Contacts of the strand formed by residues 200 - 206 (chain D) in PDB entry 5U07
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 GLU 200 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C ARG* 2.7 34.0 + - - +
14D TYR* 3.6 28.3 + - + +
198D THR* 3.1 9.4 + - - +
199D VAL* 1.3 71.6 - - - +
201D VAL* 1.3 68.8 + - - +
225D GLN* 4.6 0.4 - - - -
226D PHE 2.8 37.8 + - - +
227D SER* 5.0 2.5 - - - -
27H THR* 2.6 40.0 + - - +
28H VAL* 4.8 5.4 - - + -
29H VAL* 4.7 11.7 - - + +
37H ARG* 5.0 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C TRP* 3.5 37.5 - - + -
445C ASN* 3.0 41.3 - - + +
522C ARG* 5.4 8.4 - - - +
14D TYR* 4.2 0.7 - - - -
199D VAL 3.7 3.5 + - - +
200D GLU* 1.3 81.6 - - - +
202D ASP* 1.3 63.7 + - - +
203D PHE* 4.1 2.8 + - + +
223D ALA* 3.8 10.3 - - + -
224D GLY 3.9 6.7 - - - +
225D GLN* 4.1 7.9 - - + +
37H ARG* 4.2 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D TYR* 3.3 7.6 - - - +
200D GLU 3.7 0.6 + - - -
201D VAL* 1.3 72.0 - - - +
203D PHE* 1.3 60.7 + - - +
204D PHE* 3.5 9.2 + - - +
224D GLY* 2.8 39.6 + - - +
226D PHE* 4.3 20.0 - - + -
26H LYS* 3.6 14.1 + - - +
37H ARG* 2.8 42.9 + - - +
41H GLN* 3.4 24.7 + - - +
190H HIS* 4.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ASN* 4.9 11.7 - - - +
446C SER* 4.9 8.7 - - - -
201D VAL* 4.0 4.6 + - + +
202D ASP* 1.3 72.0 + - - +
204D PHE* 1.3 57.7 + - - +
205D THR* 3.3 24.7 - - - -
221D MET* 3.9 31.4 - - + -
222D ASN 3.1 28.9 - - - -
223D ALA* 4.0 11.2 - - + +
20H ASP* 4.5 10.3 - - + +
21H ASP* 4.2 32.1 - - + +
26H LYS* 3.1 27.5 + - - +
15K A 3.9 37.0 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ASP* 3.8 16.4 - - - +
203D PHE* 1.3 74.9 - - - +
205D THR* 1.3 66.8 + - - +
220D HIS* 3.7 5.3 - + - +
222D ASN* 2.9 68.5 + - + +
224D GLY* 3.7 22.4 - - - -
41H GLN* 3.4 28.0 - - - +
13K U 3.4 64.6 - + - +
15K A 3.7 4.7 - - - -
39M A 4.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D PHE* 3.3 25.6 - - - -
204D PHE* 1.3 78.8 + - - +
206D ALA* 1.3 58.8 + - - +
207D VAL 3.7 0.2 + - - -
218D SER* 2.9 34.5 - - - +
220D HIS 3.1 16.4 - - - +
221D MET* 4.1 9.0 - - + +
13K U 3.9 4.0 - - - -
14K G 3.1 51.2 + - - +
15K A 2.8 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D PHE* 4.4 2.0 - - - -
205D THR* 1.3 71.3 - - - +
207D VAL* 1.3 53.0 + - - +
218D SER* 2.3 26.0 + - - -
219D GLY* 2.8 13.6 + - - -
220D HIS* 2.8 29.5 + - + -
61H ARG* 5.4 2.7 - - - -
116H LEU* 3.9 17.7 - - + -
13K U 3.4 34.4 + - - +
14K G 3.8 4.5 - - - -
----------------------------------------------------------
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