Contacts of the strand formed by residues 159 - 165 (chain E) in PDB entry 1R4N
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 159 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E ARG 3.8 0.7 - - - +
155E THR* 3.7 2.6 - - - -
156E TYR* 2.7 40.3 + - + +
157E GLY 3.3 0.4 - - - -
158E LEU* 1.3 83.4 - - - +
160E GLY* 1.3 69.0 + - - +
161E TYR* 3.9 2.0 + - + +
425E LEU* 3.9 38.6 - - + -
429E LEU* 4.7 18.6 - - + -
482E PHE* 3.9 24.7 - - + -
485E TYR* 4.1 11.0 - - + +
493E ILE* 4.1 4.7 - - - +
521E ILE* 4.6 5.4 - - + -
522E TYR 3.2 7.4 - - - +
523E SER* 5.2 1.6 - - - +
525E MET* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E ARG 3.7 3.8 - - - -
158E LEU 4.0 0.6 + - - -
159E VAL* 1.3 74.6 - - - +
161E TYR* 1.3 59.5 + - - -
493E ILE* 4.6 4.3 - - - -
497E LEU* 3.8 22.4 - - - +
520E TYR* 3.6 1.7 - - - +
521E ILE* 3.4 5.7 - - - +
522E TYR* 2.6 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E ILE* 4.5 20.5 - - + +
153E CYS* 3.4 0.7 - - - -
154E ARG* 2.7 67.8 + - + +
159E VAL* 3.9 2.6 + - + +
160E GLY* 1.3 72.6 - - - +
162E MET* 1.3 67.8 + - - +
163E ARG* 3.6 30.3 - - + +
398E LEU* 5.2 3.5 - - - +
401E GLU* 4.8 1.6 + - - -
402E TYR* 4.9 7.5 + - - -
426E TYR* 4.1 23.0 - + - -
429E LEU* 3.5 34.3 - - + -
497E LEU* 3.5 2.6 - - - +
519E THR* 3.4 31.1 + - + -
520E TYR 3.8 2.2 - - - -
521E ILE* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E LEU* 4.1 11.7 - - + -
152E ILE 3.3 4.9 - - - -
153E CYS* 3.8 15.7 - - - -
161E TYR* 1.3 81.7 - - - +
163E ARG* 1.3 56.7 + - - +
497E LEU* 4.0 16.8 - - + -
500E ALA* 4.3 5.2 - - + -
501E ALA* 3.6 36.1 - - - +
504E GLU* 4.6 0.4 - - + -
516E PHE* 3.6 23.8 - - + -
519E THR* 4.5 0.7 - - - -
520E TYR* 2.8 53.5 + - + +
330F LEU* 3.3 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E LEU 4.2 0.3 - - - +
151E LEU* 3.4 4.2 - - - +
152E ILE* 2.8 42.8 + - + +
161E TYR* 3.6 21.8 - - + +
162E MET* 1.3 74.6 - - - +
164E ILE* 1.3 89.5 + - - +
165E ILE* 3.4 17.0 - - + +
395E CYS* 4.6 1.6 - - - +
396E ARG* 2.7 32.7 + - - +
397E SER 3.9 5.2 + - - -
398E LEU* 3.7 18.6 - - - +
401E GLU* 2.6 31.7 + - - +
518E ASN* 2.9 34.3 + - - +
519E THR* 3.4 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E LEU 3.7 8.5 - - - +
151E LEU* 3.8 9.0 - - + -
163E ARG* 1.3 99.9 + - - +
165E ILE* 1.3 62.7 + - - +
166E ILE* 4.0 11.2 - - + +
395E CYS* 3.9 11.5 - - - +
504E GLU* 5.3 3.1 - - + -
508E ILE* 3.8 25.6 - - + -
515E ILE* 3.7 33.9 - - + -
516E PHE* 3.5 48.6 - - + +
518E ASN 3.9 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E ALA* 3.7 21.5 - - + +
144E TRP* 3.6 33.1 - - + -
148E ILE 4.0 4.4 - - - +
149E PRO* 3.7 2.8 - - - +
150E LEU* 2.8 48.4 + - + +
152E ILE* 4.4 6.7 - - + -
163E ARG* 3.4 17.7 - - + +
164E ILE* 1.3 83.5 - - - +
166E ILE* 1.3 58.8 + - - +
395E CYS* 4.2 2.5 - - - -
396E ARG 4.7 0.9 - - - +
397E SER* 4.6 1.3 - - - -
398E LEU* 3.6 41.3 - - + +
----------------------------------------------------------
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