Contacts of the helix formed by residues 189 - 201 (chain I) in PDB entry 3Q2K
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 ALA 189 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I VAL* 4.2 15.0 - - + -
184I ALA 3.0 18.2 + - - +
185I PHE* 3.4 11.4 + - + +
188I GLN* 1.3 74.9 - - - +
190I SER* 1.3 57.3 + - - +
191I HIS 3.0 3.4 - - - -
192I TYR* 2.6 31.6 + - + -
193I VAL* 2.8 12.6 + - - +
237I ILE* 5.0 1.6 - - + -
239I VAL* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I LYS* 3.2 29.8 - - - +
104I PRO* 4.8 2.7 - - - -
130I LYS* 3.6 18.9 + - - -
185I PHE 3.0 9.1 + - - -
186I MET 3.4 21.3 - - - -
187I ASN 3.3 0.7 + - - -
188I GLN 3.1 2.0 - - - -
189I ALA* 1.3 78.8 - - - +
191I HIS* 1.3 59.7 + - - +
193I VAL* 3.5 8.5 + - - +
194I ASP* 2.9 27.2 + - - +
328I SER* 4.8 1.7 - - - -
332I LEU* 4.2 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 191 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I LYS* 3.5 29.4 - - + +
129I VAL 4.4 1.6 - - - -
130I LYS* 4.6 12.7 - - - +
131I GLN* 3.8 12.2 + - - -
132I ASN* 3.5 32.7 + - + +
188I GLN 3.7 9.9 - - - -
190I SER* 1.3 78.3 + - - +
192I TYR* 1.3 68.4 + + + +
194I ASP* 3.4 18.9 - - - +
195I LEU* 3.4 16.1 - - - +
500I NAI 3.6 13.0 + - - -
550I HP7 2.8 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 192 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I ASN* 3.8 11.9 + - - -
158I VAL* 3.9 18.1 - - + +
159I ASN 4.7 1.1 - - - -
160I VAL* 3.4 28.0 - - + -
162I TRP* 3.5 34.2 - + - -
188I GLN 4.5 0.2 - - - -
189I ALA* 2.6 22.6 + - - +
191I HIS* 1.3 89.1 - + + +
193I VAL* 1.3 64.7 + - - +
194I ASP 3.0 1.3 - - - -
195I LEU* 3.1 32.8 + - + +
196I LEU* 3.7 9.0 + - - +
237I ILE* 4.1 5.9 - - + +
250I GLY* 4.1 13.5 - - - -
251I SER 4.9 0.4 - - - -
267I ALA* 3.3 28.3 - - - +
268I VAL* 3.6 28.7 - - + +
550I HP7 5.0 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I PHE* 4.1 15.7 - - + -
189I ALA 2.8 18.4 + - - +
190I SER* 3.7 9.6 - - - +
192I TYR* 1.3 71.8 - - - +
194I ASP* 1.3 63.3 + - - +
196I LEU* 3.3 21.5 + - + +
197I ASP* 4.1 0.9 + - - +
237I ILE* 3.9 19.5 - - + +
328I SER* 4.1 8.3 - - - +
331I LEU* 3.7 35.7 - - + +
332I LEU* 3.9 32.3 - - + +
335I ILE* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 194 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I LYS* 3.9 21.9 - - + +
133I ARG* 2.8 50.5 + - - +
190I SER 2.9 15.5 + - - +
191I HIS* 3.4 16.5 - - - +
193I VAL* 1.3 77.1 - - - +
195I LEU* 1.3 65.3 + - - +
196I LEU 3.3 0.7 + - - -
197I ASP* 3.4 3.6 + - - +
198I TRP* 3.0 20.6 + - - +
324I GLU* 4.8 3.8 - - - +
327I GLN* 5.7 0.9 - - - +
328I SER* 3.8 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I ASN* 5.3 5.4 - - + +
133I ARG* 5.5 1.1 - - + -
138I LEU* 3.9 30.7 - - + -
158I VAL* 5.6 1.6 - - + -
191I HIS 3.4 18.2 - - - +
192I TYR* 3.1 28.4 + - + +
194I ASP* 1.3 78.9 - - - +
196I LEU* 1.3 68.3 + - + +
198I TRP* 4.0 19.7 - - + -
199I LEU* 2.7 36.1 + - + +
200I VAL* 3.6 1.0 + - - +
252I ILE* 4.3 36.1 - - + -
268I VAL* 4.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I VAL* 4.7 5.4 - - + +
158I VAL* 4.0 26.0 - - + -
192I TYR 4.0 6.3 - - - +
193I VAL* 3.5 18.4 - - + +
194I ASP 3.2 0.8 - - - -
195I LEU* 1.3 79.8 - - - +
197I ASP* 1.3 61.6 + - - +
200I VAL* 3.3 13.2 + - - +
201I GLY 3.6 0.3 - - - +
203I VAL* 4.3 2.9 - - + -
227I LEU* 3.4 35.2 - - + -
229I TRP* 3.2 46.3 + - + -
236I SER 5.5 0.4 - - - +
237I ILE* 4.3 15.9 - - + -
252I ILE* 5.2 1.6 - - + -
331I LEU* 3.9 19.1 - - + -
335I ILE* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 197 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I VAL 4.1 1.6 + - - +
194I ASP 3.4 4.6 + - - +
195I LEU 3.2 0.2 - - - -
196I LEU* 1.3 79.3 - - - +
198I TRP* 1.3 69.4 + - - +
201I GLY* 3.2 34.9 + - - +
202I PRO* 3.5 16.9 - - - +
203I VAL* 4.2 5.3 + - + +
324I GLU* 5.2 2.9 - - - +
327I GLN* 3.1 45.7 + - + +
328I SER* 6.1 1.3 - - - -
331I LEU* 4.6 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 198 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I ARG* 3.2 86.9 - - + +
138I LEU* 4.1 16.6 - - + -
139I GLN* 3.8 17.9 - - - -
142I LYS* 3.2 60.2 + - + +
194I ASP 3.0 17.8 + - - +
195I LEU* 4.0 16.8 - - + -
197I ASP* 1.3 82.8 + - - +
199I LEU* 1.3 87.1 + - + +
201I GLY 4.9 0.2 + - - -
319I GLU* 4.7 5.0 + - - -
324I GLU* 3.9 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I LEU* 3.8 17.0 - - + +
141I VAL* 3.8 21.5 - - + -
142I LYS* 3.5 48.0 + - + +
145I ILE* 3.0 30.2 - - + +
195I LEU* 2.7 26.4 + - + +
198I TRP* 1.3 94.8 - - + +
200I VAL* 1.3 66.9 + - + +
252I ILE* 3.9 31.4 - - + -
254I ILE* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I ILE* 4.5 7.3 - - + +
153I ILE* 4.4 14.7 - - + +
156I VAL* 4.2 27.6 - - + -
195I LEU 4.6 1.1 - - - +
196I LEU* 3.3 16.1 + - - +
199I LEU* 1.3 86.2 - - + +
201I GLY* 1.3 54.7 + - - +
229I TRP* 3.4 25.6 - - + +
231I HIS* 2.9 39.5 + - + +
233I ALA* 5.0 0.2 - - + -
252I ILE* 4.9 3.6 - - + -
254I ILE* 4.0 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 201 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197I ASP* 3.2 35.6 + - - -
198I TRP 4.9 0.2 + - - -
199I LEU 3.7 0.8 - - - -
200I VAL* 1.3 77.2 - - - +
202I PRO* 1.3 75.7 - - - +
229I TRP* 3.5 8.9 + - - -
231I HIS* 4.5 3.6 - - - -
----------------------------------------------------------
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