Contacts of the strand formed by residues 136 - 141 (chain C) in PDB entry 2BP1
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 VAL 136 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ILE* 3.9 19.5 - - + +
105C THR* 4.4 13.0 - - + -
124C LEU* 4.2 9.0 - - + -
128C LEU* 3.7 19.5 - - + +
131C LEU* 4.0 24.9 - - + -
133C CYS* 4.2 1.6 - - - -
135C GLN* 1.3 77.7 - - - +
137C ASP* 1.3 60.8 + - - +
138C LEU 3.6 19.1 - - - +
139C PHE* 4.1 6.3 - - + -
165C LYS 3.1 10.0 + - - +
166C PHE* 3.2 23.2 - - + -
167C VAL* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C GLY* 4.9 9.8 + - - -
99C CYS* 5.9 0.3 - - - -
101C VAL 4.0 3.1 - - - +
102C LYS* 3.3 39.7 + - + +
103C ILE* 3.0 37.2 + - - +
135C GLN* 5.4 3.9 + - - +
136C VAL* 1.3 74.1 - - - +
138C LEU* 1.3 62.2 + - + +
167C VAL* 3.4 18.9 - - + +
168C GLU* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLU* 4.3 7.9 - - - +
103C ILE 3.3 3.8 + - - +
104C ALA* 3.1 15.8 - - + -
105C THR 3.0 24.9 + - - +
136C VAL* 3.6 7.5 - - - +
137C ASP* 1.3 80.8 - - + +
139C PHE* 1.3 60.9 + - - +
140C TYR* 3.3 37.5 - - + +
168C GLU* 3.3 23.8 - - + +
169C LEU 3.9 2.2 - - - -
170C GLY* 3.8 20.2 - - - +
196C VAL* 3.8 31.6 - - + -
222C ARG* 5.0 1.6 - - - +
224C TYR* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C THR* 3.5 12.3 - - + -
106C LYS 4.3 2.0 - - - -
107C ALA* 3.6 38.8 - - + -
120C VAL* 3.7 25.4 - - + -
124C LEU* 3.7 41.1 - - + -
136C VAL* 4.1 1.1 - - + -
138C LEU* 1.3 74.9 - - - +
140C TYR* 1.3 62.7 + - - +
141C LEU* 4.8 3.4 - - + -
157C CYS* 4.5 8.1 - - - -
160C LEU* 5.0 0.2 - - + -
166C PHE* 3.5 49.1 - + + +
168C GLU 2.8 8.3 + - - -
169C LEU* 3.4 13.3 - - + +
170C GLY 2.7 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASP* 3.7 8.9 + - - -
104C ALA* 3.9 4.9 - - + -
105C THR 2.8 26.5 + - - +
106C LYS* 3.2 24.8 - - + -
107C ALA* 2.9 26.7 + - - -
138C LEU* 3.3 29.6 - - + +
139C PHE* 1.3 82.8 - - - +
141C LEU* 1.3 66.2 + - - +
142C HIS* 4.7 0.2 - - - -
170C GLY* 3.3 24.5 - - - -
171C LEU 3.7 14.8 - - - -
172C SER* 4.5 1.8 - - - -
196C VAL* 3.3 26.6 - - + +
198C GLN* 3.2 46.5 + - + +
224C TYR* 3.4 10.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ALA* 3.8 2.9 - - + +
115C LEU* 4.2 18.6 - - + -
120C VAL* 4.8 2.9 - - + -
139C PHE* 4.8 7.6 - - + -
140C TYR* 1.3 72.1 - - - +
142C HIS* 1.3 61.1 + - - +
143C ALA 3.4 2.4 + - - -
150C VAL* 5.4 1.1 - - + -
153C THR* 3.7 32.1 - - + -
154C LEU* 4.2 18.2 - - + -
157C CYS* 4.1 18.8 - - - -
169C LEU* 4.7 3.8 - - + -
170C GLY 3.0 11.3 + - - +
171C LEU* 3.8 17.4 - - + -
172C SER* 3.0 28.6 + - - +
174C TYR* 3.6 30.2 - - + +
182C ILE* 5.2 1.6 - - + -
----------------------------------------------------------
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