Contacts of the strand formed by residues 190 - 200 (chain A) in PDB entry 1LA5
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ARG* 4.8 7.3 - - - +
182A GLU* 2.9 35.9 + - - -
183A LEU 2.7 22.0 - - - +
184A GLU* 3.6 16.5 + - + +
188A GLY 3.8 1.9 + - - +
189A ASN* 1.4 93.1 + - - +
191A THR* 1.4 72.4 + - - +
192A PHE* 5.3 5.7 - - - -
218A THR* 5.6 2.4 - - - +
295A ARG* 4.0 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLU 3.9 0.2 - - - -
183A LEU* 2.9 53.9 + - + +
189A ASN* 5.5 0.2 - - - -
190A ARG* 1.4 80.6 - - - +
192A PHE* 1.4 65.2 + - - +
218A THR* 3.1 15.9 + - - +
219A ALA* 2.7 48.7 + - + +
281A TRP* 5.5 0.4 - - + -
284A GLY* 6.3 2.2 - - - -
291A TYR* 6.0 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ARG* 3.7 30.7 - - + +
181A VAL* 3.0 9.9 - - - +
182A GLU* 3.2 24.7 - - - +
183A LEU* 5.5 0.2 - - - -
190A ARG* 5.3 7.0 - - - -
191A THR* 1.4 77.2 + - - +
193A ALA* 1.4 68.6 + - - +
194A HIS* 5.1 1.1 - - + -
216A GLU* 3.0 48.2 - - + -
217A GLY* 3.2 8.9 - - - -
218A THR* 3.2 27.0 + - - +
219A ALA* 3.1 23.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU 3.9 0.3 - - - +
180A ARG* 3.4 5.4 - - - +
181A VAL* 2.9 33.6 + - + +
192A PHE* 1.4 80.0 - - - +
194A HIS* 1.3 60.3 + - - +
195A TYR* 3.8 16.6 - - + -
214A PHE* 3.3 24.9 - - + -
217A GLY* 4.2 1.1 - - - -
219A ALA* 4.1 3.6 - - + -
281A TRP* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLU* 5.3 5.6 - - - -
130A TRP* 4.1 18.3 - + - -
178A GLU* 2.8 48.3 + - + +
179A LEU 3.5 8.5 - - - -
180A ARG* 4.6 6.7 - - + -
192A PHE* 5.1 2.0 - - + -
193A ALA* 1.3 75.8 - - - +
195A TYR* 1.4 66.5 + - - +
196A ALA* 4.3 4.8 + - + +
214A PHE* 3.4 6.5 - - - -
215A SER* 2.7 59.2 + - - +
216A GLU* 4.3 16.2 - - + +
299A ARG* 5.5 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLU* 3.2 3.5 - - - +
179A LEU* 2.8 58.9 + - + +
181A VAL* 4.9 0.4 - - + -
193A ALA* 3.8 19.1 - - + -
194A HIS* 1.4 76.6 + - - +
196A ALA* 1.3 60.8 + - - +
198A PHE* 4.5 0.5 - - - +
211A LEU* 2.9 49.1 - - + -
212A GLY 4.0 4.5 - - - -
213A LYS 3.4 2.5 - - - +
214A PHE* 3.4 32.2 - + + -
220A GLY 4.0 1.7 + - - -
221A ASP* 2.6 35.2 + - - -
222A SER 3.7 0.7 + - - -
223A LEU* 3.3 32.7 + - + +
224A SER* 3.4 4.5 - - - -
281A TRP* 4.1 5.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLU* 3.9 12.3 - - + +
194A HIS* 4.3 5.8 + - + +
195A TYR* 1.3 75.6 - - - +
197A THR* 1.3 69.4 + - + +
198A PHE* 3.3 0.9 + - - -
211A LEU* 4.1 1.0 - - - -
212A GLY 2.6 30.5 + - - -
213A LYS* 3.2 19.7 + - + +
215A SER* 5.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ASN* 3.4 31.1 + - - +
177A TRP 3.3 6.9 + - - -
178A GLU* 4.7 0.8 + - - +
196A ALA* 1.3 89.9 - - + +
198A PHE* 1.3 60.5 + - - +
199A ARG* 3.8 6.3 + - - +
210A ALA* 3.3 16.8 - - - +
211A LEU* 3.6 4.0 - - - -
212A GLY* 3.0 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 4.6 14.6 - + - -
168A LEU* 3.8 37.2 - - + -
172A THR* 3.8 17.2 - - + +
176A ASN* 5.0 0.9 - - - +
177A TRP 2.8 26.6 + - - +
179A LEU* 2.9 49.4 - - + +
195A TYR 4.5 1.1 - - - +
196A ALA 4.1 0.9 - - - -
197A THR* 1.3 71.3 - - - +
199A ARG* 1.4 68.8 + - - +
200A LEU* 5.0 0.9 - - + -
209A LEU* 3.3 40.2 - - + -
210A ALA 3.4 9.2 - - - -
211A LEU* 4.0 7.2 - - + +
254A TRP* 5.1 7.0 - + - -
296A MET* 6.1 0.4 - - + -
298A LEU* 4.0 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A HIS* 6.2 0.4 - - - -
172A THR* 3.2 37.2 - - - +
173A LEU* 3.9 31.3 - - - +
197A THR* 3.8 7.4 + - - +
198A PHE* 1.4 80.0 - - - +
200A LEU* 1.3 75.3 + - - +
201A LEU* 5.5 9.6 - - - +
209A LEU* 3.9 3.7 - - - +
210A ALA* 2.8 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TRP* 5.8 0.2 - - + -
165A ASN* 4.1 9.9 - - - +
168A LEU* 3.0 36.1 - - + -
169A HIS* 3.0 47.5 + - + +
172A THR* 3.6 1.1 + - - -
198A PHE* 5.0 0.2 - - + -
199A ARG* 1.3 88.5 - - - +
201A LEU* 1.3 67.5 + - - +
207A TYR* 3.8 19.3 - - + +
208A GLN 3.1 12.8 - - - +
209A LEU* 3.9 9.4 - - + -
254A TRP* 4.2 21.8 - - + -
----------------------------------------------------------
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