Contacts of the strand formed by residues 171 - 178 (chain H) in PDB entry 1BGX
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 171 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H THR* 4.5 17.3 + - - +
140H GLY* 3.3 23.7 + - - -
141H TYR* 3.1 46.7 + - + +
142H PHE* 3.8 28.4 - + - -
143H PRO* 4.2 13.9 - - + -
144H GLU* 3.5 38.1 - - + +
164H ALA* 3.9 12.8 - - + -
165H VAL 3.5 13.9 - - - -
166H LEU* 3.8 28.8 - - + +
167H GLN* 3.5 1.1 - - - +
170H LEU* 1.3 74.1 - - - +
172H THR* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 172 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H LEU* 4.5 15.7 - - + -
138H VAL 3.7 4.9 - - - +
139H LYS* 3.8 33.2 + - + +
140H GLY 4.8 0.3 + - - -
163H PRO 3.9 2.9 - - - +
164H ALA* 3.4 3.9 - - - -
165H VAL* 3.4 27.6 + - - +
167H GLN* 2.9 28.4 + - - -
170H LEU* 6.1 0.2 - - - +
171H TYR* 1.3 76.1 + - - +
173H LEU* 1.3 61.7 + - - +
174H SER* 5.6 0.8 + - - -
160L LEU* 4.1 14.5 - - + +
178L THR* 5.3 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H LEU* 4.3 2.4 - - - +
138H VAL* 2.8 35.4 + - + +
141H TYR* 3.3 29.6 - - + +
144H GLU* 5.2 3.1 - - - +
145H PRO* 6.2 1.6 - - + -
146H VAL* 3.8 26.5 - - + +
148H LEU* 4.0 25.6 - - + -
161H THR* 4.5 11.7 - - + -
162H PHE 3.4 16.2 - - - +
163H PRO* 4.6 2.9 - - + -
164H ALA* 4.1 16.4 - - + +
172H THR* 1.3 74.3 - - - +
174H SER* 1.3 82.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H CYS 3.5 11.9 - - - -
137H LEU* 4.5 13.0 - - - -
148H LEU* 5.0 0.9 - - - -
161H THR* 4.2 0.2 - - - -
162H PHE* 3.1 47.5 + - - +
163H PRO 5.1 0.4 + - - -
172H THR* 6.1 0.4 - - - -
173H LEU* 1.3 85.4 - - - +
175H SER* 1.3 63.9 + - - +
133L VAL* 5.7 0.2 - - - -
135L PHE* 3.8 19.6 - - - -
162L SER* 5.9 0.2 - - - -
176L SER* 3.9 7.4 + - - -
178L THR* 5.3 4.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H GLY* 3.4 2.6 - - - -
136H CYS 3.2 27.2 + - - -
148H LEU* 3.9 29.3 - - - +
150H TRP* 3.3 20.6 + - - -
159H VAL* 4.2 2.8 - - - +
160H HIS 3.4 18.1 + - - -
161H THR* 4.0 11.5 + - - -
162H PHE* 3.9 2.0 - - - -
174H SER* 1.3 77.8 - - - +
176H SER* 1.3 69.8 + - - +
135L PHE* 3.6 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H THR* 4.8 4.9 - - - -
134H LEU 3.4 15.3 - - - -
135H GLY* 4.4 1.1 - - - -
150H TRP* 4.5 2.7 - - - -
158H GLY 3.3 3.3 - - - +
159H VAL* 3.5 2.8 - - - +
160H HIS* 3.0 30.6 + - - +
162H PHE* 3.4 17.8 - - - -
175H SER* 1.3 81.3 + - - +
177H VAL* 1.3 60.8 + - - +
178H THR* 5.5 0.7 - - - -
135L PHE* 3.9 18.6 - - - -
137L ASN* 3.6 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H THR* 3.5 2.1 - - - -
134H LEU* 2.9 54.1 + - + +
150H TRP* 4.0 30.5 - - + -
155H LEU* 3.9 25.8 - - + -
157H SER 3.6 21.1 - - - +
158H GLY 3.4 3.6 - - - +
159H VAL* 3.9 13.2 - - + -
176H SER* 1.3 75.9 - - - +
178H THR* 1.3 70.5 + - - +
179H VAL* 4.2 3.1 - - + -
189H ILE* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H SER* 4.4 7.4 - - - +
132H VAL 3.6 16.4 - - - +
133H THR* 3.5 23.1 - - - +
157H SER 4.0 10.7 - - - +
158H GLY* 3.6 16.7 + - - -
160H HIS* 5.4 3.2 + - - -
176H SER 5.5 0.5 - - - -
177H VAL* 1.3 77.6 - - - +
179H VAL* 1.3 67.7 + - - +
137L ASN* 5.3 8.1 + - - +
----------------------------------------------------------
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