Contacts of the helix formed by residues 123 - 132 (chain N) in PDB entry 1MFR
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 PRO 123 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J LEU* 3.7 19.1 - - + +
114J HIS* 3.5 43.5 - - + +
130J GLU* 4.4 6.2 - - - +
134J LEU* 3.8 16.8 - - + -
7N ASN* 3.7 11.2 - - - +
121N VAL* 3.3 17.7 - - + +
122N ASP* 1.3 85.1 - - - +
124N HIS* 1.3 57.8 + - + +
126N CYS* 3.4 8.8 + - + +
127N ASP* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J LEU* 5.7 3.6 - - + -
134J LEU* 3.5 40.2 - - + +
135J GLU* 3.0 33.4 + - + +
138J VAL* 3.3 28.6 - - + +
68N TYR* 2.8 39.8 + + - -
71N LYS* 5.4 0.9 - - + -
72N ARG* 3.6 14.2 + - - +
122N ASP* 3.3 8.1 + - - +
123N PRO* 1.3 79.4 - - + +
125N LEU* 1.3 59.9 + - - +
127N ASP* 3.5 8.3 + - - +
128N PHE* 3.1 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N TYR* 4.4 7.4 - - + -
12N CYS* 4.0 28.0 - - + -
16N VAL* 4.3 13.5 - - + -
65N PHE* 5.3 0.4 - - + -
68N TYR* 3.2 33.8 + - + +
113N LEU* 4.4 12.6 - - + -
117N ALA* 3.9 20.4 - - + -
122N ASP* 2.9 24.3 + - - +
124N HIS* 1.3 74.2 - - - +
126N CYS* 1.3 65.3 + - - +
128N PHE* 4.2 11.7 - - + -
129N LEU* 3.1 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 126 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J GLU* 5.7 3.6 - - - +
114N HIS* 3.6 22.0 - - - +
117N ALA* 3.6 19.3 - - - -
118N THR* 3.5 29.2 - - - -
122N ASP 3.4 15.5 + - - +
123N PRO* 3.5 12.6 - - + +
125N LEU* 1.3 80.8 - - - +
127N ASP* 1.3 56.7 + - - +
129N LEU* 3.4 4.0 + - - +
130N GLU* 3.1 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J ASP* 5.6 1.2 - - - +
130J GLU* 3.7 48.9 + - + +
131J SER* 5.0 3.5 + - - -
134J LEU* 6.4 0.2 - - + -
135J GLU* 5.1 7.8 - - - +
123N PRO 3.0 18.1 + - - +
124N HIS* 3.8 9.6 - - + +
126N CYS* 1.3 74.3 - - - +
128N PHE* 1.3 60.0 + - - +
130N GLU* 4.2 11.5 - - - +
131N SER* 2.9 50.1 + - - -
127Q ASP* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J GLU* 5.8 3.8 - - - -
64N LYS* 3.7 25.4 - - + -
65N PHE* 3.5 20.4 - + - -
68N TYR* 3.6 37.5 - + + -
71N LYS* 6.2 3.1 - - - -
124N HIS* 3.1 18.9 + - + +
125N LEU* 3.6 10.3 - - + +
126N CYS 3.3 0.2 - - - -
127N ASP* 1.3 78.1 + - - +
129N LEU* 1.3 67.8 + - + +
131N SER* 4.7 2.5 - - - -
132N GLU* 3.0 52.0 + - + +
133N TYR* 3.5 30.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65N PHE* 4.0 33.0 - - + -
110N LEU* 4.3 16.6 - - + +
113N LEU* 3.9 18.4 - - + +
114N HIS* 3.8 40.8 - - + +
117N ALA* 5.1 0.2 - - + -
125N LEU* 3.1 26.9 + - + +
126N CYS* 3.6 4.5 - - - +
128N PHE* 1.3 89.8 - - + +
130N GLU* 1.3 58.3 + - - +
133N TYR* 3.0 14.6 + - + +
134N LEU* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J GLU* 3.9 18.2 - - - +
114N HIS* 2.9 28.6 + - - +
126N CYS* 3.1 24.9 + - - +
127N ASP* 3.7 8.5 - - - +
129N LEU* 1.3 77.7 - - - +
131N SER* 1.3 62.8 + - - +
134N LEU* 3.9 25.2 + - + +
135N GLU* 4.1 11.4 + - - +
123Q PRO* 4.4 8.6 - - - +
126Q CYS* 5.7 2.5 - - - +
127Q ASP* 3.7 44.9 - - + +
130Q GLU* 3.9 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127N ASP* 2.9 35.1 + - - -
128N PHE* 4.2 2.2 - - - -
130N GLU* 1.3 78.7 - - - +
132N GLU* 1.3 74.5 + - - +
133N TYR 3.6 0.2 - - - -
135N GLU* 5.8 2.4 - - - +
127Q ASP* 5.3 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N HIS* 4.6 4.3 + - - -
64N LYS* 2.9 42.3 + - + +
128N PHE* 3.0 40.8 + - + +
131N SER* 1.3 91.4 - - - +
133N TYR* 1.3 78.2 + - + +
136N GLU* 4.2 11.9 - - - +
----------------------------------------------------------
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