Contacts of the helix formed by residues 134 - 153 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO* 3.8 30.3 - - + -
124A HIS* 3.5 18.5 - - + +
127A ASP* 6.1 0.9 - - + +
107H ASN* 4.8 5.5 - - - +
110H LEU* 3.9 37.2 - - + +
111H LEU* 4.6 14.4 - - + -
114H HIS* 4.2 7.9 - - + -
129H LEU* 2.9 19.5 + - + +
130H GLU* 3.9 29.8 + - + +
133H TYR* 1.3 76.7 - - + +
135H GLU* 1.3 62.1 + - - +
137H GLN* 3.5 6.2 + - - +
138H VAL* 3.3 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 5.4 0.7 - - - -
71A LYS* 2.8 32.9 + - - -
124A HIS* 3.0 34.0 + - + +
127A ASP* 5.1 7.0 - - - +
128A PHE* 5.8 3.1 - - - -
130H GLU 4.1 11.0 + - - +
131H SER 5.8 2.2 - - - +
133H TYR 3.5 0.4 - - - +
134H LEU* 1.3 75.1 - - - +
136H GLU* 1.3 67.0 + - - +
138H VAL* 3.3 3.2 + - - +
139H LYS* 3.0 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H HIS* 5.1 15.5 - - + +
132H GLU 4.2 12.7 - - - +
133H TYR* 3.3 13.6 + - - +
134H LEU 3.3 0.2 - - - -
135H GLU* 1.3 80.6 - - - +
137H GLN* 1.3 58.8 + - + +
139H LYS* 3.5 7.7 - - - +
140H ASP* 3.1 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H HIS* 5.1 1.2 - - - -
103H GLU* 3.0 48.0 + - - +
106H VAL* 3.9 10.1 - - - +
107H ASN* 3.6 22.6 - - - +
110H LEU* 3.7 19.7 - - + -
133H TYR* 3.0 19.4 + - + +
134H LEU 3.7 4.3 - - - +
135H GLU 3.2 0.2 - - - -
136H GLU* 1.3 75.9 - - + +
138H VAL* 1.3 60.0 + - - +
140H ASP* 3.3 3.4 + - - +
141H ILE* 2.9 33.8 + - - +
176H MG 3.4 16.1 - - - -
177H MG 2.7 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 4.3 22.5 - - + +
72A ARG* 4.4 15.0 - - - +
124A HIS* 3.3 44.0 - - + +
107H ASN* 5.0 11.9 - - - +
134H LEU 3.3 12.9 + - - +
135H GLU* 3.3 15.4 + - - +
137H GLN* 1.3 77.2 - - + +
139H LYS* 1.3 64.6 + - - +
141H ILE* 3.9 7.9 - - + +
142H LYS* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 4.6 11.9 - - - +
135H GLU* 3.0 32.1 + - + +
136H GLU* 3.5 13.0 - - - +
138H VAL* 1.3 79.7 - - - +
140H ASP* 1.3 59.8 + - - +
142H LYS* 3.5 4.9 + - - +
143H ARG* 3.0 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H HIS* 3.7 20.6 - - + -
57H GLU* 4.1 9.9 - - - +
61H HIS* 5.6 0.5 - - - -
103H GLU* 4.4 12.1 - - + +
136H GLU* 3.1 17.3 + - - +
137H GLN 3.7 4.7 - - - +
139H LYS* 1.3 80.2 - - - +
141H ILE* 1.3 64.8 + - - +
143H ARG* 3.2 30.6 + - - +
144H ILE* 3.1 30.1 + - - +
177H MG 2.5 29.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 3.5 35.4 - - + +
6A GLN* 3.8 22.4 - - + +
100H LEU* 3.9 21.0 - - + +
103H GLU* 3.9 26.9 - - + +
104H LYS* 4.2 7.9 - - + -
107H ASN* 3.9 24.7 - - + +
137H GLN* 2.9 23.3 + - - +
138H VAL* 3.9 7.4 - - + +
140H ASP* 1.3 74.8 - - - +
142H LYS* 1.3 60.0 + - - +
144H ILE* 3.4 1.8 + - - -
145H GLY* 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 4.0 8.7 - - + -
67A LYS* 5.9 0.8 - - - +
70A ASN* 3.3 33.7 - - - +
71A LYS* 4.1 24.7 - - + +
38G ASP* 2.9 29.7 + - - -
40G ASP* 4.0 16.8 - - + +
45G HIS* 4.0 6.3 - - - -
138H VAL 3.0 18.6 + - - +
139H LYS* 3.7 6.1 - - - +
141H ILE* 1.3 77.9 - - - +
143H ARG* 1.3 57.1 + - - +
145H GLY* 3.5 0.5 + - - -
146H ASP* 2.8 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H PHE* 3.9 12.8 - - - -
54H HIS* 3.1 31.1 + - - -
57H GLU* 5.8 1.6 + - - -
139H LYS* 3.0 22.8 + - - +
140H ASP* 3.2 30.5 + - - +
141H ILE 3.2 0.2 - - - -
142H LYS* 1.3 75.7 - - - +
144H ILE* 1.3 61.2 + - - +
146H ASP* 3.4 11.0 + - + +
