Contacts of the helix formed by residues 155 - 166 (chain A) in PDB entry 3HS3
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 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 3.6 1.3 + - - -
154A SER* 1.3 70.4 + - - +
156A ASN* 1.3 53.8 + - - +
157A THR* 3.6 10.0 + - - -
158A LYS* 2.9 45.3 + - + +
159A GLY 2.9 22.7 + - - -
307A ILE* 4.2 21.8 - - + +
308A ILE 2.8 20.8 + - - +
309A ASP* 4.6 5.6 + - - +
310A VAL* 3.6 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A SER 4.1 4.5 - - - +
154A SER* 2.7 37.0 + - - +
155A ASN* 1.3 68.9 - - - +
157A THR* 1.3 61.4 + - - +
159A GLY* 3.2 0.7 + - - -
160A GLY 2.9 24.4 + - - -
185A THR* 3.6 44.4 + - - +
188A GLU* 3.0 28.2 + - + +
189A ARG* 3.5 23.1 - - + +
262A TYR* 4.3 11.4 + - - -
280A GLN* 4.4 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASN* 3.2 7.8 - - - -
156A ASN* 1.3 78.0 - - - +
158A LYS* 1.3 63.8 + - - +
160A GLY 3.2 0.5 + - - -
161A LYS* 3.0 13.3 + - + +
188A GLU* 4.0 20.2 + - - +
192A ALA* 3.0 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASN* 2.9 33.3 + - - +
157A THR* 1.3 77.5 - - - +
159A GLY* 1.3 58.3 + - - +
161A LYS* 3.3 8.8 + - + +
162A GLU* 2.8 54.5 + - + +
309A ASP* 2.7 35.1 + - - +
310A VAL* 3.4 22.6 + - + -
311A LEU* 5.3 1.6 - - - +
312A PRO* 5.1 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASN 2.9 12.3 + - - -
156A ASN 3.2 1.3 + - - -
157A THR 3.2 0.2 - - - -
158A LYS* 1.3 77.8 - - - +
160A GLY* 1.3 55.2 + - - +
162A GLU* 3.9 0.8 - - - -
163A SER* 2.8 33.7 + - - -
262A TYR* 3.3 29.8 - - - -
278A ILE* 3.8 8.2 - - - +
310A VAL* 3.6 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ASN 2.9 11.9 + - - -
157A THR 3.8 1.8 - - - -
159A GLY* 1.3 73.0 - - - +
161A LYS* 1.3 67.0 + - - +
163A SER* 3.2 10.5 + - - -
164A ILE* 3.3 7.1 + - - +
189A ARG* 3.4 30.6 - - - +
192A ALA* 4.1 0.2 - - - -
193A MET* 3.3 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 3.0 18.6 + - + +
158A LYS* 3.7 9.2 - - + +
160A GLY* 1.3 75.9 - - - +
162A GLU* 1.3 66.2 + - + +
164A ILE* 3.2 6.8 + - - +
165A LYS* 3.1 43.7 + - + +
192A ALA* 3.9 7.1 - - + +
196A GLU* 3.5 42.7 - - + +
199A LYS* 5.2 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 2.8 50.2 + - + +
159A GLY* 4.8 0.4 - - - -
161A LYS* 1.3 76.2 - - + +
163A SER* 1.3 65.3 + - - +
165A LYS* 2.9 46.4 + - - +
166A LEU* 3.1 26.5 + - - +
278A ILE* 3.9 18.8 - - + -
310A VAL* 5.4 1.6 - - + -
312A PRO* 3.8 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY 2.8 19.8 + - - -
160A GLY 3.2 10.0 + - - -
162A GLU* 1.3 75.6 - - - +
164A ILE* 1.3 62.5 + - - +
166A LEU* 3.3 21.4 + - - +
167A LEU* 3.9 8.0 - - - +
193A MET* 4.1 18.3 - - - +
232A ILE* 4.1 16.4 - - - +
260A VAL* 4.2 12.8 - - - +
261A GLY 4.8 0.5 + - - -
262A TYR* 4.0 9.7 - - - -
278A ILE* 3.5 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLY 3.3 10.7 + - - +
161A LYS 3.2 8.6 + - - +
163A SER* 1.3 76.9 - - - +
165A LYS* 1.3 62.2 + - - +
167A LEU* 3.1 30.9 + - + +
174A VAL* 4.6 5.2 - - + -
176A ILE* 4.6 7.4 - - + -
193A MET* 3.5 34.1 - - + +
196A GLU* 3.7 19.7 - - + -
197A ALA* 4.1 15.5 - - + +
200A LEU* 3.8 17.6 - - + +
202A ILE* 4.1 14.6 - - + +
232A ILE* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LYS* 3.1 35.7 + - + +
162A GLU* 2.9 46.6 + - - +
164A ILE* 1.3 78.7 - - - +
166A LEU* 1.3 58.5 + - - +
167A LEU 3.2 7.1 + - - +
169A LYS* 4.8 8.3 + - - -
196A GLU* 3.8 19.1 - - + +
200A LEU* 5.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLU 3.1 17.6 + - - +
163A SER* 3.5 8.5 - - - +
164A ILE 3.1 0.4 - - - -
165A LYS* 1.3 75.6 - - - +
167A LEU* 1.3 64.6 + - - +
168A SER 3.8 0.7 + - - -
258A GLN* 4.6 0.5 + - - -
260A VAL* 3.8 33.0 - - + -
276A SER* 4.4 4.3 - - - -
277A THR 3.8 27.1 - - - +
278A ILE* 4.2 8.7 - - + -
312A PRO* 4.4 12.8 - - + -
314A LYS* 3.4 46.8 - - + +
318A THR* 3.9 20.1 + - + +
319A GLU* 4.4 5.5 - - - +
----------------------------------------------------------
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