Contacts of the strand formed by residues 181 - 190 (chain K) in PDB entry 1I9R
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 TYR 181 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91K THR* 5.6 3.6 - - - +
115K THR* 4.5 12.8 + - - -
149K ASP 3.2 6.4 + - - -
150K TYR* 2.8 53.3 + - + +
151K PHE* 4.5 13.0 - + - -
152K PRO* 4.2 9.9 - - + -
153K GLU* 3.9 39.7 - - + -
173K ALA* 4.2 9.4 - - + -
174K VAL* 4.0 3.8 - - - -
175K LEU* 3.2 58.9 - - + +
176K GLN* 3.1 10.9 + - - -
180K LEU* 1.3 70.0 - - - +
182K SER* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K LEU* 3.6 10.7 - - - +
147K VAL 3.4 7.0 - - - -
148K LYS* 3.3 23.0 - - - +
172K PRO 5.0 0.3 - - - +
174K VAL* 3.4 28.0 + - - +
176K GLN* 3.0 33.0 + - - -
181K TYR* 1.3 73.5 - - - +
183K LEU* 1.3 59.5 + - - +
164M GLN* 5.6 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K LEU* 3.5 3.0 - - - +
147K VAL* 2.8 43.3 + - + +
150K TYR* 3.8 6.5 - - - +
153K GLU* 4.7 3.4 - - - +
155K VAL* 3.4 37.0 - - + +
157K VAL* 4.0 23.1 - - + -
170K THR* 4.1 8.7 - - - +
171K PHE* 3.5 26.0 - - - +
172K PRO* 4.1 4.0 - - + +
173K ALA* 3.9 19.1 - - + +
182K SER* 1.3 75.4 - - - +
184K SER* 1.3 66.7 + - - +
185K SER 4.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129K LEU* 3.3 20.6 - - - +
145K CYS 3.0 14.1 + - - -
146K LEU* 3.3 16.6 - - - +
171K PHE* 3.0 43.0 + - - +
183K LEU* 1.3 78.8 - - - +
185K SER* 1.3 58.6 - - - +
186K VAL* 4.0 2.7 - - - -
137M VAL* 4.5 12.0 - - - +
180M SER* 5.2 8.0 + - - -
182M THR* 5.8 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 185 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144K GLY* 3.1 2.9 - - - -
145K CYS* 2.7 40.1 + - - +
147K VAL* 5.1 0.6 - - - +
157K VAL* 3.4 35.0 + - - +
159K TRP* 3.5 16.9 + - - -
168K VAL* 4.0 1.7 - - - +
170K THR* 2.8 33.6 - - - +
183K LEU* 4.1 2.9 - - - +
184K SER* 1.3 71.7 - - - +
186K VAL* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129K LEU* 3.6 24.2 - - + -
143K LEU 3.5 10.5 - - - +
144K GLY* 4.0 4.9 - - - +
159K TRP* 4.7 0.4 - - - -
167K GLY 3.6 0.6 - - - +
168K VAL* 3.2 5.0 - - - +
169K HIS* 2.6 50.7 + - + +
171K PHE* 4.5 12.3 - - + -
184K SER* 4.0 3.3 + - - +
185K SER* 1.3 81.7 + - - +
187K VAL* 1.3 71.1 + - - +
188K THR* 4.9 4.0 - - + -
122M PHE* 4.9 4.7 - - + -
137M VAL* 6.0 2.0 - - + -
139M LEU* 3.5 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143K LEU* 2.7 64.6 + - + +
159K TRP* 3.9 20.4 - - + -
164K LEU* 4.3 10.1 - - + -
166K SER 3.7 18.8 - - - +
167K GLY 3.2 9.2 - - - +
168K VAL* 4.1 13.2 - - + +
186K VAL* 1.3 79.1 - - - +
188K THR* 1.3 78.5 + - - +
189K VAL* 3.9 12.3 + - + -
199K TYR* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 188 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140K THR* 4.5 11.8 - - - -
141K ALA 3.3 9.0 - - - -
142K ALA* 4.4 16.2 - - + -
166K SER 4.2 7.4 - - - +
167K GLY* 3.3 14.1 + - - +
169K HIS* 5.0 0.2 - - + -
186K VAL* 4.9 5.8 - - + -
187K VAL* 1.3 84.5 - - - +
189K VAL* 1.3 64.7 + - - +
120M PHE* 4.8 4.9 - - + -
139M LEU* 5.3 0.4 - - + -
141M ASN* 3.4 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140K THR* 3.7 4.8 - - - -
141K ALA* 2.8 40.6 + - + +
143K LEU* 3.9 17.7 - - + -
164K LEU* 4.6 5.2 - - + -
166K SER 5.8 0.2 - - - +
187K VAL* 3.9 17.0 - - + -
188K THR* 1.3 79.9 - - - +
190K PRO* 1.3 69.7 - - + +
193K SER* 3.5 8.7 - - - +
194K LEU* 4.9 3.1 - - + -
199K TYR* 3.1 50.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 190 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139K GLY 4.0 5.8 - - - +
140K THR* 4.4 3.6 - - - -
189K VAL* 1.3 90.5 - - + +
191K SER* 1.3 64.3 + - - +
192K SER* 4.5 7.4 - - - +
193K SER* 2.5 45.3 + - - +
199K TYR* 4.4 1.6 - - - +
----------------------------------------------------------
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