Contacts of the strand formed by residues 182 - 190 (chain D) in PDB entry 1KTD
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 PHE 182 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP 5.3 1.3 - - - -
29C ASP* 4.7 2.2 - - - -
148D ASP* 3.1 22.3 + - - -
149D PHE* 2.9 47.2 + - + -
150D TYR* 4.0 20.4 - + - -
151D PRO 3.6 3.1 - - - -
152D GLY* 3.1 33.4 - - - -
174D LEU* 3.7 29.6 - - + -
175D VAL 3.3 13.0 - - - +
176D ARG* 3.7 50.7 - - + -
177D ASN* 3.8 1.6 - - - -
181D THR* 1.3 75.9 - - - +
183D GLN* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 3.4 20.9 - - - +
93C SER* 2.6 30.0 + - - +
94C ARG* 4.1 8.8 - - - +
95C SER* 5.2 2.8 + - - -
146D VAL 3.6 7.4 - - - -
147D SER* 4.3 13.2 - - - +
149D PHE* 4.1 1.8 - - - -
174D LEU* 4.1 1.7 - - - +
175D VAL* 2.8 45.6 + - + +
177D ASN* 2.9 28.7 + - - +
182D PHE* 1.3 76.6 - - - +
184D THR* 1.3 67.9 + - - +
185D LEU* 5.0 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D SER* 4.4 0.3 + - - -
146D VAL* 3.1 55.5 + - + +
147D SER* 5.9 0.2 - - - -
149D PHE* 4.0 11.9 - - + -
154D ILE* 5.0 3.4 - - + -
156D VAL* 4.5 12.3 - - + -
171D SER* 4.1 5.2 + - - -
172D THR* 4.1 3.0 + - - -
173D GLY 3.0 26.1 + - - -
174D LEU* 4.6 3.8 - - - -
175D VAL* 5.1 0.4 - - - -
183D GLN* 1.3 81.9 + - - +
185D LEU* 1.3 82.1 + - - +
186D VAL* 4.3 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PRO* 6.0 0.7 - - + -
129D TYR* 4.2 11.7 - - - +
143D VAL* 4.2 11.2 - - + -
144D CYS 3.7 2.2 - - - -
145D SER* 3.9 26.5 - - - +
170D VAL 3.9 0.5 - - - +
171D SER* 3.3 6.2 + - - -
172D THR* 3.1 51.6 + - + +
183D GLN* 5.0 11.7 - - - +
184D THR* 1.3 87.1 + - - +
186D VAL* 1.3 62.0 + - - +
187D MET* 3.7 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D CYS* 3.1 22.2 + - - +
156D VAL* 3.4 53.8 - - + +
157D ARG* 5.5 0.4 - - - -
158D TRP* 2.8 38.0 + - + +
169D ILE* 4.2 19.1 - - + -
170D VAL 4.1 1.3 - - - -
171D SER* 4.2 12.8 - - - +
184D THR* 4.3 9.9 - - + +
185D LEU* 1.3 73.4 - - - +
187D MET* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 3.8 15.5 - - + -
141D LEU* 4.0 31.9 - - + -
142D LEU 3.4 6.7 - - - +
143D VAL* 4.0 29.2 - - + -
158D TRP* 3.8 1.1 - - - -
169D ILE* 3.3 11.3 - - - +
170D VAL* 2.7 72.9 + - + +
172D THR* 4.1 18.2 - - + -
185D LEU* 4.4 13.5 - - + +
186D VAL* 1.3 76.5 - - - +
188D LEU* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D LEU* 3.5 7.6 - - - +
142D LEU* 2.9 39.0 + - + +
158D TRP* 3.7 26.7 - - + +
165D GLU* 3.6 29.4 - - + -
167D THR 4.2 8.5 - - - +
168D GLY 3.6 3.8 - - - +
169D ILE* 3.5 21.3 - - + -
187D MET* 1.3 76.1 - - - +
189D GLU* 1.3 68.6 + - - +
190D THR* 3.7 15.7 + - + +
198D TYR* 3.7 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A NAG 5.5 6.2 + - - -
139D HIS* 4.5 34.3 - - + +
140D ASN 3.9 4.5 - - - -
141D LEU* 3.5 23.6 - - + +
167D THR 5.0 0.9 - - - +
168D GLY* 2.8 34.4 + - - +
170D VAL* 3.9 20.3 - - + +
188D LEU* 1.3 72.8 - - - +
190D THR* 1.3 71.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D HIS* 4.8 4.0 - - - +
140D ASN* 3.3 26.5 + - - +
142D LEU* 4.2 6.9 - - - +
160D ARG* 5.3 3.4 - - - +
165D GLU* 3.6 24.2 - - - +
188D LEU* 3.7 20.5 + - + +
189D GLU* 1.3 83.7 - - - +
191D VAL* 1.3 70.7 + - - +
192D PRO* 3.5 10.2 - - - +
198D TYR* 3.4 31.6 + - - +
----------------------------------------------------------
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