Contacts of the strand formed by residues 179 - 189 (chain D) in PDB entry 1TW8
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 ASP 179 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LYS* 3.3 24.4 - - - +
20D VAL 3.1 26.0 - - - +
21D LYS* 3.6 7.1 - - + +
22D ARG* 3.9 2.7 - - - +
175D LEU* 3.1 17.9 - - - +
176D ASN* 3.5 12.8 + - - +
177D GLY* 4.4 3.5 + - - -
178D GLU* 1.3 85.4 + - - +
180D LEU* 1.3 60.9 + - - +
181D VAL* 3.7 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLN 3.5 0.7 - - - +
19D LYS* 3.0 3.6 - - - -
20D VAL* 2.7 54.7 + - + +
23D PRO* 4.3 24.9 - - + -
28D LEU* 4.0 17.3 - - + -
33D ALA* 4.4 11.4 - - - +
36D PRO* 5.7 1.3 - - + -
37D PHE* 3.7 16.6 - - + -
173D TRP* 3.4 46.2 - - + -
175D LEU* 3.8 27.1 - - + +
179D ASP* 1.3 72.3 - - - +
181D VAL* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLY* 3.7 23.6 - - - +
18D GLN 3.2 10.3 - - - +
19D LYS* 3.6 15.7 - - + +
173D TRP* 3.1 5.5 - - - -
174D GLU 3.1 36.5 + - - +
176D ASN* 4.7 11.4 - - + -
179D ASP* 3.7 13.5 - - - +
180D LEU* 1.3 81.4 - - - +
182D CYS* 1.3 72.7 + - - +
183D VAL* 3.5 8.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 3.2 23.8 - - - +
16D ILE* 3.7 18.6 - - - +
17D GLY* 3.0 20.3 + - - -
18D GLN 3.0 11.7 + - - +
37D PHE* 4.1 14.6 - - + -
171D VAL* 4.1 9.0 - - - -
172D ASP 3.3 7.2 - - - -
173D TRP* 4.2 3.6 - - - +
181D VAL* 1.3 77.4 - - - +
183D VAL* 1.3 64.0 + - - +
184D SER 3.5 20.6 - - - -
185D THR* 3.6 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 4.1 20.1 - - - +
133D ILE* 3.3 29.4 - - + -
172D ASP* 2.7 30.3 + - + +
173D TRP 4.1 0.4 - - - +
174D GLU* 3.6 29.6 - - + +
181D VAL* 3.6 13.0 - - + +
182D CYS* 1.3 78.6 - - - +
184D SER* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ASN* 5.2 0.2 + - - -
16D ILE* 4.2 9.2 - - - -
172D ASP* 2.7 50.2 + - - +
182D CYS* 3.5 3.4 - - - -
183D VAL* 1.3 86.6 - - - +
185D THR* 1.3 82.1 + - - +
186D SER* 4.7 2.1 + - - -
213D ARG* 5.2 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D TYR* 2.6 29.0 + - - -
12D ASN* 2.5 33.6 + - - +
15D LEU* 4.0 23.1 - - + -
16D ILE* 4.5 2.9 - - + -
169D LEU* 4.4 10.3 - - - -
170D GLU 3.0 15.5 - - - +
171D VAL* 4.7 3.1 - - - -
172D ASP* 4.5 1.1 - - - -
182D CYS* 3.6 19.5 - - - -
184D SER* 1.3 87.4 + - - +
186D SER* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D TYR* 3.5 5.8 - - - -
169D LEU* 3.5 8.0 - - - +
170D GLU* 2.9 38.7 + - - -
172D ASP* 4.4 3.3 + - - -
184D SER* 4.7 2.1 + - - -
185D THR* 1.3 78.3 + - - +
187D PHE* 1.3 61.4 + - - +
212D VAL* 3.3 6.5 - - - +
213D ARG* 3.3 42.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SER* 3.7 14.8 - - - -
4D ILE* 3.8 28.5 - - + -
5D LYS* 4.5 20.0 - - + -
8D TYR* 4.1 26.2 + + + -
124D GLU* 4.1 0.2 - - - -
126D LEU* 4.0 9.0 - - + -
167D ASN* 3.2 40.4 - - + -
168D TYR 3.3 17.5 - - - -
169D LEU* 4.6 10.5 - - + -
186D SER* 1.3 74.7 - - - +
188D ALA* 1.3 83.0 + - - +
189D GLU* 4.0 13.7 - - + -
212D VAL* 3.4 9.7 - - - +
217D GLN* 5.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ASN* 3.4 8.5 - - - +
168D TYR* 3.3 28.2 + - + +
187D PHE* 1.3 85.4 - - - +
189D GLU* 1.3 66.5 + - - +
190D LEU 4.1 0.4 - - - -
210D PHE* 5.5 1.8 - - + -
212D VAL* 3.8 20.4 - - + +
215D LEU* 3.7 27.1 - - + +
217D GLN* 4.4 12.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
2D SER* 4.1 16.4 - - - -
5D LYS* 4.1 17.0 - - - +
165D ASP* 5.1 8.9 - - + +
167D ASN* 3.5 28.0 - - - +
187D PHE* 4.0 6.4 - - + -
188D ALA* 1.3 82.1 - - - +
190D LEU* 1.3 56.1 + - - +
191D PHE* 3.0 5.1 - - + +
192D LYS* 2.5 66.0 + - + +
193D SER 3.6 0.5 + - - -
215D LEU* 4.2 3.5 - - - +
217D GLN* 3.4 18.4 + - - +
223D ARG* 5.8 1.0 + - - -
----------------------------------------------------------
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