Contacts of the helix formed by residues 162 - 171 (chain C) in PDB entry 3SPD
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 162 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C LYS* 1.3 83.7 - - - +
163C SER* 1.3 64.7 + - - +
164C ALA* 3.3 10.7 + - - +
165C HIS* 3.0 59.4 + - - +
166C TYR 3.4 1.9 + - - -
211C PHE* 3.4 20.4 - - - -
4G T 5.4 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ASN* 1.3 71.9 - - - +
164C ALA* 1.3 66.6 + - - +
166C TYR* 3.1 3.6 + - - +
167C ILE* 2.9 29.6 + - - +
198C LEU* 3.3 37.2 - - - +
209C ARG* 3.8 32.3 + - - -
211C PHE* 3.7 16.9 - - - +
9H C 4.6 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ASN* 3.3 10.3 + - - +
163C SER* 1.3 78.6 - - - +
165C HIS* 1.3 64.7 + - - +
167C ILE* 4.6 1.1 - - - -
168C SER* 2.9 27.0 + - - -
194C PHE* 3.6 21.5 + - + +
209C ARG* 5.5 0.2 - - - +
1G T 3.4 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 3.5 18.6 - - + +
159C SER 3.5 17.2 + - - -
160C LEU* 3.8 17.0 - - + -
161C LYS* 3.0 27.8 + - + -
162C ASN* 3.0 40.8 + - - +
164C ALA* 1.3 75.2 - - - +
166C TYR* 1.3 62.2 + - - +
168C SER* 2.7 21.1 + - - -
169C PHE* 3.3 13.5 - + - -
1G T 3.2 22.0 - - - -
2G A 5.2 0.9 - - - -
3G T 2.8 30.4 + - - -
4G T 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C HIS* 4.2 13.2 - + + -
160C LEU* 4.0 15.5 - - + -
162C ASN 3.4 6.6 + - - +
163C SER* 3.1 8.3 + - - +
165C HIS* 1.3 79.3 - - - +
167C ILE* 1.3 62.3 + - + +
169C PHE* 3.1 11.7 + - - +
170C THR* 2.7 52.0 + - + +
198C LEU* 4.1 10.3 - - + -
199C LYS* 2.7 33.5 + - + -
200C CYS* 3.4 3.6 - - - -
201C TRP* 2.8 29.1 + + - +
211C PHE* 4.6 1.8 - - + -
214C LEU* 3.6 29.8 - - + +
218C LEU* 3.9 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C SER 2.9 21.8 + - - +
164C ALA 4.1 2.5 - - - +
166C TYR* 1.3 77.8 - - + +
168C SER* 1.3 62.0 + - - +
169C PHE 3.1 1.2 + - - -
170C THR* 3.6 6.5 - - - -
171C SER* 2.8 48.1 + - - +
193C LEU* 3.8 26.9 - - + +
194C PHE* 3.7 37.5 - - + +
196C GLU* 4.1 5.8 - - + +
197C ASP 5.3 2.2 - - - +
198C LEU* 4.0 20.0 - - + -
209C ARG* 3.8 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C HIS* 3.3 38.1 + - - -
164C ALA 2.9 15.5 + - - -
165C HIS* 2.7 21.0 + - - -
166C TYR 3.2 0.2 - - - -
167C ILE* 1.3 77.0 - - - +
169C PHE* 1.3 63.1 + - - +
173C PHE* 3.6 23.4 - - - -
174C PHE* 3.5 11.9 + - - +
194C PHE* 4.0 4.7 - - - -
1G T 3.8 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 3.5 33.2 - - + -
71C HIS* 3.7 11.2 - + - -
134C LYS* 2.8 20.6 + - - +
138C HIS* 3.3 24.9 - + - -
149C HIS* 3.5 33.0 - + - -
151C MET* 3.3 21.5 - - + -
155C HIS* 3.3 25.8 - + + +
165C HIS* 3.3 21.1 - - - -
166C TYR 3.1 4.4 + - - +
167C ILE 3.1 0.6 - - - -
168C SER* 1.3 88.8 + - - +
170C THR* 1.3 58.5 + - - +
171C SER 3.7 1.3 - - - -
174C PHE* 3.6 33.0 - + - +
176C LYS* 5.5 0.9 + - - -
1G T 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG* 5.4 9.4 + - - -
134C LYS* 3.9 4.3 - - - +
155C HIS* 3.7 26.9 - - + +
166C TYR* 2.7 52.4 + - + +
167C ILE* 3.6 5.2 - - - +
169C PHE* 1.3 83.0 - - - +
171C SER* 1.3 61.6 - - - +
199C LYS* 5.5 6.5 - - - -
201C TRP* 4.2 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ILE* 2.8 31.1 + - - +
170C THR* 1.3 80.4 - - - +
172C PRO* 1.3 70.5 - - - +
173C PHE* 3.0 19.2 + - - +
174C PHE* 2.9 25.6 + - - +
193C LEU* 3.4 14.6 - - - +
----------------------------------------------------------
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