Contacts of the strand formed by residues 144 - 148 (chain H) in PDB entry 2W3S
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 144 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H GLU* 3.5 25.4 - - + +
142H GLY 3.8 3.8 + - - +
143H PRO* 1.3 71.8 - - - +
145H ILE* 1.3 61.5 + - - +
146H TRP* 3.6 26.9 - - + +
312H MET* 3.5 13.9 - - + +
328H SER* 2.6 41.0 + - - -
330H ARG* 3.6 26.0 - - - +
611H ARG* 3.9 15.5 - - - +
612H LEU* 4.9 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H PRO* 3.8 15.5 + - + +
144H VAL* 1.3 80.3 - - - +
146H TRP* 1.3 76.1 + - - +
147H ALA* 4.5 2.6 + - + -
325H ARG* 3.7 26.9 - - + +
326H ILE 3.2 10.5 - - - +
327H GLU* 3.7 32.5 - - + +
612H LEU 4.5 4.9 - - - +
613H ARG 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H VAL* 3.6 9.8 - - + +
145H ILE* 1.3 85.8 - - - +
147H ALA* 1.3 61.4 + - - +
309H ASP* 3.9 17.3 - - - -
312H MET* 3.6 40.8 - - + +
313H LEU* 3.2 38.4 - - + -
324H LEU 4.0 1.1 - - - +
325H ARG* 3.3 5.4 - - - +
326H ILE* 3.0 43.7 + - + +
404H HIS* 4.5 12.3 - + + +
405H TYR* 4.8 2.2 - - + -
609H TRP* 3.5 21.5 - + - -
611H ARG 2.9 30.1 + - - -
612H LEU 3.6 11.3 + - - -
613H ARG 4.1 5.8 - - - +
614H GLY* 3.4 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H ILE* 5.2 2.7 - - + -
146H TRP* 1.3 76.0 - - - +
148H ARG* 1.3 59.2 + - - +
149H GLY 4.2 6.9 + - - +
151H VAL* 6.1 1.6 - - + -
324H LEU 3.5 3.8 - - - -
325H ARG* 4.4 16.8 - - + +
404H HIS 5.1 2.7 - - - +
613H ARG 5.5 1.4 + - - -
615H GLN* 5.5 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 148 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H ALA* 1.3 72.6 - - - +
149H GLY* 1.3 64.1 + - - +
150H ASP 3.8 0.2 + - - -
151H VAL* 4.8 1.2 + - - +
320H PHE* 3.3 25.2 - - - -
321H VAL 3.7 18.5 + - - +
322H PRO* 3.0 27.2 + - - +
323H ALA* 3.1 4.8 - - - +
324H LEU 2.7 44.0 + - - +
402H THR* 3.3 29.3 + - - -
403H THR 3.0 30.5 + - - -
404H HIS* 3.5 31.5 - - + +
615H GLN* 5.7 2.0 - - - +
----------------------------------------------------------
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