Contacts of the strand formed by residues 148 - 155 (chain E) in PDB entry 1XSK
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 ASN 148 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E TYR* 3.1 36.4 + - + +
140E VAL 3.2 3.6 - - - +
141E GLN* 3.4 28.7 + - - +
142E ASP 4.2 0.3 + - - +
146E GLN 4.5 9.0 + - - +
147E ARG* 1.3 77.9 + - - +
149E TYR* 1.3 63.6 + - - +
233E GLU* 3.3 22.3 - - - +
234E SER 3.5 10.2 + - - +
235E GLU* 4.0 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 3.6 45.5 - - + -
14E LEU* 6.0 0.2 - - + -
139E TYR* 3.4 6.6 - - - -
140E VAL* 2.7 55.3 + - + +
142E ASP* 4.0 12.9 + - + -
145E ASN* 4.2 7.3 + - - -
147E ARG* 3.5 45.9 - - + +
148E ASN* 1.3 74.9 - - - +
150E MET* 1.3 64.9 + - - +
231E SER* 4.7 3.4 - - - -
232E VAL* 3.4 9.4 - - - +
233E GLU* 3.5 38.5 + - + -
234E SER 4.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 150 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E PHE* 4.0 12.1 - - + -
69E ILE* 3.3 46.4 - - + +
70E GLU* 4.3 3.8 - - - -
71E HIS* 4.3 3.4 - - - -
138E GLY* 3.3 17.9 - - - +
139E TYR* 3.8 22.9 - - - -
149E TYR* 1.3 72.2 - - - +
151E PHE* 1.3 60.6 + - - +
231E SER* 3.3 3.5 - - - -
232E VAL* 3.1 34.9 + - + +
234E SER 3.4 18.7 + - - +
235E GLU 3.6 5.2 - - - +
236E TYR 3.4 20.4 - - - +
237E LEU* 3.7 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ILE* 3.6 24.7 - - + -
16E LEU* 5.0 2.0 - - + -
18E HIS* 3.8 21.1 - + - -
69E ILE* 5.3 0.5 - - - +
135E LYS 4.4 1.8 - - - -
136E ASN 3.2 21.5 - - - -
137E ASN* 3.0 27.3 - - - +
138E GLY* 2.9 47.7 + - - -
139E TYR 4.2 1.8 - - - -
140E VAL* 3.6 24.9 - - + -
150E MET* 1.3 77.2 - - - +
152E GLU* 1.3 64.5 + - - +
153E ARG* 3.9 26.9 - - + -
229E GLN* 4.7 1.6 - - + -
230E PHE 3.4 6.3 - - - +
231E SER* 3.6 18.6 - - - -
237E LEU* 3.6 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ILE* 4.2 1.6 - - + +
120E LEU* 4.1 0.7 - - - +
132E SER* 2.7 36.7 + - - -
136E ASN 3.5 4.5 - - - -
137E ASN* 3.2 20.0 + - + +
151E PHE* 1.3 77.0 - - - +
153E ARG* 1.3 77.7 + - - +
154E LEU* 4.1 9.0 - - + -
228E VAL 3.7 0.9 - - - +
229E GLN* 3.3 3.5 - - - +
230E PHE* 2.8 57.7 + - + -
237E LEU* 3.6 17.5 - - + -
239E TYR* 2.7 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ILE* 3.7 20.6 - - - +
4E SER* 4.0 4.8 - - - +
16E LEU* 6.0 0.2 - - - +
131E GLY 3.6 8.8 - - - +
132E SER* 3.8 7.3 + - - -
133E GLN 4.8 0.3 + - - -
135E LYS 4.0 12.5 + - - -
136E ASN* 3.0 43.3 + - + +
151E PHE* 3.9 12.6 - - + -
152E GLU* 1.3 95.5 + - - +
154E LEU* 1.3 62.0 + - - +
155E ASP* 3.9 1.7 + - - +
223E GLU* 2.8 26.0 + - - -
224E LYS* 3.8 35.8 - - - +
227E LYS* 4.2 14.1 - - + +
228E VAL 3.3 4.5 - - - -
229E GLN* 2.6 30.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E PHE* 3.9 20.4 - - + -
130E THR* 3.9 13.0 - - + +
131E GLY* 3.5 23.8 - - - +
152E GLU* 4.1 16.6 - - + -
153E ARG* 1.3 72.6 - - - +
155E ASP* 1.3 64.6 + - - +
156E LEU* 4.8 0.2 - - - +
200E TYR* 3.5 26.0 - - - +
206E TYR* 5.6 0.2 - - - +
208E VAL* 4.2 15.5 - - + -
227E LYS* 3.3 1.7 - - - -
228E VAL* 2.8 37.8 + - - +
230E PHE* 3.9 23.8 - - + -
239E TYR* 4.2 13.2 - - + +
241E VAL* 4.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E ARG* 2.6 32.8 + - - +
129E ILE 4.9 0.2 - - - +
130E THR* 2.8 25.5 + - - +
131E GLY 3.1 17.4 + - - +
133E GLN* 3.1 19.4 - - - +
153E ARG 4.9 1.0 - - - +
154E LEU* 1.3 75.7 - - - +
156E LEU* 1.3 63.4 + - - +
157E GLY 4.2 0.2 - - - -
160E GLU* 4.0 0.9 - - - +
206E TYR* 3.6 9.5 + - - -
226E SER 3.6 4.9 - - - +
227E LYS* 2.6 39.6 + - - +
488F GLU* 6.5 0.4 - - + -
----------------------------------------------------------
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