Contacts of the helix formed by residues 190 - 202 (chain A) in PDB entry 1JR9
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 190 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS 4.2 7.2 + - - +
88A LEU* 3.7 6.7 + - - +
89A MET 4.0 23.2 + - - +
90A SER* 4.1 16.8 + - - -
93A GLY* 4.7 3.8 - - - -
94A GLY 4.5 4.0 - - - +
188A VAL 3.1 2.5 + - - -
189A VAL* 1.3 72.8 - - - +
191A TRP* 1.3 60.8 + - - +
192A ASP* 2.6 18.6 + - - +
193A GLU* 2.6 37.7 + - - +
194A VAL* 3.5 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLY 3.8 17.3 + - - +
95A GLY 3.7 13.7 + - - -
96A LYS 3.9 12.3 - - - +
97A PRO* 3.4 36.8 - - + -
98A THR* 4.3 13.9 - - + +
101A VAL* 4.7 3.5 - - + +
105A ILE* 4.0 10.5 - - + -
112A PHE* 3.5 32.0 - + - -
115A PHE* 4.0 16.4 - + - -
134A LEU* 5.2 2.5 - - + -
161A LEU* 4.7 8.7 - - + -
186A TRP* 3.7 19.3 + + - -
189A VAL* 3.5 26.8 + - + +
190A ASN* 1.3 69.9 - - - +
192A ASP* 1.3 68.6 + - - +
194A VAL* 3.3 34.1 + - + +
195A ALA* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR* 4.8 12.0 - - - +
190A ASN* 2.6 22.5 + - - +
191A TRP* 1.3 74.4 + - - +
193A GLU* 1.3 59.8 + - - +
195A ALA* 3.0 23.3 - - - +
196A ALA* 3.2 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 3.5 47.0 + - - +
88A LEU* 3.7 7.6 - - + -
190A ASN* 2.6 25.5 + - - +
192A ASP* 1.3 73.6 - - - +
194A VAL* 1.3 62.9 + - - +
195A ALA 3.1 0.2 + - - -
196A ALA* 3.1 13.1 + - - +
197A GLN* 2.8 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.4 3.6 - - + +
101A VAL* 3.7 25.1 - - + -
134A LEU* 4.8 3.6 - - + -
160A ILE* 3.8 32.3 - - + +
161A LEU* 3.6 30.1 - - + -
189A VAL* 4.6 0.2 - - + -
190A ASN 3.6 15.3 - - - +
191A TRP* 3.5 30.3 - - + +
193A GLU* 1.3 77.4 - - - +
195A ALA* 1.3 56.7 + - - +
197A GLN* 3.3 4.8 + - - +
198A TYR* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR* 4.4 14.8 - - + +
99A GLY* 5.5 3.6 - - - -
101A VAL* 3.4 18.9 - - + +
191A TRP 3.0 11.7 + - - +
192A ASP* 3.0 15.0 - - - +
194A VAL* 1.3 76.1 - - - +
196A ALA* 1.3 56.4 + - - +
198A TYR* 2.8 29.3 + - - +
199A SER* 3.1 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASP 3.2 6.2 + - - +
193A GLU* 3.1 18.3 + - - +
195A ALA* 1.3 79.2 - - - +
197A GLN* 1.3 58.8 + - - +
198A TYR 3.0 4.3 + - - -
199A SER* 3.3 7.7 + - - +
200A GLN* 3.2 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.1 34.7 - - + +
87A LYS* 4.8 4.4 - - - +
88A LEU* 3.3 2.4 - - - +
159A PRO 4.5 4.0 - - - +
160A ILE* 2.7 55.9 - - + +
193A GLU* 2.8 56.6 + - - +
194A VAL 3.5 6.3 - - - +
196A ALA* 1.3 73.1 - - + +
198A TYR* 1.3 59.0 + - - +
200A GLN* 4.3 7.5 - - - +
201A ALA* 3.6 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU* 3.9 30.5 - - + -
101A VAL* 3.5 24.7 - - + -
104A LYS* 3.1 35.5 + - + -
136A VAL* 4.0 23.1 - - + +
139A GLY* 4.1 8.5 + - - -
141A ILE* 3.8 23.3 - - + -
160A ILE* 4.2 12.3 - - + -
194A VAL 2.9 10.6 + - - +
195A ALA 2.8 14.3 + - - +
197A GLN* 1.3 77.9 - - - +
199A SER* 1.3 68.7 + - - -
200A GLN 3.3 0.2 + - - -
201A ALA* 3.3 3.6 + - - +
202A ALA* 3.2 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU* 4.5 13.0 + - - -
195A ALA 3.1 7.6 + - - -
196A ALA* 3.3 8.9 + - - -
198A TYR* 1.3 81.5 - - - +
200A GLN* 1.3 60.1 + - - +
202A ALA* 2.8 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 5.8 0.6 + - - -
196A ALA* 3.2 17.5 + - + +
197A GLN* 4.5 6.0 - - - +
199A SER* 1.3 79.3 - - - +
201A ALA* 1.3 71.0 + - - +
202A ALA 3.8 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL* 4.4 16.2 - - + -
158A LYS* 4.0 44.3 + - + +
159A PRO 5.5 0.4 - - - +
160A ILE* 4.7 2.5 - - + -
197A GLN 3.6 13.8 + - - +
198A TYR* 3.3 9.7 + - - +
200A GLN* 1.3 80.6 - - - +
202A ALA* 1.3 69.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL* 4.9 3.9 - - + +
138A ASN 4.9 13.7 - - - +
139A GLY* 5.9 2.7 - - - -
198A TYR* 3.2 29.9 + - + +
199A SER* 2.8 19.3 - - - +
200A GLN 3.8 2.6 - - - +
201A ALA* 1.3 86.8 - - - +
----------------------------------------------------------
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