Contacts of the strand formed by residues 126 - 130 (chain D) in PDB entry 1MWA
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 LYS 126 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D PRO* 3.6 5.3 + - + +
125D PRO* 1.3 70.7 - - - +
127D VAL* 1.3 61.3 + - - +
128D SER* 3.7 7.8 + - - +
148D LEU* 4.9 0.3 - - - +
149D ALA* 4.5 0.9 - - - -
150D ARG 3.0 35.7 + - - +
151D GLY* 3.7 21.0 + - - +
152D PHE* 4.3 2.0 - - - -
237D ILE* 4.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D PRO 3.5 1.2 + - - -
126D LYS* 1.3 68.8 - - - +
128D SER* 1.3 69.8 + - - +
147D CYS* 3.5 15.5 - - - -
148D LEU 3.0 23.6 - - - +
149D ALA 4.4 0.2 - - - +
212D CYS* 4.0 3.1 - - - -
214D VAL* 3.5 19.5 - - + -
237D ILE* 3.4 15.0 - - + +
238D SER* 3.2 38.8 - - - +
239D ALA* 3.6 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ASP* 4.9 8.3 - - - -
126D LYS* 3.7 6.7 + - - +
127D VAL* 1.3 82.5 - - - +
129D LEU* 1.3 67.2 + - - +
130D PHE* 4.5 7.4 - - - -
147D CYS* 3.6 0.9 - - - -
148D LEU* 3.3 47.9 + - - +
150D ARG* 5.1 5.5 + - - -
239D ALA* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ASP* 2.6 28.5 + - - +
133C PRO* 3.1 20.1 - - + +
128D SER* 1.3 83.0 - - - +
130D PHE* 1.3 74.8 + - - +
131D GLU* 5.3 3.1 - - + -
145D LEU* 6.2 2.5 - - + -
146D VAL 3.7 14.4 - - - +
147D CYS* 4.4 10.8 - - + +
148D LEU* 3.8 3.5 - - - +
161D TRP* 5.4 7.9 - - + -
203D TRP* 6.3 2.7 - - + -
212D CYS* 4.9 2.7 - - + -
239D ALA* 3.9 34.1 - - + +
240D GLU* 4.3 15.5 - - - +
241D ALA* 4.8 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LEU* 3.4 41.1 - - + -
129C LYS 3.3 15.9 - - - +
132C ASP* 4.0 11.4 - - + -
135C SER* 6.1 0.2 - - - -
138C SER* 3.3 38.6 - - - -
140C LEU* 3.4 21.3 - - + -
181C ILE* 6.5 0.2 - - + -
183C TRP* 4.8 13.5 - + - -
128D SER* 4.5 7.4 - - - -
129D LEU* 1.3 91.9 - - - +
131D GLU* 1.3 61.5 + - - +
145D LEU* 4.8 1.6 - - - +
146D VAL* 3.2 24.7 + - + +
148D LEU* 3.6 37.9 - - + +
150D ARG* 5.9 1.3 - - - -
----------------------------------------------------------
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