Contacts of the strand formed by residues 135 - 140 (chain L) in PDB entry 2BDI
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 SER 135 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133L GLY 3.4 3.2 + - - -
134L ASN* 1.3 86.1 + - - +
136L CYS* 1.3 62.4 + - - +
159L ASN* 3.6 22.7 + - - +
160L VAL 3.9 0.9 + - - -
161L SER* 3.7 16.5 + - - -
201L CYS* 4.9 2.4 - - - -
202L ASN* 5.0 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 136 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L ASN* 4.2 3.1 - - - -
135L SER* 1.3 77.3 + - - +
137L LEU* 1.3 63.0 + - - +
159L ASN* 3.0 15.3 + - - +
160L VAL* 3.0 32.4 + - - +
162L VAL* 3.8 24.9 - - - -
199L LEU* 4.2 13.9 - - + -
200L ILE 2.9 13.2 - - - +
201L CYS* 2.1 44.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L GLN* 3.6 35.9 - - - +
136L CYS* 1.3 78.5 - - - +
138L VAL* 1.3 68.0 + - - +
139L SER* 5.2 1.1 - - - +
157L CYS* 3.8 14.6 - - + -
158L VAL 3.2 32.1 - - - +
159L ASN* 3.9 17.5 - - - +
199L LEU* 3.2 5.1 - - - +
200L ILE* 2.8 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L ILE* 3.8 19.0 - - + +
137L LEU* 1.3 79.7 - - - +
139L SER* 1.3 64.5 + - - +
157L CYS* 3.4 2.9 - - - -
158L VAL* 3.0 46.6 + - + +
160L VAL* 3.8 14.1 - - + -
190L SER* 3.9 17.3 - - - +
198L PRO* 3.2 17.3 - - - +
199L LEU* 3.5 19.1 - - + -
213L VAL* 4.2 13.7 - - + -
228L TYR* 4.1 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L ILE* 3.7 8.1 - - - +
27L GLN* 4.1 12.2 + - - +
30L GLN* 2.8 36.1 + - - +
137L LEU* 5.2 1.9 - - - +
138L VAL* 1.3 78.2 - - - +
140L GLY* 1.3 58.1 + - - +
155L LEU* 4.1 7.4 - - - -
156L GLN 2.8 17.9 - - - -
157L CYS* 3.7 15.7 - - - -
194L ASP* 5.2 1.7 - - - +
197L GLY* 4.2 5.7 - - - -
198L PRO* 3.5 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L ILE* 3.5 5.2 - - - +
30L GLN* 3.7 5.6 - - - -
43L SER* 4.5 5.4 - - - -
139L SER* 1.3 76.4 - - - +
141L TRP* 1.3 57.7 + - - -
142L GLY 3.3 5.2 - - - -
155L LEU* 3.3 16.0 - - - +
156L GLN* 2.9 34.8 + - - +
194L ASP* 3.4 12.8 - - - -
----------------------------------------------------------
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