Contacts of the helix formed by residues 155 - 162 (chain G) in PDB entry 5IXM
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 155 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G PRO* 5.5 2.7 - - - -
153G VAL* 3.1 11.5 + - + +
154G PHE* 1.3 83.8 - - - +
156G ALA* 1.3 60.4 + - - +
157G ALA* 4.7 1.6 - - - -
158G GLY* 3.5 18.4 + - - -
159G ASN* 2.9 27.3 + - - +
111H LEU* 4.4 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G PRO* 6.1 1.0 - - - +
155G THR* 1.3 72.7 - - - +
157G ALA* 1.3 59.4 + - - +
159G ASN* 3.3 5.2 + - - +
160G SER* 2.9 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G THR* 3.5 1.7 + - - +
156G ALA* 1.3 78.6 - - - +
158G GLY* 1.3 57.0 + - - +
160G SER* 3.1 7.8 + - - -
161G ASN* 2.9 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 158 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G VAL* 3.6 9.5 - - - +
155G THR* 3.3 20.2 + - - -
156G ALA 3.2 1.0 - - - -
157G ALA* 1.3 78.9 - - - +
159G ASN* 1.3 60.5 + - - +
161G ASN* 3.4 2.7 + - - +
162G ALA* 3.1 26.2 + - - +
110H PRO 5.1 0.5 - - - +
111H LEU* 3.7 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 159 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G PHE 3.3 22.2 - - - +
152G GLN* 3.8 7.8 - - - +
153G VAL* 3.4 29.3 + - - +
155G THR 2.9 17.8 + - - +
156G ALA* 3.7 5.2 - - - +
158G GLY* 1.3 74.9 - - - +
160G SER* 1.3 62.6 + - - +
162G ALA* 3.7 9.0 + - - +
164G ARG* 3.9 22.4 + - - +
195G VAL* 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G ALA 2.9 14.8 + - - -
157G ALA* 3.1 14.1 + - - -
159G ASN* 1.3 79.8 - - - +
161G ASN* 1.3 61.4 + - - +
162G ALA 3.7 0.3 + - - -
194G SER* 4.1 1.6 - - - -
195G VAL* 3.8 16.7 + - - +
196G ASN* 3.1 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 161 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G ALA* 2.9 30.5 + - - +
158G GLY* 3.8 2.9 - - - +
160G SER* 1.3 78.2 + - - +
162G ALA* 1.3 62.4 + - - +
163G TYR* 3.2 17.8 + - - -
194G SER* 4.6 0.9 - - - -
196G ASN* 3.0 29.5 + - - +
199G ASN* 3.0 19.4 + - - +
111H LEU 5.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G PHE* 4.9 12.6 - - + +
153G VAL* 3.6 20.9 - - + -
158G GLY 3.1 17.4 + - - +
159G ASN* 3.7 7.2 + - - +
160G SER 3.4 2.2 - - - -
161G ASN* 1.3 75.9 - - - +
163G TYR* 1.3 63.9 + - - +
164G ARG* 2.9 30.1 + - + +
194G SER* 3.8 4.4 - - - -
110H PRO 5.4 1.6 - - - +
111H LEU 5.3 7.4 - - - +
113H ALA* 5.6 6.3 - - + +
----------------------------------------------------------
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