Contacts of the strand formed by residues 181 - 188 (chain D) in PDB entry 1T5A
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 ILE 181 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LEU* 4.4 25.8 - - + -
174D ILE 3.8 0.7 - - - +
175D TYR* 3.3 3.6 - - - +
176D VAL* 2.8 56.0 + - + +
177D ASP* 4.7 6.1 - - + +
179D GLY 4.7 1.1 - - - -
180D LEU* 1.3 88.4 - - + +
182D SER* 1.3 64.8 + - - +
183D LEU* 4.6 4.0 - - + -
197D VAL* 4.7 0.4 - - + -
199D ASN 3.3 16.8 - - - +
200D GLY* 2.9 34.3 - - - +
201D GLY* 4.0 4.7 - - - +
202D SER 3.8 23.3 - - - +
203D LEU* 5.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ARG* 5.6 0.4 - - - -
173D LYS* 5.3 0.4 - - - -
174D ILE 3.4 4.0 - - - -
175D TYR* 3.6 31.0 - - - -
179D GLY 5.5 0.4 - - - -
181D ILE* 1.3 74.6 - - - +
183D LEU* 1.3 72.6 + - - +
197D VAL* 3.8 0.7 - - - -
198D GLU* 2.9 49.9 + - - +
199D ASN* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LEU* 3.8 13.0 - - + -
140D LEU* 3.6 23.6 - - + -
142D ILE* 4.3 18.4 - - + -
157D LEU* 4.5 7.4 - - + -
173D LYS* 3.1 11.3 - - - +
174D ILE* 2.8 47.4 + - + +
176D VAL* 4.6 6.5 - - + -
181D ILE* 4.6 6.3 - - + +
182D SER* 1.3 85.2 - - - +
184D GLN* 1.3 60.2 + - - +
195D THR* 3.8 19.5 - - - +
196D GLU 3.6 4.9 - - - -
197D VAL* 3.7 30.3 - - + -
198D GLU* 4.3 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D GLY* 3.0 28.8 + - - +
172D SER 3.2 6.5 - - - +
173D LYS* 3.3 19.9 - - - +
183D LEU* 1.3 75.7 - - - +
185D VAL* 1.3 67.2 - - - +
186D LYS* 3.0 30.3 + - - +
195D THR* 3.0 24.8 - - - -
196D GLU* 3.1 21.9 + - + +
198D GLU* 3.5 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D VAL* 3.4 29.2 - - + -
169D GLU 3.1 23.8 - - - +
170D VAL* 3.5 15.7 - - + +
171D GLY* 2.6 32.2 + - - +
172D SER* 2.8 17.4 + - - +
174D ILE* 4.0 20.6 - - + -
184D GLN* 1.3 70.2 - - - +
186D LYS* 1.3 61.0 + - - +
187D GLN 4.4 13.5 - - - +
188D LYS* 4.6 2.5 - - + +
193D LEU* 4.3 15.5 - - + -
194D VAL 5.1 0.2 - - - +
195D THR* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D THR* 5.8 2.0 - - + -
170D VAL* 3.2 20.9 - - - +
171D GLY* 6.2 0.2 - - - -
184D GLN* 3.6 38.4 + - - +
185D VAL* 1.3 73.4 - - - +
187D GLN* 1.3 72.3 + - + +
194D VAL* 2.9 20.9 + - + +
195D THR 3.7 13.2 - - - +
196D GLU* 3.1 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D VAL* 4.5 1.8 - - - -
185D VAL* 4.4 4.4 - - - +
186D LYS* 1.3 90.7 - - + +
188D LYS* 1.3 63.0 + - - +
189D GLY 3.5 1.2 + - - -
193D LEU* 3.6 2.9 - - - +
194D VAL* 2.9 65.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D CYS* 3.2 21.3 + - + +
166D LYS* 5.6 2.2 + - - +
168D VAL* 3.2 20.4 + - + +
169D GLU* 2.9 29.2 + - - +
170D VAL* 3.9 20.5 - - + +
185D VAL* 4.8 2.7 - - + -
187D GLN* 1.3 70.6 - - - +
189D GLY* 1.3 73.6 + - - +
193D LEU* 3.6 23.3 - - + -
----------------------------------------------------------
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