Contacts of the helix formed by residues 134 - 153 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K PRO* 3.7 30.5 - - + -
124K HIS* 3.5 17.8 - - + +
127K ASP* 6.4 0.7 - - + -
107P ASN* 4.8 5.9 - - - +
110P LEU* 3.9 37.9 - - + +
111P LEU* 4.6 13.9 - - + -
114P HIS* 4.2 8.3 - - + -
129P LEU* 2.9 21.2 + - + +
130P GLU* 3.9 30.0 + - + +
133P TYR* 1.3 75.6 - - + +
135P GLU* 1.3 61.3 + - - +
137P GLN* 3.5 6.8 + - - +
138P VAL* 3.3 26.3 + - - +
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Residues in contact with GLU 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K TYR* 5.4 0.9 - - - -
71K LYS* 2.8 32.5 + - - -
124K HIS* 3.0 34.7 + - + +
127K ASP* 5.0 7.2 - - - +
128K PHE* 5.7 3.1 - - - -
130P GLU 4.1 11.6 + - - +
131P SER 5.8 2.2 - - - +
133P TYR 3.5 0.4 - - - +
134P LEU* 1.3 74.8 - - - +
136P GLU* 1.3 66.9 + - - +
138P VAL* 3.3 2.7 + - - +
139P LYS* 3.0 30.5 + - + +
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Residues in contact with GLU 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P HIS* 5.1 14.8 - - + +
132P GLU 4.2 12.5 - - - +
133P TYR* 3.3 13.5 + - - +
134P LEU 3.3 0.2 - - - -
135P GLU* 1.3 80.6 - - - +
137P GLN* 1.3 57.8 + - + +
139P LYS* 3.5 8.0 - - - +
140P ASP* 3.1 35.9 + - - +
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Residues in contact with GLN 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P HIS* 5.1 1.4 - - - -
103P GLU* 3.0 48.4 + - - +
106P VAL* 3.9 8.1 - - - +
107P ASN* 3.6 23.4 - - - +
110P LEU* 3.7 20.0 - - + -
133P TYR* 3.0 19.8 + - + +
134P LEU 3.7 3.4 - - - +
135P GLU 3.2 0.2 - - - -
136P GLU* 1.3 75.1 - - + +
138P VAL* 1.3 61.6 + - - +
140P ASP* 3.3 2.7 + - - +
141P ILE* 2.9 34.3 + - - +
176P MG 3.4 15.9 - - - -
177P MG 2.7 21.2 - - - -
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Residues in contact with VAL 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K LYS* 4.3 21.7 - - + +
72K ARG* 4.4 16.2 - - - +
124K HIS* 3.3 43.7 - - + +
107P ASN* 5.0 11.4 - - - +
134P LEU 3.3 12.8 + - - +
135P GLU* 3.3 16.0 + - - +
137P GLN* 1.3 77.3 - - + +
139P LYS* 1.3 65.5 + - - +
141P ILE* 3.9 7.5 - - + +
142P LYS* 3.0 26.0 + - - +
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Residues in contact with LYS 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K LYS* 4.6 11.9 - - - +
135P GLU* 3.0 32.4 + - + +
136P GLU* 3.5 12.8 - - - +
138P VAL* 1.3 79.7 - - - +
140P ASP* 1.3 59.7 + - - +
142P LYS* 3.5 5.6 + - - +
143P ARG* 3.0 34.2 + - - +
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Residues in contact with ASP 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P HIS* 3.7 19.6 - - + -
57P GLU* 4.1 9.6 - - - +
61P HIS* 5.6 0.9 - - - -
103P GLU* 4.4 12.1 - - - +
136P GLU* 3.1 18.9 + - - +
137P GLN* 3.7 3.8 - - - +
139P LYS* 1.3 81.2 - - - +
141P ILE* 1.3 63.9 + - - +
143P ARG* 3.2 29.9 + - - +
144P ILE* 3.1 31.5 + - + +
177P MG 2.5 29.1 - - - -
