Contacts of the strand formed by residues 177 - 186 (chain H) in PDB entry 1UB5
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 LEU 177 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H LYS 5.4 0.9 - - - +
120H THR* 4.2 15.5 - - + +
147H GLY* 3.6 36.8 - - - +
148H TYR 3.5 11.2 - - - +
149H PHE* 4.1 10.3 - - + -
173H LEU* 3.6 4.3 - - - -
174H GLN* 2.6 45.3 + - - +
175H SER* 4.7 4.3 - - - +
176H GLY* 1.3 91.0 - - - +
178H TYR* 1.3 59.9 + - - +
179H THR* 4.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H GLY 3.1 14.7 + - - -
148H TYR* 2.8 54.3 + - + +
149H PHE* 3.7 23.5 - + - -
150H PRO 3.9 3.8 - - - -
151H GLU* 3.5 60.8 + - + +
171H ALA* 4.4 6.1 - - + -
172H LEU 3.4 3.6 - - - -
173H LEU* 3.5 47.5 - - + +
177H LEU* 1.3 70.3 - - - +
179H THR* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H LEU* 3.9 16.8 - - + -
145H VAL 3.2 12.8 - - - +
146H LYS* 3.3 34.9 + - + +
147H GLY 4.0 1.6 + - - -
148H TYR* 4.0 0.4 - - - -
170H PRO 4.3 0.7 - - - +
171H ALA* 3.3 1.2 - - - -
172H LEU* 2.8 43.3 + - - +
174H GLN* 3.8 13.2 + - - +
177H LEU* 4.4 3.8 + - - +
178H TYR* 1.3 79.8 + - - +
180H MET* 1.3 65.8 + - - +
165L LEU* 6.1 2.9 - - + -
183L THR* 6.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 180 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H LEU* 4.0 3.5 - - - +
145H VAL* 2.7 52.9 + - + +
148H TYR* 3.3 25.6 - - + +
151H GLU* 5.3 1.6 - - + +
153H VAL* 3.5 25.4 - - + +
155H VAL* 4.5 13.2 - - - -
168H THR* 3.8 27.6 - - + -
169H PHE* 3.6 16.2 - - - +
170H PRO* 4.8 2.0 - - + -
171H ALA* 3.6 22.7 - - + +
179H THR* 1.3 78.2 - - - +
181H SER* 1.3 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 181 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H CYS 3.3 11.9 - - - -
144H LEU* 4.3 16.2 - - - -
145H VAL* 5.5 0.4 - - - -
155H VAL* 6.0 0.2 - - - -
168H THR* 3.9 2.4 - - - +
169H PHE* 3.2 32.0 + - - +
180H MET* 1.3 78.3 - - - +
182H SER* 1.3 62.5 + - - +
138L VAL* 4.8 6.3 - - - +
140L PHE* 3.5 27.4 - - - -
181L SER* 3.7 16.3 + - - -
183L THR* 5.2 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H GLY* 3.0 4.0 - - - -
143H CYS 2.9 34.1 + - - -
155H VAL* 3.8 25.0 - - - +
157H TRP* 3.2 23.1 + - - -
166H VAL* 4.9 0.7 - - - +
167H HIS 3.4 8.6 + - - -
168H THR* 3.0 24.6 + - - -
181H SER* 1.3 76.6 - - - +
183H SER* 1.3 63.0 + - - +
140L PHE* 4.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H THR* 4.2 3.4 - - - -
141H LEU 3.2 6.7 - - - -
157H TRP* 4.7 0.4 - - - -
165H SER 3.8 1.0 - - - +
166H VAL* 3.3 5.0 - - - +
167H HIS* 2.8 47.4 + - - +
169H PHE* 3.9 3.0 - - - -
182H SER* 1.3 75.3 + - - +
184H VAL* 1.3 61.3 + - - +
185H THR* 5.8 0.2 + - - -
140L PHE* 3.2 37.4 - - - -
142L ASN* 3.0 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H VAL 3.6 0.3 - - - +
140H THR* 3.4 5.0 - - - +
141H LEU* 2.8 50.4 + - + +
157H TRP* 3.5 48.0 - - + -
161H GLY* 5.7 2.7 - - - -
165H SER* 3.6 9.4 - - - +
166H VAL* 4.3 17.0 - - + -
183H SER* 1.3 75.2 - - - +
185H THR* 1.3 74.6 + - - +
186H VAL* 4.5 9.4 - - + -
196H VAL* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H SER* 4.4 21.3 - - - +
139H VAL 3.4 10.1 - - - +
140H THR* 4.1 14.4 + - - +
165H SER* 3.0 37.9 + - - +
167H HIS* 5.6 2.8 - - - -
183H SER* 5.8 0.2 + - - -
184H VAL* 1.3 82.4 + - - +
186H VAL* 1.3 76.1 + - - +
142L ASN* 5.1 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H SER* 3.9 3.1 - - - -
139H VAL* 2.7 50.2 + - + +
141H LEU* 4.6 13.5 - - + -
184H VAL* 4.5 14.4 - - + +
185H THR* 1.3 87.8 - - - +
187H PRO* 1.3 75.7 - - + +
190H THR* 4.2 10.8 - - + +
191H TRP* 4.7 7.6 - - + -
196H VAL* 4.7 13.5 - - + -
----------------------------------------------------------
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