Contacts of the helix formed by residues 184 - 196 (chain A) in PDB entry 5MQI
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 SER 184 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ALA* 1.3 76.9 - - - +
185A ALA* 1.3 60.2 + - - +
187A ASP* 3.3 8.8 + - - +
188A GLN* 2.8 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 4.1 21.0 - - + +
122A GLU* 4.1 34.8 - - + +
125A ALA* 5.1 2.5 - - - +
183A ALA 3.3 4.7 - - - +
184A SER* 1.3 77.5 - - - +
186A HIS* 1.3 62.3 + - - +
188A GLN* 3.2 14.2 + - - +
189A LEU* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 3.0 29.1 + - - +
167A LEU* 3.2 39.6 - - + +
183A ALA* 3.5 12.1 + - - +
184A SER 3.3 0.4 - - - -
185A ALA* 1.3 77.9 - - - +
187A ASP* 1.3 64.8 + - - +
189A LEU* 3.0 7.1 + - - +
190A LEU* 2.9 42.2 + - + +
224A LEU 2.8 29.0 + - - -
225A MET* 3.9 7.8 + - - -
227A ARG* 3.3 24.1 + - + +
228A ASP* 4.1 16.6 - - + +
229A GLN* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ALA 3.0 19.3 + - - +
184A SER* 3.4 13.7 - - - +
186A HIS* 1.3 77.6 - - - +
188A GLN* 1.3 62.5 + - + +
190A LEU* 3.2 13.4 + - - +
191A TRP* 3.0 24.1 + - - +
228A ASP* 4.9 4.2 - - - +
229A GLN* 4.8 0.3 + - - -
334A SER* 2.8 46.0 + - - -
335A ALA* 3.3 10.2 + - - +
338A VAL* 3.9 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 6.1 3.4 - - - +
125A ALA* 3.6 34.0 - - + +
184A SER* 2.8 37.7 + - - +
185A ALA* 3.6 11.3 - - - +
187A ASP* 1.3 72.1 - - + +
189A LEU* 1.3 62.1 + - - +
191A TRP* 3.3 7.3 + - - +
192A ALA* 3.0 23.4 + - - +
1602A SO4 5.7 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 3.7 31.9 - - + +
124A PHE 3.7 30.5 - - - -
125A ALA* 3.8 2.2 - - - +
130A PHE* 3.7 18.9 - - + -
166A ILE* 3.4 42.4 - - + +
167A LEU* 4.1 18.6 - - + -
185A ALA 3.0 16.2 + - - +
186A HIS* 3.4 7.0 - - - +
188A GLN* 1.3 74.6 - - - +
190A LEU* 1.3 59.6 + - - +
192A ALA* 3.2 5.7 + - - +
193A ILE* 2.8 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 4.4 10.3 - - + -
186A HIS* 2.9 30.1 + - + +
187A ASP* 3.5 14.6 - - - +
189A LEU* 1.3 75.8 - - - +
191A TRP* 1.3 58.1 + - - +
193A ILE* 3.3 7.2 + - + +
194A HIS* 2.9 27.0 + - - +
225A MET* 3.6 59.0 - - + +
229A GLN* 5.0 3.1 - - - +
338A VAL* 3.8 16.2 - - + -
341A PHE* 3.5 12.4 - - + -
342A LEU* 3.8 24.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
187A ASP 3.0 16.5 + - - +
188A GLN* 3.8 6.5 - - - +
189A LEU 3.2 0.2 - - - -
190A LEU* 1.3 78.7 - - - +
192A ALA* 1.3 55.5 + - - +
194A HIS* 3.1 32.4 + + + +
195A LEU* 2.8 71.4 + - + +
337A ASN* 3.2 53.1 - - + +
338A VAL* 4.1 16.4 - - + +
341A PHE* 4.2 6.3 - + + -
1602A SO4 3.9 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA 5.0 0.7 - - - -
126A SER 4.1 24.0 - - - +
127A GLU* 4.3 7.6 - - - +
130A PHE* 3.7 24.4 - - + +
188A GLN 3.0 16.5 + - - +
189A LEU* 3.6 5.4 - - - +
191A TRP* 1.3 78.1 - - - +
193A ILE* 1.3 57.8 + - - +
195A LEU* 4.4 5.3 - - - +
196A SER* 3.0 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.8 27.1 - - + -
163A VAL* 4.7 4.0 - - + -
167A LEU* 3.9 37.2 - - + -
189A LEU 2.8 25.9 + - - +
190A LEU* 3.5 8.5 - - - +
192A ALA* 1.3 72.8 - - - +
194A HIS* 1.3 63.6 + - - +
196A SER* 3.2 15.1 + - - -
198A LEU* 3.3 12.5 + - + -
199A ASP* 3.3 37.4 + - + +
202A LEU* 4.6 4.7 - - + -
221A ILE* 5.6 0.4 - - + -
225A MET* 4.3 25.4 - - + -
341A PHE* 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU 2.9 12.9 + - - +
191A TRP* 3.1 45.9 + + + +
193A ILE* 1.3 78.5 - - - +
195A LEU* 1.3 72.6 + - + +
197A GLY* 3.2 10.9 + - - -
199A ASP* 3.0 33.5 + - - +
341A PHE* 3.3 33.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 3.6 44.0 - - + +
191A TRP* 2.8 61.3 + - + +
192A ALA* 4.4 0.9 - - - +
194A HIS* 1.3 85.7 - - + +
196A SER* 1.3 60.4 + - - +
197A GLY 3.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 4.3 8.0 - - - +
130A PHE* 3.7 31.5 - - - +
131A GLY* 3.7 9.0 - - - -
134A SER* 3.1 15.8 + - - -
192A ALA 3.0 20.3 + - - -
193A ILE* 3.2 3.8 + - - -
195A LEU* 1.3 77.2 - - - +
197A GLY* 1.3 55.9 + - - +
198A LEU* 3.1 23.4 + - - +
----------------------------------------------------------
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