Contacts of the helix formed by residues 186 - 198 (chain H) in PDB entry 1GN2
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 186 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H LYS 3.1 21.8 + - - +
82H ASN 2.8 19.4 + - - +
83H LEU 4.1 1.0 + - - -
84H SER* 3.4 31.2 + - - -
87H GLY* 4.7 3.4 - - - -
184H VAL 3.3 0.2 + - - -
185H VAL* 1.3 74.6 - - - +
187H TRP* 1.3 54.6 + - - +
188H ALA* 3.0 20.2 + - - +
189H ASP* 2.9 28.7 + - - +
190H VAL* 3.6 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 187 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H GLY* 5.5 1.0 - - - -
88H GLY* 3.6 23.1 + - - -
89H ASP 3.5 14.1 + - - -
90H LYS 4.1 8.3 - - - +
91H PRO* 3.7 38.6 - - + -
95H LEU* 4.1 2.7 - - + -
99H ILE* 4.1 9.6 - - + -
106H PHE* 3.5 34.3 - + - -
109H PHE* 4.3 6.5 - + - -
128H LEU* 5.8 0.9 - - + -
157H LEU* 4.2 13.2 - - + -
182H TRP* 3.8 25.1 + + - -
185H VAL* 3.5 25.1 + - + +
186H ASN* 1.3 70.0 - - - +
188H ALA* 1.3 61.1 + - - +
189H ASP 3.1 0.7 - - - -
190H VAL* 4.0 29.6 - - + -
191H GLN* 3.0 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H ASN* 2.9 13.1 + - - +
187H TRP* 1.3 78.3 - - - +
189H ASP* 1.3 58.3 + - - +
191H GLN* 4.0 8.4 - - - +
192H SER* 3.2 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H LYS* 3.7 21.3 - - - +
82H ASN* 2.8 21.1 + - - +
186H ASN* 2.9 27.5 + - - +
188H ALA* 1.3 79.1 - - - +
190H VAL* 1.3 65.8 + - - +
192H SER* 2.9 9.2 + - - -
193H ARG* 2.7 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H ASN* 4.3 5.4 - - - +
95H LEU* 3.4 21.8 - - + -
128H LEU* 4.7 8.1 - - + -
156H LEU* 4.1 27.4 - - + +
157H LEU* 4.0 32.1 - - + -
185H VAL* 4.6 0.9 - - + -
186H ASN 3.6 14.1 + - - +
187H TRP* 4.1 24.5 - - + +
188H ALA 3.6 0.2 - - - -
189H ASP* 1.3 73.5 + - - +
191H GLN* 1.3 50.4 + - - +
193H ARG* 3.0 10.3 + - - +
194H TYR* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 191 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H LYS 4.9 0.2 - - - +
91H PRO* 3.6 4.7 - - - +
92H THR* 2.6 52.7 + - - +
95H LEU* 3.1 38.1 - - + +
187H TRP* 3.0 22.2 + - - +
188H ALA* 4.0 7.7 - - - +
190H VAL* 1.3 78.5 - - - +
192H SER* 1.3 64.3 + - - +
194H TYR* 3.3 5.2 + - - +
195H ALA* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H ALA 3.2 14.5 + - - -
189H ASP* 2.9 15.5 + - - -
191H GLN* 1.3 81.6 - - - +
193H ARG* 1.3 61.3 + - - +
195H ALA* 3.2 9.2 + - - +
196H ALA* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H THR* 6.1 1.2 - - - +
78H ILE* 3.9 37.3 - - - +
81H LYS* 3.8 21.6 - - - +
82H ASN* 3.8 2.2 - - - +
154H VAL* 5.3 2.2 - - + +
155H PRO 4.0 11.0 + - - +
156H LEU* 3.3 37.0 - - + +
189H ASP* 2.7 50.2 + - - +
190H VAL* 3.4 5.2 - - - +
192H SER* 1.3 75.7 - - - +
194H TYR* 1.3 60.2 - - - +
196H ALA* 3.4 6.0 + - - +
197H ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 194 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H GLU* 4.2 22.9 + - + -
95H LEU* 3.6 32.8 - - + -
98H ALA* 3.4 30.6 - - + +
130H TRP* 4.2 19.3 - + - -
137H LEU* 4.3 8.5 - - + -
156H LEU* 3.8 26.0 - - + +
190H VAL 2.8 15.2 + - - +
191H GLN 3.6 4.7 - - - +
193H ARG* 1.3 78.9 - - - +
195H ALA* 1.3 53.4 + - + +
197H ALA* 3.2 2.6 + - + +
198H THR* 2.7 71.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H GLN 3.1 13.7 + - - +
192H SER* 3.3 12.6 - - - +
194H TYR* 1.3 81.7 - - + +
196H ALA* 1.3 60.3 + - - +
198H THR* 3.5 8.8 + - - -
199H SER* 3.4 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192H SER 3.1 9.6 + - - +
193H ARG* 3.9 8.7 - - - +
195H ALA* 1.3 77.0 - - - +
197H ALA* 1.3 66.8 + - - +
199H SER* 3.2 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H TRP* 3.7 40.8 + - + -
132H THR* 5.2 3.1 - - - +
154H VAL* 4.2 22.4 - - + +
156H LEU* 4.2 3.6 - - + -
193H ARG 2.9 19.0 + - - +
194H TYR* 3.5 5.6 - - + +
196H ALA* 1.3 79.9 - - - +
198H THR* 1.3 58.8 + - - +
199H SER 3.1 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 198 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H TRP* 3.7 32.8 - - + +
194H TYR* 2.7 66.9 + - + +
195H ALA* 3.6 9.7 + - - -
196H ALA 3.3 0.4 - - - -
197H ALA* 1.3 72.7 - - - +
199H SER* 1.3 60.4 + - - +
----------------------------------------------------------
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