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Residues in contact with ILE 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K VAL* 3.5 35.0 - - + +
6K GLN* 3.8 23.3 - - + +
100P LEU* 3.9 22.4 - - + +
103P GLU* 3.9 26.5 - - + +
104P LYS* 4.2 8.3 - - + -
107P ASN* 3.9 24.2 - - + +
137P GLN* 2.9 22.9 + - - +
138P VAL* 3.9 7.2 - - - +
140P ASP* 1.3 74.3 - - - +
142P LYS* 1.3 60.1 + - - +
144P ILE* 3.4 1.2 + - - -
145P GLY* 2.9 25.1 + - - -
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Residues in contact with LYS 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K VAL* 4.0 8.5 - - + +
67K LYS* 6.0 0.8 - - - +
70K ASN* 3.3 32.8 - - - +
71K LYS* 4.1 24.2 - - + +
138P VAL 3.0 19.2 + - - +
139P LYS* 3.7 5.6 - - - +
141P ILE* 1.3 78.3 - - - +
143P ARG* 1.3 55.7 + - - +
145P GLY* 3.9 0.5 - - - -
146P ASP* 2.8 65.4 + - - +
38W ASP* 3.0 28.6 + - - -
40W ASP* 3.9 18.4 - - + +
45W HIS* 4.0 6.5 - - - -
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Residues in contact with ARG 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50P PHE* 3.9 11.9 - - - -
54P HIS* 3.1 30.9 + - - -
57P GLU* 5.8 1.6 + - - -
139P LYS* 3.0 21.7 + - - +
140P ASP* 3.2 31.8 + - - +
141P ILE 3.2 0.2 - - - -
142P LYS* 1.3 75.6 - - - +
144P ILE* 1.3 61.9 + - - +
146P ASP* 3.4 11.4 + - + +
147P PHE* 3.0 55.7 + - + -
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Residues in contact with ILE 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TYR* 4.3 4.3 - - - +
50P PHE* 4.5 23.6 - - + -
54P HIS* 4.9 5.8 - - + -
96P MET* 3.4 37.2 - - - +
99P ALA* 4.1 15.3 - - + +
100P LEU* 3.9 16.8 - - + +
103P GLU* 3.9 28.9 - - + +
140P ASP* 3.1 17.9 + - - +
141P ILE 4.0 2.9 - - - +
143P ARG* 1.3 75.2 - - + +
145P GLY* 1.3 61.8 + - - +
147P PHE* 3.2 8.4 + - - +
148P ILE* 2.9 28.7 + - + +
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Residues in contact with GLY 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K GLN* 3.2 29.7 + - - -
4K VAL* 4.0 11.0 - - - -
100P LEU* 4.5 3.0 - - - +
141P ILE 2.9 16.3 + - - -
142P LYS 3.9 1.8 - - - -
143P ARG 3.3 0.2 - - - -
144P ILE* 1.3 75.9 - - - +
146P ASP* 1.3 61.9 + - - +
148P ILE* 3.1 6.2 + - - +
149P THR* 3.0 19.8 + - - -
40W ASP* 4.4 3.1 - - - -
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Residues in contact with ASP 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142P LYS* 2.8 53.9 + - - +
143P ARG* 3.4 12.4 - - + +
144P ILE 3.3 0.2 - - - -
145P GLY* 1.3 75.8 - - - +
147P PHE* 1.3 64.9 + - + +
149P THR* 3.4 1.7 + - - -
150P ASN* 3.0 31.5 + - - +
40W ASP* 3.3 17.0 - - - -
43W ALA* 3.8 14.7 - - + +
45W HIS* 3.1 24.7 + - + +
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Residues in contact with PHE 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P PHE* 3.7 32.1 - + - -
96P MET* 3.9 27.1 - - + -
143P ARG* 3.0 41.3 + - + -
144P ILE* 3.2 12.1 + - - +
146P ASP* 1.3 80.6 - - + +
148P ILE* 1.3 52.2 + - - +
150P ASN* 3.2 4.3 + - + +
151P LEU* 2.7 43.3 + - + +
166P PHE* 3.6 23.5 - + + -
