Contacts of the helix formed by residues 131 - 143 (chain C) in PDB entry 5T0H
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 VAL 131 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASN* 4.5 20.0 - - - +
129C ASN* 5.5 1.8 - - - +
130C LYS* 1.3 76.0 - - - +
132C ASP* 1.3 75.1 + - + +
133C PRO* 3.3 3.1 - - + +
134C LEU* 3.0 18.5 + - - +
135C VAL* 3.2 16.7 + - + +
223C PHE* 3.7 18.7 - - + -
224C ILE* 5.7 2.9 - - + -
237C MET* 4.9 10.8 - - + -
240C GLU* 4.7 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C VAL* 1.3 85.0 - - + +
133C PRO* 1.3 58.8 - - + +
134C LEU 3.0 0.2 - - - -
135C VAL* 2.7 17.2 + - - +
136C SER* 2.3 45.0 + - - +
237C MET* 3.2 27.7 - - - +
240C GLU* 3.8 7.2 - - - +
241C HIS* 2.6 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LYS* 3.5 31.4 - - + -
131C VAL* 3.5 11.7 - - + +
132C ASP* 1.3 91.2 - - + +
134C LEU* 1.3 55.8 + - - +
136C SER* 3.3 10.3 + - - +
137C LEU* 3.1 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LYS* 5.3 2.5 - - - +
131C VAL* 3.0 13.4 + - - +
132C ASP 3.0 0.6 - - - -
133C PRO* 1.3 76.7 - - - +
135C VAL* 1.3 64.1 + - - +
137C LEU* 3.5 3.3 + - - +
138C MET* 3.0 44.8 + - + +
219C LEU* 5.8 5.4 - - + +
220C VAL* 6.0 1.3 - - + -
223C PHE* 3.6 42.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C VAL* 3.3 16.4 - - + +
132C ASP* 2.7 29.3 + - - +
134C LEU* 1.3 72.8 - - - +
136C SER* 1.3 51.7 + - - +
138C MET* 3.0 9.7 + - + +
139C MET* 2.7 53.1 + - + +
212C ILE* 5.7 5.8 - - + -
220C VAL* 6.4 2.2 - - + -
223C PHE* 3.4 24.5 - - + -
224C ILE* 4.4 5.6 - - + -
237C MET* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ASP* 2.3 43.3 + - - +
133C PRO* 3.3 12.5 + - - +
135C VAL* 1.3 69.7 - - - +
137C LEU* 1.3 52.1 + - - -
139C MET* 3.3 12.4 - - - +
140C VAL* 2.5 38.5 + - - +
210C THR* 6.0 2.2 - - - -
211C PHE 5.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C PRO 3.1 20.9 + - - +
134C LEU* 3.8 4.5 - - - +
135C VAL 3.1 0.6 - - - -
136C SER* 1.3 79.7 + - - +
138C MET* 1.3 59.0 + - - +
140C VAL* 3.4 14.3 - - + +
141C GLU* 2.6 60.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C LEU* 3.0 34.7 + - + +
135C VAL* 3.0 10.6 + - + +
137C LEU* 1.3 76.5 - - + +
139C MET* 1.3 73.6 + - + +
141C GLU* 3.2 49.2 - - - +
142C LYS* 3.9 9.9 + - - +
217C SER* 5.5 5.8 - - - +
218C GLU 5.7 2.0 - - - +
219C LEU* 5.7 8.7 - - + -
220C VAL* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C VAL* 2.7 36.6 + - + +
136C SER* 3.3 14.8 - - - +
138C MET* 1.3 80.8 - - + +
140C VAL* 1.3 63.8 + - - +
141C GLU 3.0 1.6 + - - -
142C LYS* 3.0 22.2 + - - +
143C VAL* 4.0 2.4 + - - +
201C ARG* 5.9 2.0 - - - +
211C PHE* 4.0 22.6 - - + +
212C ILE* 3.7 12.3 - - + -
213C ARG* 3.1 60.9 + - + +
214C VAL 4.9 4.5 - - - +
216C GLY* 6.1 2.0 - - - -
220C VAL* 6.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C SER 2.5 23.0 + - - +
137C LEU* 3.4 20.6 - - + +
139C MET* 1.3 69.2 - - - +
141C GLU* 1.3 70.2 + - - +
142C LYS 3.4 0.2 - - - -
143C VAL 3.7 14.6 - - - +
144C PRO* 5.6 2.0 - - + -
201C ARG* 3.3 39.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 2.6 39.4 + - + +
138C MET* 3.2 52.5 - - - +
140C VAL* 1.3 77.2 - - - +
142C LYS* 1.3 69.5 + - + +
143C VAL* 4.5 0.3 - - - -
144C PRO* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C MET 3.9 8.5 - - - +
139C MET* 3.0 7.2 + - + +
141C GLU* 1.3 83.9 - - + +
143C VAL* 1.3 61.2 + - - +
144C PRO* 4.5 2.4 - - - +
213C ARG* 3.3 35.4 - - - +
249C ASP* 3.2 37.8 + - - +
250C GLU* 5.4 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C MET 4.0 1.2 + - - +
140C VAL* 3.7 16.9 - - - +
141C GLU 3.5 0.8 + - - -
142C LYS* 1.3 80.6 - - + +
144C PRO* 1.3 85.1 - - + +
197C THR* 3.6 30.7 - - + +
198C LEU* 4.0 14.1 - - + -
201C ARG* 3.4 23.9 + - + -
211C PHE* 4.7 0.4 - - + -
213C ARG* 3.3 25.1 - - - +
----------------------------------------------------------
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