Contacts of the strand formed by residues 159 - 165 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G ARG 3.8 0.9 - - - +
155G THR* 3.7 3.6 - - - -
156G TYR* 2.7 37.6 + - + +
157G GLY 3.3 0.4 + - - -
158G LEU* 1.3 84.0 - - - +
160G GLY* 1.3 69.7 + - - +
161G TYR* 3.8 2.0 + - + +
425G LEU* 3.9 36.8 - - + -
429G LEU* 4.7 19.1 - - + -
482G PHE* 3.8 26.0 - - + -
485G TYR* 4.1 11.2 - - + +
493G ILE* 4.2 3.7 - - - +
521G ILE* 4.6 5.2 - - + -
522G TYR 3.2 7.0 - - - +
523G SER* 5.2 0.7 - - - -
525G MET* 5.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G ARG 3.7 4.0 - - - -
158G LEU 4.0 0.6 + - - -
159G VAL* 1.3 73.5 - - - +
161G TYR* 1.3 59.2 + - - -
493G ILE* 4.6 4.5 - - - -
497G LEU* 3.8 22.2 - - - +
520G TYR* 3.6 1.7 - - - +
521G ILE* 3.4 6.8 - - - +
522G TYR* 2.6 52.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152G ILE* 4.5 22.1 - - + +
153G CYS* 3.5 0.7 - - - -
154G ARG* 2.7 68.9 + - + +
159G VAL* 3.8 2.6 + - + -
160G GLY* 1.3 71.9 - - - +
162G MET* 1.3 70.7 + - - +
163G ARG* 3.6 28.0 - - + +
398G LEU* 5.2 2.6 - - - +
401G GLU* 4.8 1.6 + - - -
402G TYR* 4.9 8.4 + - - -
426G TYR* 4.1 21.4 - + - -
429G LEU* 3.6 32.1 - - + -
497G LEU* 3.5 3.3 - - - +
519G THR* 3.4 30.7 + - + -
520G TYR 3.8 2.5 - - - -
521G ILE* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 162 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G LEU* 4.1 11.7 - - + -
152G ILE 3.3 5.6 - - - -
153G CYS* 3.7 16.4 - - - -
161G TYR* 1.3 80.8 - - - +
163G ARG* 1.3 56.1 + - - +
497G LEU* 4.0 17.5 - - + -
500G ALA* 4.3 4.3 - - + -
501G ALA* 3.6 35.4 - - - +
504G GLU* 4.6 0.9 - - + -
516G PHE* 3.6 23.4 - - + -
519G THR* 4.4 0.2 - - - -
520G TYR* 2.7 55.7 + - + +
330H LEU* 3.2 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G LEU 4.2 0.3 - - - +
151G LEU* 3.5 4.1 - - - +
152G ILE* 2.8 43.6 + - + +
161G TYR* 3.6 21.8 - - + +
162G MET* 1.3 73.0 - - - +
164G ILE* 1.3 90.0 + - - +
165G ILE* 3.4 17.1 + - + +
395G CYS* 4.6 2.0 - - - +
396G ARG* 2.7 32.7 + - - +
397G SER 3.9 5.0 + - - -
398G LEU* 3.7 18.6 - - - +
401G GLU* 2.6 31.7 + - - +
518G ASN* 2.9 33.8 + - - +
519G THR* 3.3 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G LEU 3.7 7.6 - - - +
151G LEU* 3.8 9.2 - - + -
163G ARG* 1.3 98.7 + - - +
165G ILE* 1.3 63.8 + - - +
166G ILE* 4.0 11.9 - - + +
395G CYS* 3.8 12.3 - - - -
504G GLU* 5.3 2.9 - - + -
508G ILE* 3.8 26.2 - - + -
515G ILE* 3.7 33.7 - - + -
516G PHE* 3.4 48.2 - - + +
518G ASN* 3.9 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G ALA* 3.7 21.1 - - + +
144G TRP* 3.6 32.8 - - + -
148G ILE 4.0 4.2 - - - +
149G PRO* 3.8 2.6 - - - +
150G LEU* 2.7 50.8 + - + +
152G ILE* 4.4 7.4 - - + -
163G ARG* 3.4 17.0 - - - +
164G ILE* 1.3 82.6 - - - +
166G ILE* 1.3 59.5 + - - +
395G CYS* 4.2 2.0 - - - -
396G ARG 4.7 1.6 - - - +
397G SER* 4.5 0.9 - - - -
398G LEU* 3.6 42.2 - - + +
----------------------------------------------------------
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