197D LEU* 2.9 28.9 + - - +
600D ADP 4.2 10.7 + - - -
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Residues in contact with GLY 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ILE* 3.9 10.6 - - - +
189D GLU* 5.6 1.8 - - - +
190D ARG 3.2 7.1 + - - -
191D THR 2.8 11.0 + - - -
193D GLU* 1.3 76.4 - - - +
195D ASN* 1.3 60.1 + - - -
197D LEU* 3.3 2.5 + - - +
198D TYR* 3.0 23.9 + - - +
219D PHE* 3.9 32.4 - - - -
221D GLN* 4.7 4.0 - - - -
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Residues in contact with ASN 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ILE* 3.8 18.8 - - + +
141C ARG* 2.7 54.2 + - + +
142C ARG* 3.4 1.4 + - - +
143C SER* 3.3 25.1 - - - +
191D THR 3.0 6.6 + - - +
192D ARG* 3.2 14.8 + - - +
194D GLY* 1.3 76.0 - - - +
196D ASP* 1.3 57.1 + - - +
198D TYR* 3.3 7.4 + - - +
199D ARG* 2.9 33.4 + - - +
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Residues in contact with ASP 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C SER* 3.2 33.7 + - - -
168D GLN* 4.9 8.5 - - - +
192D ARG* 2.8 44.4 + - - +
193D GLU* 3.7 10.1 - - + +
194D GLY 3.3 0.4 - - - -
195D ASN* 1.3 76.4 + - - +
197D LEU* 1.3 58.3 + - - +
199D ARG* 3.3 8.0 + - - +
200D GLU* 2.9 36.5 + - + +
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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
----------------------------------------------------------
168D GLN* 4.2 29.8 - - + +
171D ILE* 4.8 10.3 - - + -
184D PHE* 3.6 55.2 - - + -
193D GLU 2.9 16.5 + - - +
194D GLY* 3.9 6.1 - - - +
196D ASP* 1.3 77.0 - - - +
198D TYR* 1.3 59.3 + - - +
200D GLU* 4.5 4.5 - - + +
201D MET* 2.9 58.4 + - + +
217D LEU* 4.8 4.5 - - + -
219D PHE* 4.5 5.4 - - + -
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Residues in contact with TYR 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ILE* 4.4 11.9 - - + -
139C LEU* 4.8 20.4 - - + +
93D GLY 4.6 8.2 + - - -
95D ILE* 3.6 31.4 - - + -
104D ASP* 5.0 11.3 + - + +
106D ARG* 5.2 2.8 + - - +
194D GLY 3.0 17.2 + - - +
195D ASN* 3.3 11.6 + - - +
197D LEU* 1.3 78.0 - - - +
199D ARG* 1.3 57.5 + - + +
201D MET* 3.8 1.9 - - - +
202D LYS* 3.0 60.8 + - + +
207D ILE* 3.8 16.4 - - + -
209D LEU* 3.9 21.5 - - - +
217D LEU* 3.8 19.9 - - + +
219D PHE* 5.5 0.2 - - - -
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Residues in contact with ARG 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ARG* 4.2 21.1 - - - +
143C SER* 3.4 31.5 + - - +
145C HIS* 6.1 0.4 + - - -
195D ASN* 2.9 23.5 + - - +
196D ASP* 3.6 8.7 - - - +
198D TYR* 1.3 78.7 - - + +
200D GLU* 1.3 66.7 + - + +
202D LYS* 3.3 17.1 + - - +
203D GLU* 2.9 53.5 + - + +
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Residues in contact with GLU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D GLN* 4.3 17.3 - - - +
196D ASP* 2.9 22.8 + - + +
197D LEU* 3.4 8.0 + - + +
199D ARG* 1.3 84.2 + - - +
201D MET* 1.3 64.6 + - + +
203D GLU* 4.4 11.8 - - - +
204D THR* 2.9 42.5 + - - +
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Residues in contact with MET 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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171D ILE* 4.0 27.1 - - + -
172D ASN* 6.5 0.2 - - - -
175D ALA* 5.1 5.4 - - + -
197D LEU* 2.9 38.5 + - + +
198D TYR* 5.1 0.2 - - - -
200D GLU* 1.3 75.7 - - - +
202D LYS* 1.3 64.4 + - - +
204D THR* 4.8 4.9 - - - +
205D GLY 3.4 0.6 + - - -
206D VAL* 3.4 44.6 + - + -
207D ILE* 3.0 46.1 + - + -
215D VAL* 3.9 25.1 - - + -
217D LEU* 5.4 5.2 - - + -
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Residues in contact with LYS 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 TYR* 3.0 55.0 + - + +
199D ARG* 3.5 17.5 - - - +
200D GLU 3.2 0.2 - - - -
201D MET* 1.3 76.2 - - - +
203D GLU* 1.3 64.6 + - + +
205D GLY* 2.9 23.2 + - - -
207D ILE* 3.8 25.9 - - + +
209D LEU* 4.5 19.0 - - + +
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Residues in contact with GLU 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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199D ARG* 2.9 46.8 + - + +
200D GLU* 4.5 13.0 - - - +
202D LYS* 1.3 77.0 - - + +
204D THR* 1.3 64.5 + - - +
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Residues in contact with THR 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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172D ASN* 4.7 6.2 + - - +
176D LYS* 3.5 37.0 + - + +
200D GLU* 2.9 26.7 + - - +
201D MET* 4.7 4.5 - - - -
203D GLU* 1.3 78.3 - - - +
205D GLY* 1.3 57.2 + - - +
206D VAL* 4.2 17.0 - - + -
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Residues in contact with GLY 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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201D MET 3.4 1.8 + - - -
202D LYS 2.9 17.3 + - - -
204D THR* 1.3 80.1 - - - +
206D VAL* 1.3 67.8 + - - +
207D ILE 3.3 9.9 - - - +
208D ASN* 4.1 8.2 + - - +
212D GLU 5.2 0.2 - - - +
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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