Contacts of the helix formed by residues 189 - 198 (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 PHE 189 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G ARG* 3.7 31.2 - - + +
187G LYS 5.2 0.7 - - - +
188G PRO* 1.3 74.8 - - - +
190G PRO* 1.3 79.4 - - + +
191G GLU* 3.4 24.7 - - + -
192G LEU* 3.2 44.8 + - + +
193G ARG* 2.8 23.2 + - - +
325G VAL* 4.2 9.0 - - + -
345G VAL* 4.1 11.0 - - + -
346G TYR* 4.3 17.5 - + - -
349G LYS* 3.4 53.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 190 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G PRO 4.7 0.4 - - - +
189G PHE* 1.3 85.8 - - + -
191G GLU* 1.3 63.6 + - - +
193G ARG* 2.6 20.4 + - + +
194G GLU* 2.6 47.2 + - + +
349G LYS* 5.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G PHE* 3.4 22.9 - - + -
190G PRO* 1.3 87.2 - - - +
192G LEU* 1.3 51.6 + - - +
194G GLU* 3.2 14.1 + - - +
195G HIS* 2.7 35.2 + - - +
345G VAL* 4.0 13.3 - - + +
348G GLU* 6.4 1.6 - - + -
349G LYS* 4.2 15.3 + - + +
352G LYS* 3.3 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G LEU 3.9 11.9 - - - +
184G ARG 3.7 23.6 - - - +
185G LEU* 5.0 0.9 - - + -
188G PRO* 3.9 10.5 - - + -
189G PHE* 3.2 32.7 + - + +
190G PRO 2.9 1.4 + - - -
191G GLU* 1.3 76.0 - - - +
193G ARG* 1.3 57.6 + - - +
195G HIS* 2.8 22.7 + - + +
196G PHE* 2.9 55.1 + - + -
342G LEU* 4.4 3.1 - - + -
345G VAL* 3.6 14.1 - - + +
346G TYR* 3.5 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G PRO* 5.0 13.2 - - + +
189G PHE 2.8 13.3 + - - +
190G PRO* 2.6 17.5 + - + +
192G LEU* 1.3 72.0 - - - +
194G GLU* 1.3 65.7 + - - +
196G PHE* 3.1 16.1 + - + +
197G GLN* 2.9 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G PRO* 2.6 24.4 + - + +
191G GLU* 3.5 20.6 + - - +
193G ARG* 1.3 75.1 - - + +
195G HIS* 1.3 63.1 + - - +
197G GLN* 3.5 24.1 + - - +
198G SER* 3.3 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 195 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G GLU 2.7 17.8 + - - +
192G LEU* 2.8 16.3 + - + +
194G GLU* 1.3 72.7 - - - +
196G PHE* 1.3 74.8 + + - +
198G SER* 2.9 25.6 + - - -
199G TYR* 3.8 34.6 + + - -
216G VAL* 4.8 2.8 - - + +
341G LYS* 3.9 38.6 + - + -
342G LEU* 3.7 38.4 - - + +
345G VAL* 3.7 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 196 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G LEU* 3.6 20.2 - - + -
188G PRO* 5.0 4.7 - - + -
192G LEU* 2.9 58.0 + - + -
193G ARG* 3.4 11.2 - - + +
195G HIS* 1.3 86.7 - + - +
197G GLN* 1.3 57.1 + - - +
199G TYR* 2.9 16.9 + - - +
215G ILE* 3.6 28.5 - - + -
216G VAL* 4.2 20.4 - - + -
219G ALA* 3.7 23.6 - - + -
220G LYS* 2.7 30.8 + - + +
342G LEU* 4.8 2.0 - - + -
346G TYR* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 197 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G ARG* 2.9 48.6 + - + +
194G GLU* 3.6 24.4 + - - +
195G HIS 3.2 0.2 - - - -
196G PHE* 1.3 75.8 - - - +
198G SER* 1.3 57.9 + - - +
199G TYR 3.1 9.7 + - - +
220G LYS* 3.8 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194G GLU 3.3 7.9 + - - -
195G HIS* 2.9 21.5 + - - -
197G GLN* 1.3 78.4 - - - +
199G TYR* 1.3 67.2 + - - +
341G LYS* 4.6 13.2 + - - -
----------------------------------------------------------
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