Contacts of the strand formed by residues 198 - 203 (chain D) in PDB entry 1LNU
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 198 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LEU* 3.9 17.7 - - + -
158D TRP* 4.3 7.0 - - + -
159D PHE 3.2 12.8 - - - +
160D ARG* 2.7 35.8 + - + -
188D LEU* 3.9 20.9 - - + -
190D MET* 3.8 20.6 - - + -
191D THR 2.5 34.4 + - - -
192D PRO* 4.5 2.7 - - + -
196D GLU* 2.7 29.3 + - + -
197D VAL* 1.3 75.0 - - - +
199D THR* 1.3 65.6 + - - +
215D TRP* 2.6 66.1 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D ILE* 6.0 0.2 - - - -
157D ARG 3.9 0.2 - - - +
158D TRP* 3.4 10.5 - - - -
159D PHE* 3.1 50.5 + - - +
197D VAL* 4.3 10.6 + - + +
198D TYR* 1.3 81.8 - - - +
200D CYS* 1.3 62.6 + - - +
212D THR* 5.4 6.1 - - - -
213D VAL 2.9 10.3 - - - -
214D GLU* 3.2 32.1 - - + -
215D TRP 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D VAL* 5.8 1.8 - - + +
128D ILE* 4.1 11.9 - - + +
144D CYS* 2.0 54.3 - - + -
156D VAL* 4.1 19.7 - - - -
157D ARG 3.6 4.9 - - - -
158D TRP* 4.2 8.3 - - + -
159D PHE* 5.6 0.2 - - - -
199D THR* 1.3 75.0 - - - +
201D HIS* 1.3 60.6 + - - +
202D VAL* 3.9 9.3 + - - +
211D ILE* 3.8 1.2 - - - +
212D THR* 3.3 7.2 - - - -
213D VAL* 2.8 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LYS 3.6 1.4 - - - +
156D VAL* 3.3 4.9 - - - +
157D ARG* 2.8 65.8 + - + +
159D PHE* 3.8 24.3 - + + -
199D THR 4.1 0.4 + - - -
200D CYS* 1.3 71.8 - - - +
202D VAL* 1.3 63.7 + - - +
203D GLU* 3.8 16.7 + - + -
210D PRO* 3.3 36.1 - - + +
211D ILE 3.7 1.6 - - - -
212D THR* 3.4 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D PRO* 3.8 15.3 - - + -
126D VAL* 3.9 13.9 - - + -
146D VAL* 3.8 21.5 - - + -
154D ILE* 3.7 27.8 - - + -
155D LYS 3.4 3.4 - - - -
156D VAL* 3.7 16.4 - - + -
200D CYS* 3.9 14.8 + - - +
201D HIS* 1.3 78.9 - - - +
203D GLU* 1.3 71.3 + - - +
207D LEU* 5.0 1.8 - - + -
210D PRO* 3.5 2.3 - - - +
211D ILE* 3.1 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D LYS* 5.7 2.3 + - - -
154D ILE* 3.7 0.2 - - - +
155D LYS* 3.0 57.0 + - + +
157D ARG* 3.5 23.1 + - - +
201D HIS* 3.8 12.4 + - + +
202D VAL* 1.3 82.2 - - - +
204D HIS* 1.3 70.3 + - + +
205D PRO* 3.5 7.5 - - - +
207D LEU* 4.7 4.5 - - - -
210D PRO* 3.8 26.5 - - + +
----------------------------------------------------------
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