Contacts of the helix formed by residues 123 - 132 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L ASN* 3.7 11.4 - - - +
121L VAL* 3.3 16.8 - - + +
122L ASP* 1.3 84.8 - - - +
124L HIS* 1.3 58.8 + - - +
126L CYS* 3.4 8.2 + - + +
127L ASP* 3.0 28.6 + - - +
111M LEU* 3.7 19.5 - - + +
114M HIS* 3.5 46.2 - - + +
130M GLU* 4.4 5.6 - - - +
134M LEU* 3.7 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68L TYR* 2.8 39.4 + + - -
71L LYS* 5.4 1.1 - - + -
72L ARG* 3.6 13.9 + - - +
122L ASP* 3.3 7.9 + - - +
123L PRO* 1.3 78.9 - - + +
125L LEU* 1.3 60.0 + - - +
127L ASP* 3.5 8.6 + - - +
128L PHE* 3.1 24.8 + - + +
111M LEU* 5.7 3.8 - - + -
134M LEU* 3.4 40.0 - - + +
135M GLU* 3.0 32.7 + - + +
138M VAL* 3.3 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L TYR* 4.4 6.3 - - + -
12L CYS* 4.0 28.3 - - + -
16L VAL* 4.3 13.9 - - + -
65L PHE* 5.3 0.2 - - + -
68L TYR* 3.2 33.6 + - + +
113L LEU* 4.4 12.3 - - + -
117L ALA* 3.9 21.3 - - + -
122L ASP* 2.9 24.9 + - - +
124L HIS* 1.3 74.4 - - - +
126L CYS* 1.3 65.7 + - - +
128L PHE* 4.2 11.9 - - + -
129L LEU* 3.1 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 126 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L HIS* 3.6 23.2 - - + +
117L ALA* 3.6 19.1 - - - -
118L THR* 3.5 28.5 - - - -
122L ASP 3.4 14.5 + - - +
123L PRO* 3.5 11.7 - - + +
125L LEU* 1.3 81.2 - - - +
127L ASP* 1.3 57.0 - - - +
129L LEU* 3.4 3.8 + - - +
130L GLU* 3.1 37.1 + - - +
130M GLU* 5.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L PRO 3.0 17.2 + - - +
124L HIS* 3.8 8.8 - - + +
126L CYS* 1.3 74.7 - - - +
128L PHE* 1.3 61.7 + - - +
130L GLU* 4.2 11.5 - - - +
131L SER* 2.9 49.6 + - - -
127M ASP* 5.6 1.2 - - - +
130M GLU* 3.6 47.2 + - + +
131M SER* 4.9 4.0 + - - -
134M LEU* 6.1 1.2 - - + +
135M GLU* 5.1 8.0 - - - +
127T ASP* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L LYS* 3.7 24.9 - - + -
65L PHE* 3.5 20.2 - + - -
68L TYR* 3.6 38.8 - + + -
71L LYS* 6.2 2.7 - - - -
124L HIS* 3.1 19.0 + - + +
125L LEU* 3.6 9.9 - - + +
127L ASP* 1.3 77.5 + - - +
129L LEU* 1.3 69.1 + - + +
131L SER* 4.7 2.9 - - - -
132L GLU* 3.0 52.5 + - + +
133L TYR* 3.5 30.9 - + - -
135M GLU* 5.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65L PHE* 4.0 33.0 - - + -
110L LEU* 4.2 17.3 - - + +
113L LEU* 3.9 19.1 - - + +
114L HIS* 3.8 40.8 - - + +
117L ALA* 5.1 0.2 - - + -
125L LEU* 3.1 25.6 + - + +
126L CYS* 3.6 4.9 - - - +
127L ASP 3.2 0.2 - - - -
128L PHE* 1.3 90.1 - - + +
130L GLU* 1.3 58.5 + - - +
133L TYR* 3.0 16.3 + - + +
134L LEU* 2.9 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L HIS* 2.9 28.4 + - - +
126L CYS* 3.1 25.1 + - - +
127L ASP* 3.7 9.2 - - - +
129L LEU* 1.3 76.9 - - - +
131L SER* 1.3 62.5 + - - +
134L LEU* 3.9 24.8 + - + +
135L GLU* 4.1 12.0 + - - +
130M GLU* 3.9 17.5 - - - +
123T PRO* 4.4 7.4 - - - +
126T CYS* 5.7 2.5 - - - +
127T ASP* 3.7 47.2 - - + +
130T GLU* 3.9 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127L ASP* 2.9 35.6 + - - -
128L PHE* 4.2 2.5 - - - -
130L GLU* 1.3 79.1 - - - +
132L GLU* 1.3 74.7 + - - +
135L GLU* 5.8 3.0 - - - +
127T ASP* 5.3 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L HIS* 4.6 4.0 + - - -
64L LYS* 2.9 41.9 + - + +
128L PHE* 3.0 40.5 + - + +
131L SER* 1.3 90.4 - - - +
133L TYR* 1.3 78.9 + - + +
136L GLU* 4.2 12.0 - - - +
----------------------------------------------------------
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