Contacts of the helix formed by residues 134 - 153 (chain T) 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 LEU 134 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123M PRO* 3.8 30.3 - - + -
124M HIS* 3.5 19.2 - - + +
127M ASP* 6.4 0.7 - - + -
107T ASN* 4.8 6.1 - - - +
110T LEU* 3.9 37.5 - - + +
111T LEU* 4.6 13.0 - - + -
114T HIS* 4.2 7.6 - - + -
129T LEU* 2.9 20.5 + - + +
130T GLU* 3.9 30.0 + - + +
133T TYR* 1.3 75.3 - - + +
135T GLU* 1.3 62.5 + - - +
137T GLN* 3.5 6.4 + - - +
138T VAL* 3.3 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M TYR* 5.3 0.3 - - - -
71M LYS* 2.8 32.3 + - - -
124M HIS* 3.0 35.6 + - + +
127M ASP* 5.1 6.7 + - - +
128M PHE* 5.8 3.3 - - - -
130T GLU 4.1 10.3 + - - +
131T SER 5.8 2.5 - - - +
133T TYR 3.5 0.4 - - - +
134T LEU* 1.3 74.8 - - - +
136T GLU* 1.3 66.5 + - - +
138T VAL* 3.3 3.1 + - - +
139T LYS* 3.0 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61T HIS* 5.1 15.7 - - + +
132T GLU 4.2 13.2 - - - +
133T TYR* 3.3 13.1 + - - +
134T LEU 3.3 0.2 - - - -
135T GLU* 1.3 81.0 - - - +
137T GLN* 1.3 57.2 + - + +
139T LYS* 3.5 7.5 - - - +
140T ASP* 3.1 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61T HIS* 5.1 1.6 - - - -
103T GLU* 3.0 47.4 + - - +
106T VAL* 3.9 10.1 - - - +
107T ASN* 3.6 22.4 - - - +
110T LEU* 3.7 20.9 - - + -
133T TYR* 3.0 19.2 + - + +
134T LEU* 3.7 3.8 - - - +
135T GLU 3.2 0.4 - - - -
136T GLU* 1.3 75.7 - - + +
138T VAL* 1.3 60.5 + - - +
140T ASP* 3.3 3.3 + - - +
141T ILE* 2.9 34.0 + - - +
176T MG 3.4 16.1 - - - -
177T MG 2.7 21.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M LYS* 4.3 25.9 - - + +
72M ARG* 4.4 12.8 - - - +
124M HIS* 3.3 42.0 - - + +
107T ASN* 5.0 11.7 - - - +
134T LEU 3.3 13.6 + - - +
135T GLU* 3.3 15.2 + - - +
137T GLN* 1.3 77.4 - - + +
139T LYS* 1.3 65.4 + - - +
141T ILE* 3.9 7.4 - - + +
142T LYS* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M LYS* 4.6 11.4 - - - +
135T GLU* 3.0 33.0 + - + +
136T GLU* 3.5 12.8 - - - +
138T VAL* 1.3 78.9 - - - +
140T ASP* 1.3 60.1 + - - +
142T LYS* 3.5 5.6 + - - +
143T ARG* 3.0 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54T HIS* 3.7 20.4 - - + -
57T GLU* 4.1 10.7 - - - +
61T HIS* 5.6 0.7 - - - -
103T GLU* 4.4 12.3 - - + +
136T GLU* 3.1 17.5 + - - +
137T GLN* 3.7 4.3 - - - +
139T LYS* 1.3 80.1 - - - +
141T ILE* 1.3 64.6 + - - +
143T ARG* 3.2 30.9 + - - +
144T ILE* 3.1 30.0 + - - +
177T MG 2.5 29.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M VAL* 3.4 35.4 - - + +
6M GLN* 3.8 22.0 - - + +
100T LEU* 3.9 22.0 - - + +
103T GLU* 3.9 26.5 - - + +
104T LYS* 4.2 8.1 - - + -
107T ASN* 3.9 24.5 - - + +
137T GLN* 2.9 23.8 + - - +
138T VAL* 3.9 7.0 - - + +
140T ASP* 1.3 73.0 - - - +
142T LYS* 1.3 61.5 + - - +
144T ILE* 3.4 1.8 + - - -
145T GLY* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M VAL* 3.9 9.6 - - + +
67M LYS* 6.0 0.6 - - - +
70M ASN* 3.3 32.3 - - - +
71M LYS* 4.1 23.8 - - + +
38S ASP* 2.9 29.0 + - - -
40S ASP* 3.9 16.4 - - + +
45S HIS* 4.0 6.5 - - - -
138T VAL 3.0 18.6 + - - +
139T LYS* 3.7 5.6 - - - +
141T ILE* 1.3 78.1 - - - +
143T ARG* 1.3 56.6 + - - +
145T GLY* 3.5 0.5 + - - -
146T ASP* 2.8 66.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50T PHE* 3.9 12.4 - - - -
54T HIS* 3.1 31.1 + - - -
57T GLU* 5.8 1.6 + - - -
139T LYS* 3.0 21.9 + - - +
140T ASP* 3.2 30.1 + - - +
141T ILE 3.2 0.2 - - - -
142T LYS* 1.3 75.7 - - - +
144T ILE* 1.3 60.8 + - + +
146T ASP* 3.4 10.2 + - + +
