Contacts of the helix formed by residues 189 - 209 (chain D) in PDB entry 3LOC
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 ASP 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184D GLY 4.7 0.9 - - - +
185D ALA* 3.5 10.5 - - + -
186D THR* 3.0 34.2 + - - +
187D LEU 3.2 2.0 - - - +
188D ARG* 1.3 75.0 - - - +
190D GLU* 1.3 55.2 + - - +
191D VAL* 3.2 2.8 + - + +
192D PHE* 3.3 12.9 + - + +
193D PHE* 2.8 34.5 + - - +
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Residues in contact with GLU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU 6.2 0.4 - - - +
56B TYR* 4.3 22.4 - - - -
59B PRO* 4.5 8.1 - - + +
187D LEU 5.1 0.2 - - - -
188D ARG 3.3 20.3 + - - +
189D ASP* 1.3 71.7 - - - +
191D VAL* 1.3 60.3 + - + +
193D PHE* 3.5 11.0 - - - +
194D ASN* 3.2 25.8 + - - +
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Residues in contact with VAL 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.8 25.6 - - + +
59B PRO* 4.6 23.0 - - + +
189D ASP* 3.2 1.9 - - + +
190D GLU* 1.3 77.2 - - + +
192D PHE* 1.3 62.8 + - - +
194D ASN* 3.0 8.1 + - - +
195D GLN* 2.8 42.5 + - + +
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Residues in contact with PHE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C GLN* 5.9 0.9 - - - -
160C HIS* 3.8 22.0 - + - -
163C PHE* 5.4 0.2 - + - -
172D TYR* 4.4 2.9 - + - -
179D VAL* 3.9 21.5 - - + -
183D THR* 3.4 29.4 - - + -
185D ALA* 3.5 22.4 - - + -
186D THR 3.2 29.2 - - - +
187D LEU* 4.2 10.3 - - + -
189D ASP* 3.3 12.8 + - + +
191D VAL* 1.3 78.1 - - - +
193D PHE* 1.3 67.7 + - - +
195D GLN* 3.4 21.1 - - - +
196D THR* 2.8 44.7 + - - -
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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
----------------------------------------------------------
98D ARG* 4.5 12.8 - - - -
101D LEU* 3.7 30.3 - - + -
102D GLU* 3.8 25.1 - - + -
105D ARG* 3.6 31.0 - - + +
187D LEU* 3.5 32.5 - - + +
189D ASP 2.8 21.6 + - - +
190D GLU* 3.5 11.9 - - - +
192D PHE* 1.3 76.2 - - - +
194D ASN* 1.3 66.2 + - + +
196D THR* 3.1 7.0 + - - -
197D VAL* 2.9 47.5 + - + +
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Residues in contact with ASN 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PRO* 3.8 32.0 - - + +
60B SER* 3.9 11.3 + - - -
63B ALA* 4.9 3.2 - - - +
98D ARG* 2.4 35.0 + - - +
190D GLU 3.2 14.1 + - - +
191D VAL 3.0 5.4 + - - +
193D PHE* 1.3 83.5 - - + +
195D GLN* 1.3 65.0 + - - +
197D VAL* 3.3 2.6 + - - +
198D GLU* 2.9 51.5 + - - +
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Residues in contact with GLN 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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157C ASP* 3.5 21.2 - - - +
159C GLN* 5.7 0.3 - - - +
160C HIS* 3.7 13.6 + - - +
191D VAL* 2.8 32.1 + - + +
192D PHE* 3.4 21.8 - - + +
194D ASN* 1.3 71.6 - - - +
196D THR* 1.3 64.7 + - - +
198D GLU* 3.2 9.2 + - - +
199D ASN* 2.9 37.0 + - - +
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Residues in contact with THR 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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160C HIS* 3.1 20.5 - - - -
