Contacts of the helix formed by residues 192 - 205 (chain D) in PDB entry 1LBI
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 VAL 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D PRO* 4.5 3.2 - - + +
128D LEU 3.5 28.7 - - - +
129D ASP* 4.0 2.1 + - - +
130D ASP* 5.0 7.4 - - + +
149D ASP* 3.6 26.5 - - - +
150D VAL* 3.8 8.3 - - - -
151D SER* 4.0 21.1 - - - +
190D SER 3.6 1.4 + - - -
191D SER* 1.3 71.9 - - - +
193D SER* 1.3 62.1 + - - +
195D ARG* 3.2 23.7 - - - +
196D LEU* 2.8 50.9 + - + +
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Residues in contact with SER 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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149D ASP* 3.3 29.3 + - - -
150D VAL 5.8 0.9 - - - -
163D HIS* 5.9 0.3 - - - +
191D SER* 3.6 12.3 - - - -
192D VAL* 1.3 79.3 - - - +
194D ALA* 1.3 63.3 + - - +
196D LEU* 3.0 9.7 + - - +
197D ARG* 2.9 52.3 + - - +
220D TRP* 4.2 8.5 - - - -
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Residues in contact with ALA 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D ALA* 5.4 0.5 - - - +
187D GLY* 3.7 32.5 + - - +
188D PRO 3.7 22.0 - - - +
189D LEU* 4.2 3.9 - - + +
191D SER* 3.3 7.7 + - - -
193D SER* 1.3 75.0 + - - +
195D ARG* 1.3 66.9 + - - +
196D LEU 3.0 2.8 + - - -
197D ARG* 3.1 17.4 + - - +
198D LEU* 3.1 16.8 + - - +
220D TRP* 3.9 12.7 - - + -
245D ALA* 5.6 0.9 - - - -
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Residues in contact with ARG 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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129D ASP* 2.8 41.8 + - - +
189D LEU* 2.9 41.2 + - + +
190D SER* 3.1 17.0 + - - +
191D SER 2.8 18.7 + - - +
192D VAL* 3.2 30.6 - - - +
194D ALA* 1.3 78.7 - - - +
196D LEU* 1.3 59.9 + - + +
198D LEU* 4.2 2.8 + - - +
199D ALA* 3.8 17.5 + - - +
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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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150D VAL 4.5 5.2 - - - +
151D SER* 4.3 23.6 - - - +
152D ASP* 5.2 0.4 - - - +
160D ILE* 6.4 0.4 - - + -
163D HIS* 4.0 49.6 + - + +
167D THR* 4.2 4.3 - - - +
192D VAL* 2.8 43.0 + - + +
193D SER* 3.0 8.0 + - - +
194D ALA 3.0 0.6 - - - -
195D ARG* 1.3 80.1 - - + +
197D ARG* 1.3 63.6 + - - +
198D LEU 3.3 1.3 - - - -
199D ALA* 3.9 9.5 - - + +
200D GLY* 3.6 13.3 + - - -
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Residues in contact with ARG 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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163D HIS* 5.2 3.6 - - + +
167D THR* 3.1 17.7 - - + +
193D SER* 2.9 32.6 + - - +
194D ALA* 3.1 7.6 + - - +
196D LEU* 1.3 75.6 - - - +
198D LEU* 1.3 58.0 + - - +
199D ALA 3.4 0.2 + - - -
200D GLY 3.4 0.3 + - - -
201D TRP* 3.0 40.7 + - + +
220D TRP* 4.0 17.0 - - - -
245D ALA* 3.0 38.2 + - + -
273D TYR* 3.3 50.5 + - + +
274D ASP* 3.6 12.5 + - - -
291D GLN* 3.4 21.2 + - - +
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Residues in contact with LEU 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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184D LEU* 3.5 32.3 - - + -
186D ALA* 3.3 33.7 - - + -
189D LEU* 3.8 20.9 - - + -
194D ALA 3.1 14.8 + - - +
195D ARG 4.4 4.0 - - - +
197D ARG* 1.3 78.7 - - - +
199D ALA* 1.3 60.9 + - - +
201D TRP* 3.4 11.4 + - + +
202D HIS* 3.2 36.4 + - + -
215D GLU* 3.7 14.6 - - + +
