Contacts of the helix formed by residues 114 - 123 (chain N) in PDB entry 6MZL
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 114 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113N SER* 1.3 87.4 + - - +
115N PRO* 1.3 71.9 - - - +
116N LEU 3.3 4.2 + - - -
117N VAL* 3.3 25.9 - - - +
118N ASP* 3.1 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 115 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C HIS* 5.5 7.2 - - + +
108C GLU* 2.8 40.7 - - - +
113N SER* 3.7 10.7 - - - +
114N THR* 1.3 85.3 - - - +
116N LEU* 1.3 61.1 + - + +
118N ASP* 3.7 11.7 - - + +
119N PHE* 2.9 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLN* 5.3 5.2 - - - +
104C LEU* 4.0 47.6 - - + +
105C HIS* 4.3 30.1 - - + +
108C GLU* 5.5 1.8 - - + -
114N THR 3.3 1.6 - - - -
115N PRO* 1.3 78.4 - - - +
117N VAL* 1.3 61.7 + - - +
119N PHE* 3.2 21.1 + - + +
120N LEU* 2.9 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N THR* 3.3 31.6 - - - +
116N LEU* 1.3 75.6 - - - +
118N ASP* 1.3 67.2 + - - +
120N LEU* 3.3 16.6 + - + +
121N MET* 2.9 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 118 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLU* 5.0 1.6 - - - +
113N SER* 3.0 28.6 + - - +
114N THR* 3.1 9.6 + - - +
115N PRO* 3.7 12.3 - - + +
116N LEU 3.2 0.4 - - - -
117N VAL* 1.3 81.8 - - - +
119N PHE* 1.3 59.4 + - - +
121N MET* 3.3 9.4 + - - +
122N GLN* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU 5.4 0.2 - - - -
107C LEU* 4.2 21.1 - - + -
108C GLU* 3.3 38.3 + - + +
111C ILE* 3.5 31.2 - - + -
115N PRO 2.9 9.1 + - - +
116N LEU* 3.3 25.6 - - + +
118N ASP* 1.3 73.9 - - - +
120N LEU* 1.3 68.5 + - + +
122N GLN* 3.3 6.9 + - - +
123N LEU* 3.0 52.8 + - + +
126N TYR* 3.9 13.5 - + - -
154N LEU* 3.8 28.0 - - + -
157N LEU* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 4.0 37.2 - - + +
91C ASP* 4.2 19.1 - - - +
116N LEU* 2.9 28.4 + - + +
117N VAL* 3.3 19.7 + - + +
119N PHE* 1.3 87.6 - - + +
121N MET* 1.3 70.7 + - + +
123N LEU* 3.7 34.6 - - + +
150N ARG* 4.4 5.9 + - - -
154N LEU* 5.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 121 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 5.6 2.2 - - + -
931D ASP* 5.2 10.1 - - + +
933D ARG* 5.1 12.8 - - + -
934D TYR* 4.9 18.6 - - + +
117N VAL* 2.9 32.6 + - + +
118N ASP* 3.6 13.0 - - - +
119N PHE 3.2 0.2 - - - -
120N LEU* 1.3 86.5 - - + +
122N GLN* 1.3 57.8 + - - +
123N LEU 3.2 4.3 + - - -
124N GLU* 3.5 24.7 + - - +
150N ARG* 4.6 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLU* 3.7 24.0 + - - +
112C HIS* 5.4 4.2 + - - -
118N ASP* 2.9 20.5 + - - +
119N PHE* 3.3 11.8 + - - +
121N MET* 1.3 72.7 - - - +
123N LEU* 1.3 63.2 + - - +
124N GLU* 3.1 5.2 - - - +
125N ASP* 3.1 30.9 + - + +
126N TYR* 2.7 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 3.9 20.4 - - + -
111C ILE* 5.6 0.9 - - + -
119N PHE* 3.0 45.7 + - + +
120N LEU* 3.7 38.6 - - + +
121N MET 3.2 1.4 - - - -
122N GLN* 1.3 75.9 - - - +
124N GLU* 1.3 59.0 + - - +
125N ASP 3.1 2.6 + - - -
126N TYR* 3.6 12.6 + - + -
150N ARG* 3.5 32.9 - - + +
153N ARG* 3.4 29.4 - - + -
154N LEU* 4.7 15.0 - - + +
157N LEU* 6.2 1.6 - - + -
----------------------------------------------------------
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