147T PHE* 3.0 56.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T TYR* 4.3 4.0 - - - +
50T PHE* 4.5 24.2 - - + -
54T HIS* 4.9 5.4 - - + -
96T MET* 3.4 37.5 - - - +
99T ALA* 4.1 15.9 - - + +
100T LEU* 3.9 17.5 - - + +
103T GLU* 3.9 28.3 - - + +
140T ASP 3.1 18.9 + - - +
141T ILE* 4.0 3.1 - - - +
143T ARG* 1.3 74.7 - - + +
145T GLY* 1.3 60.1 + - - +
147T PHE* 3.2 8.5 + - - +
148T ILE* 2.9 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLN* 3.2 29.9 + - - -
4M VAL* 4.0 10.5 - - - -
40S ASP* 4.3 3.4 - - - -
100T LEU* 4.5 3.1 - - - +
141T ILE 2.9 17.4 + - - -
142T LYS 3.9 1.8 - - - -
144T ILE* 1.3 75.9 - - - +
146T ASP* 1.3 61.2 + - - +
148T ILE* 3.1 6.1 + - - +
149T THR* 3.0 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S ASP* 3.3 17.5 - - - +
43S ALA* 3.8 14.9 - - + +
45S HIS* 3.0 27.8 + - + +
142T LYS* 2.8 50.5 + - - +
143T ARG* 3.4 12.6 - - + +
145T GLY* 1.3 74.5 - - - +
147T PHE* 1.3 66.2 + - + +
149T THR* 3.4 1.6 + - - -
150T ASN* 3.0 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50T PHE* 3.7 32.5 - + - -
96T MET* 3.9 27.4 - - + -
143T ARG* 3.0 40.1 + - + -
144T ILE* 3.2 12.5 + - - +
146T ASP* 1.3 79.9 - - + +
148T ILE* 1.3 52.2 + - - +
150T ASN* 3.2 4.4 + - + +
151T LEU* 2.7 43.6 + - + +
166T PHE* 3.6 22.8 - + + -
170T SER* 3.5 32.8 - - - -
171T VAL* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLN* 3.6 15.9 - - - +
93T LEU* 3.9 14.6 - - + -
96T MET* 3.7 35.4 - - + +
97T GLN* 4.0 17.7 - - + +
100T LEU* 3.7 33.4 - - + -
144T ILE 2.9 18.5 + - - +
145T GLY 3.1 6.7 + - - +
147T PHE* 1.3 73.9 - - - +
149T THR* 1.3 57.7 + - - +
151T LEU* 3.3 8.7 + - - +
152T LYS* 2.9 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLN* 3.5 11.8 + - - -
40S ASP 2.9 28.0 + - - +
41S ASP* 3.5 27.7 - - - +
43S ALA* 3.9 6.1 - - + -
145T GLY 3.0 5.1 + - - -
146T ASP 3.6 5.4 - - - -
147T PHE 3.2 0.2 - - - -
148T ILE* 1.3 77.0 - - - +
150T ASN* 1.3 58.6 + - - +
152T LYS* 3.4 9.0 + - - +
153T ARG* 3.0 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43S ALA* 3.2 33.5 + - - +
44S LEU* 3.9 6.1 - - - +
45S HIS* 5.9 0.2 - - - -
164S TYR* 3.2 34.0 - - + -
168S LYS* 4.9 1.1 + - - -
146T ASP* 3.0 26.1 + - - +
147T PHE* 3.7 6.9 - - + +
149T THR* 1.3 73.4 - - - +
151T LEU* 1.3 65.0 + - - +
153T ARG* 3.3 22.4 + - - +
154T LEU* 3.1 30.6 + - - +
166T PHE* 4.6 6.3 - - + -
170T SER* 4.8 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92T THR* 4.1 8.3 - - + +
93T LEU* 3.9 17.0 - - + +
96T MET* 3.8 29.8 - - + -
147T PHE 2.7 30.1 + - - +
148T ILE* 3.5 7.6 - - - +
150T ASN* 1.3 74.9 - - - +
152T LYS* 1.3 59.1 + - - +
154T LEU* 3.3 9.7 + - + +
155T GLY 3.3 0.2 + - - -
156T LEU* 3.0 62.3 + - + +
163T GLU* 5.3 0.2 - - - -
166T PHE* 3.5 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLN* 5.0 4.8 + - - -
93T LEU* 4.3 17.9 - - + -
97T GLN* 4.1 14.6 + - - -
148T ILE* 2.9 38.9 + - + +
149T THR* 3.7 7.9 - - - +
151T LEU* 1.3 76.4 - - - +
153T ARG* 1.3 59.7 + - - +
155T GLY* 2.9 18.9 + - - +
156T LEU* 4.3 4.7 - - - +
157T PRO* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S VAL* 2.5 36.3 + - - +
44S LEU* 3.4 25.1 - - - +
160S GLY* 3.3 51.3 + - - +
161S MET 3.6 0.7 + - - -
163S GLU* 3.5 20.9 + - - +
164S TYR* 4.1 13.5 - - - +
149T THR* 3.0 28.6 + - - +
150T ASN* 3.3 34.4 + - - +
151T LEU 3.3 0.2 - - - -
152T LYS* 1.3 70.8 - - - +
154T LEU* 1.3 59.2 + - + +
155T GLY* 3.0 9.4 + - - -
----------------------------------------------------------
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