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Residues in contact with ALA 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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195D ARG 3.8 15.9 + - - +
196D LEU* 3.8 13.4 + - + +
197D ARG 3.3 0.2 - - - -
198D LEU* 1.3 76.8 - - - +
200D GLY* 1.3 61.4 + - - +
202D HIS* 3.2 9.6 - - - +
203D LYS* 2.9 26.2 + - - +
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Residues in contact with GLY 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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164D GLU* 5.5 2.5 - - - -
167D THR* 3.5 26.0 - - - -
196D LEU 3.6 4.6 + - - -
197D ARG 3.4 2.6 + - - -
198D LEU 3.3 0.2 - - - -
199D ALA* 1.3 76.6 - - - +
201D TRP* 1.3 68.3 + - - +
202D HIS 2.8 3.1 + - - -
203D LYS* 3.0 17.9 + - - -
204D TYR* 3.0 19.2 + - - +
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Residues in contact with TRP 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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166D GLY 3.9 5.4 - - - -
167D THR* 3.4 29.6 - - - -
170D GLY* 4.1 5.6 - - - -
171D VAL* 3.4 18.1 - - + +
184D LEU* 3.9 33.7 - - + -
185D LEU 4.6 8.4 + - - -
186D ALA* 5.8 0.7 - - - -
197D ARG* 3.0 36.2 + - + +
198D LEU* 3.4 22.2 - - + +
200D GLY* 1.3 75.5 - - - +
202D HIS* 1.3 56.6 + - - +
205D LEU* 3.0 34.8 + - - +
243D LEU* 3.6 41.9 + - + -
244D VAL 3.6 22.9 + - - -
245D ALA* 4.6 3.6 - - - +
272D GLY 5.2 2.0 - - - -
273D TYR* 3.9 27.6 - + + -
289D ILE* 4.8 1.8 - - + -
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Residues in contact with HIS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D LEU* 3.5 21.2 - - + +
198D LEU* 3.2 17.8 + - + +
199D ALA* 3.2 12.7 - - - +
200D GLY 2.8 0.4 + - - -
201D TRP* 1.3 77.5 - - - +
203D LYS* 1.3 57.4 + - - +
204D TYR 3.1 1.8 - - - -
205D LEU* 2.8 5.6 + - - -
206D THR* 2.7 45.7 + - + +
211D GLN* 5.9 0.4 - - - -
212D PRO* 3.8 16.7 - - + +
215D GLU* 3.0 41.3 + - - -
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Residues in contact with LYS 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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164D GLU* 3.7 25.0 + - - +
199D ALA 2.9 20.0 + - - +
200D GLY* 3.0 7.7 + - - +
202D HIS* 1.3 70.3 - - - +
204D TYR* 1.3 83.4 + - + +
206D THR* 3.6 7.1 + - - -
207D ARG* 3.1 51.3 + - + +
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Residues in contact with TYR 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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164D GLU* 2.8 53.3 + - - +
167D THR* 3.6 12.1 - - - -
168D ARG* 3.5 39.8 + - + -
171D VAL* 3.4 24.9 - - + +
172D GLU* 4.9 4.5 - - + -
200D GLY* 3.0 23.5 + - - +
203D LYS* 1.3 93.8 - - + +
205D LEU* 1.3 63.7 + - - +
206D THR 3.4 0.2 - - - -
207D ARG* 3.8 35.1 + - - +
208D ASN* 2.5 34.9 + - - +
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Residues in contact with LEU 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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171D VAL* 3.6 21.1 - - + +
175D VAL* 4.9 0.7 - - + -
182D ILE* 3.7 33.7 - - + -
184D LEU* 3.8 28.3 - - + -
201D TRP 3.0 25.8 + - - +
202D HIS* 2.8 5.7 + - - +
204D TYR* 1.3 77.3 - - - +
206D THR* 1.3 59.7 + - + +
208D ASN* 3.0 10.8 + - - -
210D ILE* 2.8 52.3 + - + +
212D PRO* 3.8 21.8 - - + -
243D LEU* 4.4 6.5 - - + -
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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