Contacts of the helix formed by residues 160 - 172 (chain L) in PDB entry 6AH0
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 THR 160 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159L LEU* 1.3 73.7 - - - +
161L ASN* 1.3 62.0 + - - +
162L ALA 3.2 3.1 - - - -
163L THR* 3.1 7.7 + - - +
164L ILE* 2.8 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 161 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159L LEU 3.8 1.4 + - - -
160L THR* 1.3 70.6 - - - +
162L ALA* 1.3 63.4 + - - +
164L ILE* 3.7 2.3 - - - +
165L MET* 3.0 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160L THR 3.2 1.2 - - - -
161L ASN* 1.3 76.3 - - - +
163L THR* 1.3 61.1 + - - +
165L MET* 3.2 1.9 + - - -
166L VAL* 3.1 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128L LEU 6.1 1.3 - - - -
160L THR* 3.1 11.1 + - - +
162L ALA* 1.3 72.4 - - - +
164L ILE* 1.3 64.7 + - - +
166L VAL* 3.1 2.7 + - - +
167L VAL* 2.9 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L CYS 5.8 0.2 - - - -
150L LYS* 5.0 13.6 + - - +
159L LEU* 5.3 3.2 - - - +
160L THR 2.8 17.6 + - - +
161L ASN* 3.2 4.5 + - - +
163L THR* 1.3 71.1 - - - +
165L MET* 1.3 56.3 + - - +
167L VAL* 3.6 0.9 + - - +
168L SER* 3.0 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 165 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L LYS* 6.3 0.2 - - - +
161L ASN 3.0 13.3 + - - -
162L ALA* 3.6 3.6 - - - +
163L THR 3.1 0.2 - - - -
164L ILE* 1.3 75.6 - - - +
166L VAL* 1.3 63.2 + - - +
168L SER* 3.9 0.8 - - - +
169L VAL* 3.1 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162L ALA 3.1 13.4 + - - -
163L THR* 3.1 4.0 + - - +
165L MET* 1.3 76.0 - - - +
167L VAL* 1.3 61.7 + - - +
169L VAL* 3.5 1.4 + - - +
170L THR* 3.0 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163L THR 2.9 14.7 + - - -
164L ILE* 4.0 1.1 - - - +
166L VAL* 1.3 77.1 - - - +
168L SER* 1.3 50.7 + - - +
170L THR* 3.0 2.9 + - - +
171L ALA* 2.7 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 168 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L CYS* 5.7 4.3 - - - +
150L LYS* 5.2 11.4 - - - +
164L ILE 3.0 17.2 + - - -
165L MET* 3.5 2.2 + - - +
167L VAL* 1.3 74.1 - - - +
169L VAL* 1.3 61.0 - - - +
171L ALA* 3.3 10.0 + - - +
172L SER* 3.3 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165L MET 3.1 14.1 + - - -
166L VAL* 3.9 3.4 - - - +
168L SER* 1.3 75.3 - - - +
170L THR* 1.3 59.9 + - - +
171L ALA 3.6 0.2 + - - -
172L SER* 3.6 9.5 + - - +
173L THR* 4.0 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 170 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L VAL 3.0 14.8 + - - -
167L VAL* 3.0 4.9 + - - +
169L VAL* 1.3 74.5 - - - +
171L ALA* 1.3 63.7 + - - +
172L SER 3.3 0.2 - - - -
173L THR* 3.5 3.1 + - - +
174L THR* 3.1 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146L LEU* 5.7 13.4 - - - +
147L ASP* 6.0 1.6 - - - -
167L VAL 2.7 14.3 + - - -
168L SER* 3.3 4.2 + - - +
170L THR* 1.3 74.8 - - - +
172L SER* 1.3 62.0 + - - +
173L THR 3.0 6.3 + - - -
174L THR* 3.1 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 172 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168L SER 3.3 11.5 + - - -
169L VAL 3.6 5.9 + - - -
170L THR 3.3 0.4 - - - -
171L ALA* 1.3 77.0 - - - +
173L THR* 1.3 56.3 + - - +
174L THR 3.7 0.2 - - - -
----------------------------------------------------------
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