Contacts of the strand formed by residues 150 - 160 (chain B) in PDB entry 3UR9
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 150 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 5.2 12.8 - - + +
146B LYS* 3.3 5.3 - - - -
147B ARG* 2.8 45.8 + - + +
148B GLY 3.2 0.4 - - - -
149B ASN* 1.3 92.6 + - - +
151B TRP* 1.3 66.0 + - - +
152B VAL* 3.8 9.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B MET 3.5 32.8 - - - -
1B ALA* 4.0 11.4 - - + -
2B PRO* 3.9 18.8 - - + +
5B LEU* 3.6 25.6 - - + -
71B MET* 3.5 38.3 - - + +
72B VAL* 4.0 4.9 + - - +
84B SER* 5.8 3.6 - - - -
144B VAL* 4.1 18.4 - - + -
145B HIS* 3.6 20.9 - - - -
146B LYS* 3.8 49.3 - - + +
149B ASN 4.0 3.3 + - - -
150B ASP* 1.3 75.9 - - - +
152B VAL* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET* 3.9 3.4 - - - -
72B VAL* 3.6 17.5 - - + +
74B GLU* 3.7 31.6 - - + -
144B VAL* 3.2 6.4 - - - +
145B HIS* 2.7 60.0 + - + +
147B ARG* 4.1 31.2 - - + +
150B ASP* 4.0 13.2 - - + +
151B TRP* 1.3 79.0 - - - +
153B VAL* 1.3 67.6 + - - +
154B CYS* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 3.9 24.9 - - + -
20B VAL* 4.4 9.2 - - + -
26B ILE* 4.0 11.9 - - + -
71B MET* 3.8 7.8 - - + +
72B VAL 3.1 13.3 + - - +
73B LEU* 3.4 19.0 - - + +
74B GLU 2.9 22.9 + - - -
142B PRO* 3.9 18.4 - - + -
143B TYR 3.4 12.1 - - - +
144B VAL* 4.1 4.3 - - + -
152B VAL* 1.3 74.3 - - - +
154B CYS* 1.3 65.6 + - - +
155B GLY 3.9 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 5.5 0.4 - - - -
73B LEU* 4.6 3.4 - - - -
74B GLU* 3.4 13.7 - - + +
76B GLY* 3.1 45.9 + - - +
77B CYS* 4.0 18.2 - - + -
83B CYS* 3.9 25.1 - - - -
101B MET* 6.0 0.4 - - - -
117B GLN* 5.3 0.4 - - - -
143B TYR* 2.9 22.8 + - - -
145B HIS* 4.0 12.1 - - + -
153B VAL* 1.3 75.6 - - - +
155B GLY* 1.3 57.9 + - - +
169B CYS* 4.7 3.3 - - - -
171B VAL* 3.5 8.5 - - - +
172B GLN 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 4.5 6.3 - - - -
73B LEU* 5.0 1.2 - - - +
142B PRO* 3.4 4.9 - - - +
143B TYR* 2.9 27.1 + - - -
153B VAL* 3.8 7.4 - - - +
154B CYS* 1.3 78.5 - - - +
156B VAL* 1.3 66.8 + - - +
169B CYS* 4.0 14.1 - - - -
170B ALA 3.2 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 5.3 0.7 - - + -
26B ILE* 3.9 31.2 - - + -
27B THR* 3.6 23.1 - - - +
28B THR* 3.2 18.8 + - - +
55B PHE* 3.9 12.3 - - + -
140B GLY* 3.7 19.3 - - - +
141B ALA 3.3 4.0 - - - +
142B PRO* 4.7 3.1 - - + -
155B GLY* 1.3 78.0 - - - +
157B HIS* 1.3 65.1 + - - +
169B CYS* 3.1 4.3 - - - +
170B ALA* 2.8 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 2.7 21.3 + - - -
85B VAL* 4.7 3.5 - - + +
87B ILE* 6.2 0.2 - - + -
134B THR* 3.6 21.1 + - + +
138B ASP* 3.8 33.0 - - + +
139B CYS* 3.3 17.5 - - - +
140B GLY 2.9 12.3 + - - -
141B ALA* 2.7 22.7 + - + +
143B TYR* 2.8 35.9 + - + -
156B VAL* 1.3 72.1 - - - +
158B ALA* 1.3 57.5 + - - +
159B ALA 3.1 25.5 + - - -
167B VAL* 4.0 4.5 - - + -
168B VAL 3.7 0.9 + - - -
203B K36 2.8 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 4.1 16.6 - - + -
30B HIS* 3.5 5.7 - - + -
54B GLU* 5.1 1.3 - - + -
114B VAL* 4.6 17.0 - - + -
139B CYS* 3.3 11.3 - - - -
157B HIS* 1.3 75.5 - - - +
159B ALA* 1.3 65.0 + - + +
168B VAL* 2.9 14.0 + - + +
169B CYS 4.4 0.4 - - - -
170B ALA* 3.9 20.9 - - + +
203B K36 2.9 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 3.8 32.3 - - + -
157B HIS* 3.1 13.3 + - - -
158B ALA* 1.3 80.8 - - + +
160B ALA* 1.3 63.6 + - - +
168B VAL* 2.9 32.3 + - + -
203B K36 3.2 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 3.6 11.7 - - - +
159B ALA* 1.3 78.4 - - - +
161B THR* 1.3 68.1 + - - +
164B GLY* 4.7 7.9 - - - -
166B THR 3.3 14.1 - - - +
167B VAL* 4.2 6.1 - - + +
168B VAL* 5.4 1.8 - - - -
203B K36 2.9 55.7 + - + +
----------------------------------------------------------
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