Contacts of the helix formed by residues 164 - 175 (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 GLU 164 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D SER* 4.2 6.3 - - - +
163D HIS* 1.3 102.5 + - + +
165D ASP* 1.3 68.0 + - - +
167D THR* 3.2 5.7 + - - -
168D ARG* 3.1 23.6 + - - +
200D GLY* 5.5 2.1 - - - -
203D LYS* 3.7 20.1 + - - +
204D TYR* 2.8 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D SER* 2.9 27.0 + - - +
163D HIS 3.3 0.2 - - - -
164D GLU* 1.3 76.4 - - - +
166D GLY* 1.3 70.3 + - - +
168D ARG* 2.6 42.9 + - - +
169D LEU* 2.7 29.3 + - + -
320D PRO* 4.8 10.0 - - - +
321D VAL* 4.3 8.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D SER 3.5 5.7 + - - -
163D HIS 3.5 2.4 + - - -
165D ASP* 1.3 79.4 - - - +
167D THR* 1.3 57.0 + - - +
169D LEU* 4.5 0.2 - - - -
170D GLY 3.3 14.7 + - - -
201D TRP* 3.9 2.1 - - - -
273D TYR* 3.3 32.7 - - - -
289D ILE* 3.4 29.7 - - - +
321D VAL* 3.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D HIS* 2.8 29.7 + - - +
164D GLU* 3.2 9.7 + - - -
165D ASP 2.7 3.6 + - - -
166D GLY* 1.3 70.8 - - - -
168D ARG* 1.3 58.2 + - - +
171D VAL* 2.8 36.0 + - - +
196D LEU 4.2 1.8 - - - +
197D ARG* 3.1 46.2 - - + +
200D GLY* 3.5 27.1 - - - -
201D TRP* 3.4 14.2 - - + +
204D TYR* 3.6 6.7 - - - -
273D TYR* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D GLU* 3.1 18.3 + - - +
165D ASP* 2.6 43.5 + - - +
167D THR* 1.3 69.8 - - - +
169D LEU* 1.3 80.0 + - - +
170D GLY 3.1 1.6 - - - -
171D VAL* 3.1 1.2 + - - -
172D GLU* 2.7 73.6 + - + +
204D TYR* 3.5 38.5 + - + -
207D ARG* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D ASP* 2.7 37.3 + - + +
166D GLY* 4.5 0.2 - - - -
168D ARG* 1.3 97.9 - - - +
170D GLY* 1.3 55.2 + - - +
172D GLU* 4.4 3.0 - - - +
173D HIS* 3.3 28.9 + - - +
289D ILE* 3.9 13.7 - - + -
321D VAL* 3.8 25.8 - - + +
322D SER* 4.0 15.3 - - - -
323D LEU* 4.4 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D GLY 3.3 13.2 + - - -
168D ARG 3.1 0.6 - - - -
169D LEU* 1.3 78.0 - - - +
171D VAL* 1.3 61.4 + - - +
172D GLU 3.2 0.4 - - - -
173D HIS* 4.3 2.5 - - - +
174D LEU* 3.4 21.3 + - - +
201D TRP* 4.1 2.7 - - - -
243D LEU* 3.3 26.6 - - - +
271D VAL* 4.2 8.9 - - - +
289D ILE* 3.8 10.9 - - - +
323D LEU* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D THR 2.8 24.3 + - - +
168D ARG 3.1 3.3 + - - +
170D GLY* 1.3 76.5 - - - +
172D GLU* 1.3 60.9 + - + +
174D LEU* 4.2 3.5 - - - +
175D VAL* 2.8 27.5 + - + +
201D TRP* 3.4 39.7 - - + +
204D TYR* 3.4 38.4 - - + +
205D LEU* 3.6 15.6 - - + +
208D ASN* 4.6 2.0 - - - +
243D LEU* 3.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ARG* 2.7 65.7 + - + +
169D LEU* 4.4 3.3 - - + +
171D VAL* 1.3 79.9 - - + +
173D HIS* 1.3 60.3 + - - +
174D LEU 3.1 2.2 - - - -
175D VAL* 3.7 4.9 - - - +
176D ALA* 2.9 31.2 + - - +
204D TYR* 4.9 3.9 - - + -
207D ARG* 5.2 4.7 + - - -
208D ASN* 4.3 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU 3.3 18.3 + - - +
170D GLY* 4.3 3.4 - - - +
172D GLU* 1.3 76.9 - - - +
174D LEU* 1.3 62.5 + - + +
176D ALA* 4.5 5.0 - - - +
177D LEU* 2.9 46.3 + - + +
271D VAL* 4.7 5.6 - - + -
287D THR* 4.4 1.7 - - + +
323D LEU* 3.3 23.1 - - + +
325D LYS* 3.7 37.6 - - + +
329D THR* 3.0 44.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D GLY 3.4 13.3 + - - +
171D VAL 4.3 4.5 - - - +
172D GLU 3.1 0.4 - - - -
173D HIS* 1.3 81.1 - - - +
175D VAL* 1.3 60.0 + - - +
177D LEU* 3.5 1.3 + - + -
178D GLY 3.4 2.6 + - - -
179D HIS* 2.9 58.3 + - + +
182D ILE* 4.2 14.6 - - + -
241D ALA* 3.8 23.8 - - + -
242D MET 4.2 7.4 - - - +
243D LEU* 3.6 33.7 - - + -
269D SER* 4.2 2.0 - - - -
271D VAL* 4.0 8.1 - - + -
329D THR* 4.0 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D VAL* 2.8 28.9 + - + +
172D GLU* 3.3 6.8 + - - +
174D LEU* 1.3 74.0 - - - +
176D ALA* 1.3 57.4 + - - +
177D LEU 3.0 1.8 - - - -
178D GLY* 2.7 25.5 + - - -
179D HIS 4.4 5.2 - - - +
182D ILE* 4.8 4.0 - - + -
205D LEU* 4.9 0.4 - - + -
208D ASN* 4.0 35.0 - - + +
210D ILE* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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