Contacts of the strand formed by residues 151 - 154 (chain H) in PDB entry 2R0L
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 THR 151 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H VAL* 1.3 72.8 + - - +
152H VAL* 1.3 75.0 + - - +
153H SER* 4.8 5.2 - - - +
197H ASN 3.5 1.5 - - - +
198H VAL* 3.3 6.8 - - - +
199H ASN* 2.8 48.9 + - + -
201H LYS* 5.2 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H CYS* 5.7 0.2 - - + -
142H VAL* 4.6 9.4 - - + -
150H VAL* 4.3 10.3 - - + +
151H THR* 1.3 84.7 - - - +
153H SER* 1.3 70.9 + - - +
154H TRP* 4.4 3.4 - - - +
163H VAL* 5.9 0.9 - - - +
165H THR* 3.9 34.6 + - + +
178H LEU* 4.2 16.2 - - + -
180H SER* 3.8 23.8 - - - +
196H CYS* 4.4 9.4 - - + -
197H ASN 3.5 5.4 - - - +
198H VAL* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H THR* 4.8 5.4 - - - +
152H VAL* 1.3 75.4 - - - +
154H TRP* 1.3 67.5 + - - +
156H SER* 4.3 4.4 - - - -
157H GLY* 4.1 15.9 - - - -
196H CYS* 3.3 6.1 - - - +
197H ASN* 2.8 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 154 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H LEU* 3.7 20.0 - - + -
139H GLY* 3.5 28.5 - - - -
140H CYS* 3.7 2.9 - - - -
152H VAL* 4.4 2.8 - - + +
153H SER* 1.3 78.4 + - - +
155H ASN* 1.3 63.2 + - - +
156H SER 3.2 1.8 - - - -
157H GLY* 2.8 26.6 + - - +
159H LEU* 3.5 38.9 + - + +
163H VAL* 3.6 28.7 - - + +
180H SER* 3.0 44.9 + - - -
181H VAL 4.7 0.8 + - - -
182H VAL* 4.4 14.1 - - + -
194H TYR* 4.3 6.5 - - + -
195H ILE 3.4 26.5 - - - -
196H CYS* 3.7 29.4 - - + -
211H VAL* 4.2 6.7 - - + -
----------------------------------------------------------
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