147H PHE* 3.0 55.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 4.3 4.0 - - - +
50H PHE* 4.5 23.6 - - + -
54H HIS* 4.9 5.4 - - + -
96H MET* 3.4 38.1 - - - +
99H ALA* 4.1 15.5 - - + +
100H LEU* 3.9 17.7 - - + +
103H GLU* 3.9 29.2 - - + +
140H ASP 3.1 18.4 + - - +
141H ILE* 4.0 2.5 - - - +
143H ARG* 1.3 76.0 - - + +
145H GLY* 1.3 61.9 + - - +
147H PHE* 3.2 8.7 + - - +
148H ILE* 2.9 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.2 29.8 + - - -
4A VAL* 4.0 10.8 - - - -
40G ASP* 4.3 2.9 - - - -
100H LEU* 4.5 3.1 - - - +
141H ILE 2.9 17.4 + - - -
142H LYS 3.9 1.3 - - - -
144H ILE* 1.3 75.2 - - - +
146H ASP* 1.3 61.7 + - - +
148H ILE* 3.1 6.4 + - - +
149H THR* 3.0 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ASP* 3.3 17.7 - - - +
43G ALA* 3.8 15.3 - - + +
45G HIS* 3.0 27.7 + - + +
142H LYS* 2.8 50.4 + - - +
143H ARG* 3.4 12.6 - - + +
145H GLY* 1.3 76.2 - - - +
147H PHE* 1.3 65.4 + - + +
149H THR* 3.4 2.1 + - - -
150H ASN* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H PHE* 3.7 32.5 - + - -
96H MET* 3.9 27.1 - - + -
143H ARG* 3.0 40.0 + - + -
144H ILE* 3.2 12.1 + - - +
146H ASP* 1.3 80.7 - - + +
148H ILE* 1.3 52.8 + - - +
150H ASN* 3.2 4.4 + - + +
151H LEU* 2.8 43.7 + - + +
166H PHE* 3.6 23.0 - + + -
170H SER* 3.5 32.5 - - - -
171H VAL* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.6 15.3 - - - +
93H LEU* 3.9 15.0 - - + -
96H MET* 3.7 35.2 - - + +
97H GLN* 4.0 17.7 - - + +
100H LEU* 3.7 33.0 - - + -
144H ILE 2.9 19.8 + - - +
145H GLY 3.1 6.3 + - - +
147H PHE* 1.3 73.7 - - - +
149H THR* 1.3 57.9 + - - +
151H LEU* 3.3 8.2 + - - +
152H LYS* 2.9 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.5 11.4 + - - -
40G ASP 2.8 28.8 + - - +
41G ASP* 3.5 28.1 - - - +
43G ALA* 3.9 5.4 - - + -
145H GLY 3.0 5.3 + - - -
146H ASP 3.6 5.4 - - - -
148H ILE* 1.3 77.0 - - - +
150H ASN* 1.3 57.3 + - - +
152H LYS* 3.4 9.9 + - - +
153H ARG* 3.0 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ALA* 3.1 34.1 + - - +
44G LEU* 3.9 5.7 - - - +
45G HIS* 5.8 0.2 - - - -
164G TYR* 3.2 34.1 - - + -
168G LYS* 4.8 1.3 + - - -
146H ASP* 3.0 25.5 + - - +
147H PHE* 3.7 6.9 - - + +
149H THR* 1.3 74.7 - - - +
151H LEU* 1.3 65.0 + - - +
153H ARG* 3.3 22.0 + - - +
154H LEU* 3.1 30.0 + - - +
166H PHE* 4.6 7.0 - - + -
170H SER* 4.8 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H THR* 4.1 8.5 - - + +
93H LEU* 3.9 16.8 - - + +
96H MET* 3.8 30.3 - - + -
147H PHE 2.8 29.1 + - - +
148H ILE* 3.6 7.4 - - - +
150H ASN* 1.3 73.9 - - - +
152H LYS* 1.3 61.3 + - - +
154H LEU* 3.3 10.1 + - + +
156H LEU* 3.0 63.1 + - + +
163H GLU* 5.3 0.2 - - - -
166H PHE* 3.5 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 4.9 4.2 + - - -
93H LEU* 4.3 18.2 - - + -
97H GLN* 4.1 15.0 + - - -
148H ILE* 2.9 39.1 + - + +
149H THR* 3.6 7.9 - - - +
151H LEU* 1.3 75.6 - - - +
153H ARG* 1.3 58.9 + - - +
155H GLY* 2.9 18.9 + - - +
156H LEU* 4.3 4.7 - - - +
157H PRO* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G ASP 5.5 0.6 + - - -
42G VAL* 2.5 36.9 + - - +
44G LEU* 3.4 24.7 - - - +
160G GLY* 3.3 51.7 - - - +
161G MET 3.6 0.9 + - - -
163G GLU* 3.5 20.9 + - - +
164G TYR* 4.1 14.1 - - - +
149H THR* 3.0 28.8 + - - +
150H ASN* 3.3 33.1 + - - +
151H LEU 3.3 0.2 - - - -
152H LYS* 1.3 71.3 - - - +
154H LEU* 1.3 58.8 + - + +
155H 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