170P SER* 3.5 31.6 - - - -
171P VAL* 4.3 9.6 - - + -
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Residues in contact with ILE 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K GLN* 3.6 16.4 - - - +
93P LEU* 3.9 14.6 - - + -
96P MET* 3.7 35.7 - - + +
97P GLN* 4.0 17.9 - - + +
100P LEU* 3.7 33.2 - - + -
144P ILE 2.9 19.6 + - - +
145P GLY* 3.5 6.1 - - - +
147P PHE* 1.3 73.9 - - - +
149P THR* 1.3 57.6 + - - +
151P LEU* 3.3 7.5 + - - +
152P LYS* 2.9 48.4 + - + +
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Residues in contact with THR 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K GLN* 3.5 13.5 + - - -
145P GLY 3.0 4.9 + - - -
146P ASP 3.6 5.8 - - - -
147P PHE 3.2 0.2 - - - -
148P ILE* 1.3 76.2 - - - +
150P ASN* 1.3 58.3 + - - +
152P LYS* 3.4 9.6 + - - +
153P ARG* 3.0 47.5 + - - +
40W ASP 2.9 28.5 + - - +
41W ASP* 3.5 25.7 - - - +
43W ALA* 3.9 5.4 - - + -
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Residues in contact with ASN 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146P ASP* 3.0 27.3 + - - +
147P PHE* 3.7 6.5 - - + +
149P THR* 1.3 74.5 - - - +
151P LEU* 1.3 64.9 + - - +
153P ARG* 3.3 22.9 + - - +
154P LEU* 3.1 31.0 + - - +
166P PHE* 4.6 6.7 - - + -
170P SER* 4.8 2.2 - - - +
43W ALA* 3.2 32.9 + - - +
44W LEU* 4.0 5.4 - - - +
45W HIS* 5.9 0.2 - - - -
164W TYR* 3.2 34.3 - - + -
168W LYS* 4.9 0.9 + - - -
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Residues in contact with LEU 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P THR* 4.1 8.7 - - + +
93P LEU* 3.9 17.9 - - + +
96P MET* 3.8 29.4 - - + -
147P PHE 2.7 29.3 + - - +
148P ILE* 3.3 7.4 + - - +
150P ASN* 1.3 74.9 - - - +
152P LYS* 1.3 60.1 + - - +
154P LEU* 3.3 9.7 + - + +
155P GLY 3.3 0.2 + - - -
156P LEU* 3.0 63.0 + - + +
163P GLU* 5.3 0.2 - - - -
166P PHE* 3.5 41.7 - - + -
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Residues in contact with LYS 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K GLN* 4.9 4.6 + - - -
93P LEU* 4.3 17.5 - - + -
97P GLN* 4.1 14.0 + - - -
148P ILE* 2.9 40.5 + - + +
149P THR* 3.6 8.3 - - - +
151P LEU* 1.3 75.2 - - - +
153P ARG* 1.3 60.2 + - - +
155P GLY* 2.9 18.9 + - - +
156P LEU* 4.3 4.5 - - - +
157P PRO* 5.7 1.3 - - + -
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Residues in contact with ARG 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P THR* 3.0 29.4 + - - +
150P ASN* 3.3 35.6 + - - +
151P LEU 3.3 0.2 - - - -
152P LYS* 1.3 70.9 - - - +
154P LEU* 1.3 60.3 + - + +
155P GLY* 3.0 8.7 + - - -
41W ASP 5.5 0.4 + - - -
42W VAL* 2.5 36.1 + - - +
44W LEU* 3.5 23.1 - - - +
160W GLY* 3.3 51.6 - - - +
161W MET 3.6 0.9 + - - -
163W GLU* 3.5 20.1 + - - +
164W TYR* 4.1 13.9 - - - +
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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) + - + + + + + -
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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