101D LEU* 3.9 15.5 - - + -
172D TYR* 3.4 45.1 - - + +
187D LEU* 4.4 5.2 - - + -
192D PHE* 2.8 33.8 + - - -
193D PHE 3.4 8.3 - - - -
195D GLN* 1.3 72.4 - - - +
197D VAL* 1.3 63.2 + - - +
199D ASN* 3.1 3.3 + - - +
200D VAL* 3.0 30.6 + - + +
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ILE* 4.5 0.9 - - - +
98D ARG* 3.2 46.7 - - + +
101D LEU* 3.7 25.4 - - + -
193D PHE* 2.9 46.2 + - + +
194D ASN* 3.7 7.0 - - - +
196D THR* 1.3 73.8 - - - +
198D GLU* 1.3 65.4 + - + +
200D VAL* 4.3 0.3 - - - -
201D GLN* 3.1 48.4 + - + +
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Residues in contact with GLU 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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60B SER* 2.8 34.0 + - - -
62B GLU* 3.5 29.3 - - - +
63B ALA* 4.5 1.4 + - - +
98D ARG* 5.7 2.2 - - - +
194D ASN* 2.9 34.7 + - - +
195D GLN* 3.8 8.0 - - - +
197D VAL* 1.3 81.3 - - + +
199D ASN* 1.3 59.3 + - - +
201D GLN* 3.6 12.6 + - - +
202D ARG* 3.0 30.0 + - - +
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Residues in contact with ASN 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ILE* 3.7 13.0 - - + +
157C ASP* 3.0 40.1 + - - +
160C HIS* 3.6 33.2 - - + -
195D GLN* 2.9 34.7 + - - +
196D THR 3.9 0.9 - - - +
198D GLU* 1.3 79.0 - - - +
200D VAL* 1.3 64.8 + - - +
202D ARG* 3.3 5.8 + - - +
203D ILE* 3.3 31.8 + - + +
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Residues in contact with VAL 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C HIS* 5.5 1.3 - - + +
164C MSE 4.1 17.0 - - + -
97D ILE* 3.4 24.9 - - + +
101D LEU* 4.0 14.6 - - + -
168D SER* 4.0 15.7 - - - +
169D THR* 4.5 4.7 - - + -
172D TYR* 4.6 13.7 - - + +
196D THR* 3.0 28.4 + - + +
197D VAL 4.6 0.4 - - - +
199D ASN* 1.3 73.1 - - + +
201D GLN* 1.3 65.0 + - - +
204D ILE* 3.2 40.9 + - + +
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Residues in contact with GLN 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LYS* 2.9 51.0 + - + +
97D ILE* 3.8 23.3 - - + -
98D ARG* 3.9 14.4 + - - +
197D VAL* 3.1 42.7 + - - +
198D GLU* 3.7 12.0 - - - +
200D VAL* 1.3 78.7 - - - +
202D ARG* 1.3 54.9 + - - +
205D ILE* 2.7 44.6 + - + +
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Residues in contact with ARG 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ALA* 6.1 2.4 - - + -
155C PRO* 3.4 35.5 - - - +
156C ILE* 3.5 18.6 - - + +
207C GLY 4.6 3.1 - - - +
198D GLU 3.0 18.4 + - - +
199D ASN* 3.3 3.1 + - - +
201D GLN* 1.3 78.8 - - - +
203D ILE* 1.3 63.7 + - - +
205D ILE* 4.8 1.1 - - - -
206D GLU* 3.8 28.9 - - + -
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Residues in contact with ILE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ILE* 3.7 25.4 - - + -
160C HIS* 4.6 2.5 - - + +
161C LEU* 4.0 33.7 - - + +
164C MSE 3.7 34.3 - - + -
203C ILE* 3.8 2.3 - - + +
204C ILE* 4.1 32.8 - - + +
207C GLY* 3.4 14.6 - - - +
208C ILE* 4.5 7.4 - - + -
199D ASN* 3.3 15.4 + - + +
202D ARG* 1.3 77.4 + - - +
204D ILE* 1.3 62.8 + - + +
207D GLY* 2.7 27.7 + - - -
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Residues in contact with ILE 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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164C MSE 4.0 11.9 - - + -
203C ILE* 4.1 9.2 - - + -
93D ILE* 4.7 2.7 - - + -
97D ILE* 4.0 12.8 - - + -
161D LEU* 3.6 28.7 - - + -
164D MSE 4.4 20.0 - - + -
165D ILE* 3.9 23.3 - - + -
168D SER* 3.9 14.1 - - - +
200D VAL* 3.2 34.8 + - + +
203D ILE* 1.3 78.3 - - - +
205D ILE* 1.3 66.0 + - - +
207D GLY* 2.9 12.5 + - - -
208D ILE* 3.0 20.7 + - + +
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Residues in contact with ILE 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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127B ASP* 4.4 9.9 - - - +
90D LEU* 3.7 27.5 - - + +
93D ILE* 3.8 18.6 - - + -
94D LYS* 3.6 46.9 - - + +
97D ILE* 4.7 1.8 - - + -
201D GLN* 2.7 35.1 + - + +
202D ARG* 4.7 1.6 - - - -
204D ILE* 1.3 73.6 - - - +
206D GLU* 1.3 63.7 + - - +
208D ILE* 3.3 7.3 + - + +
209D ARG* 3.1 46.4 + - - +
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Residues in contact with GLU 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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206C GLU* 3.8 10.0 - - - +
207C GLY* 3.7 24.2 - - - +
211C ARG* 4.3 20.7 + - - -
202D ARG* 3.8 28.3 - - + +
203D ILE 3.4 1.0 + - - -
204D ILE 3.2 0.4 - - - -
205D ILE* 1.3 79.6 - - + +
207D GLY* 1.3 62.1 + - - +
208D ILE 3.3 0.7 + - - -
209D ARG* 3.2 55.4 + - - +
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Residues in contact with GLY 207 (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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202C ARG* 3.0 30.1 + - - +
203C ILE* 3.3 31.3 - - - -
206C GLU* 3.8 3.5 - - - +
207C GLY* 3.4 7.6 - - - -
156D ILE* 4.7 1.6 - - - +
203D ILE 2.7 14.8 + - - -
204D ILE 2.9 4.9 + - - -
206D GLU* 1.3 74.9 - - - +
208D ILE* 1.3 62.7 + - - +
209D ARG 4.8 0.2 - - - +
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Residues in contact with ILE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ILE* 4.1 20.6 - - + -
90D LEU* 4.0 8.5 - - + -
93D ILE* 3.6 37.7 - - + -
153D LEU* 3.5 27.2 - - + +
154D ALA* 2.8 31.3 + - - +
156D ILE* 4.2 13.7 - - + -
161D LEU* 4.2 25.4 - - + -
204D ILE* 3.0 16.5 + - + +
205D ILE* 3.5 13.7 - - - +
207D GLY* 1.3 77.8 - - - +
209D ARG* 1.3 61.5 + - - +
210D PRO 3.4 0.3 - - - -
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Residues in contact with ARG 209 (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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126B MSE 5.2 7.5 - - - +
127B ASP* 3.4 28.9 + - - -
202C ARG* 5.1 1.4 + - - -
211C ARG* 4.9 10.8 + - - +
90D LEU* 3.3 31.3 - - + +
94D LYS* 5.4 1.0 - - - +
154D ALA* 3.6 7.1 - - - +
205D ILE* 3.1 22.7 + - - +
206D GLU* 3.2 48.8 + - - +
207D GLY 4.8 0.9 - - - +
208D ILE* 1.3 79.9 - - - +
210D PRO* 1.3 83.8 - - + +
211D ARG* 3.4 5.9 + - - +
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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
------------------------------------------------------------
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