Contacts of the helix formed by residues 134 - 153 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123R PRO* 3.8 31.4 - - + -
124R HIS* 3.5 18.6 - - + +
127R ASP* 6.4 0.9 - - + -
107S ASN* 4.8 5.6 - - - +
110S LEU* 3.9 37.5 - - + +
111S LEU* 4.6 14.4 - - + -
114S HIS* 4.2 8.1 - - + -
129S LEU* 2.9 20.2 + - + +
130S GLU* 3.9 28.6 + - + +
133S TYR* 1.3 75.3 - - + +
135S GLU* 1.3 62.7 + - - +
137S GLN* 3.5 6.3 + - - +
138S VAL* 3.3 26.3 + - - +
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Residues in contact with GLU 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R TYR* 5.4 0.7 - - - -
71R LYS* 2.8 31.8 + - - -
124R HIS* 3.0 35.3 + - + +
127R ASP* 5.1 7.6 + - - +
128R PHE* 5.8 2.9 - - - -
130S GLU 4.1 11.0 + - - +
131S SER 5.8 2.2 - - - +
133S TYR 3.5 0.6 - - - +
134S LEU* 1.3 74.6 - - - +
136S GLU* 1.3 66.9 + - - +
138S VAL* 3.3 3.0 + - - +
139S LYS* 3.0 30.5 + - + +
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Residues in contact with GLU 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61S HIS* 5.1 15.7 - - + +
132S GLU 4.2 12.1 - - - +
133S TYR* 3.3 13.3 + - - +
134S LEU 3.3 0.6 - - - -
135S GLU* 1.3 79.8 - - - +
137S GLN* 1.3 56.6 + - + +
139S LYS* 3.5 7.6 - - - +
140S ASP* 3.1 34.7 + - - +
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Residues in contact with GLN 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61S HIS* 5.1 1.4 - - - -
103S GLU* 3.0 47.8 + - - +
106S VAL* 3.9 9.5 - - - +
107S ASN* 3.6 23.2 - - - +
110S LEU* 3.7 20.2 - - + -
133S TYR* 3.0 20.3 + - + +
134S LEU 3.7 3.6 - - - +
135S GLU 3.2 0.4 - - - -
136S GLU* 1.3 75.8 - - + +
138S VAL* 1.3 61.2 + - - +
140S ASP* 3.3 2.8 + - - +
141S ILE* 2.9 33.5 + - - +
176S MG 3.4 16.3 - - - -
177S MG 2.7 21.2 - - - -
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Residues in contact with VAL 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R LYS* 4.3 22.8 - - + +
72R ARG* 4.4 16.8 - - - +
124R HIS* 3.3 43.1 - - + +
107S ASN* 5.0 11.7 - - - +
134S LEU 3.3 13.4 + - - +
135S GLU* 3.3 15.0 + - - +
137S GLN* 1.3 78.0 - - + +
139S LYS* 1.3 65.1 + - - +
141S ILE* 3.9 8.0 - - + +
142S LYS* 3.0 26.2 + - - +
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Residues in contact with LYS 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R LYS* 4.6 11.4 - - - +
135S GLU* 3.0 33.0 + - + +
136S GLU* 3.5 11.9 - - - +
137S GLN 3.2 0.2 - - - -
138S VAL* 1.3 77.8 - - - +
140S ASP* 1.3 61.1 + - - +
142S LYS* 3.5 5.6 + - - +
143S ARG* 3.0 33.3 + - - +
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Residues in contact with ASP 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54S HIS* 3.7 19.9 - - + -
57S GLU* 4.1 9.8 - - - +
61S HIS* 5.6 0.3 - - - -
103S GLU* 4.4 11.9 - - - +
136S GLU* 3.1 18.7 + - - +
137S GLN* 3.3 3.8 + - - +
139S LYS* 1.3 80.0 - - - +
141S ILE* 1.3 65.5 + - - +
143S ARG* 3.2 30.3 + - - +
144S ILE* 3.1 30.8 + - + +
177S MG 2.5 29.1 - - - -
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Residues in contact with ILE 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R VAL* 3.4 35.8 - - + +
6R GLN* 3.8 22.0 - - + +
100S LEU* 3.9 21.6 - - + +
103S GLU* 3.9 25.8 - - + +
104S LYS* 4.2 8.7 - - + -
107S ASN* 3.9 24.7 - - + +
137S GLN* 2.9 23.5 + - - +
138S VAL* 3.9 7.6 - - + +
140S ASP* 1.3 75.3 - - - +
142S LYS* 1.3 59.2 + - - +
144S ILE* 3.4 1.6 + - - -
145S GLY 2.9 24.8 + - - -
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Residues in contact with LYS 142 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N ASP* 2.9 29.9 + - - -
40N ASP* 3.9 16.4 - - + +
45N HIS* 3.9 6.5 - - - -
4R VAL* 3.9 8.5 - - + +
67R LYS* 6.0 0.6 - - - +
70R ASN* 3.3 32.5 - - - +
71R LYS* 4.1 23.3 - - + +
138S VAL 3.0 18.9 + - - +
139S LYS* 3.7 5.6 - - - +
141S ILE* 1.3 78.4 - - - +
143S ARG* 1.3 56.9 + - - +
145S GLY* 3.5 0.3 + - - -
146S ASP* 2.8 66.8 + - - +
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Residues in contact with ARG 143 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S PHE* 3.9 12.1 - - - -
54S HIS* 3.1 30.9 + - - -
57S GLU* 5.8 1.6 + - - -
139S LYS* 3.0 22.4 + - - +
140S ASP* 3.2 30.2 + - - +
141S ILE 3.2 0.4 - - - -
142S LYS* 1.3 75.1 - - - +
144S ILE* 1.3 61.5 + - - +
146S ASP* 3.4 10.8 + - + +
147S PHE* 3.0 56.3 + - + -
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Residues in contact with ILE 144 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S TYR* 4.3 4.3 - - + +
50S PHE* 4.5 23.1 - - + -
54S HIS* 4.9 5.4 - - + -
96S MET* 3.4 38.6 - - - +
99S ALA* 4.1 15.3 - - + +
100S LEU* 3.9 17.7 - - + +
103S GLU* 3.9 29.4 - - + +
140S ASP 3.1 18.2 + - - +
141S ILE* 4.0 2.7 - - - +
143S ARG* 1.3 75.4 - - + +
145S GLY* 1.3 61.3 + - - +
147S PHE* 3.2 7.9 + - - +
148S ILE* 2.9 28.7 + - + +
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Residues in contact with GLY 145 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N ASP* 4.3 3.1 - - - -
3R GLN* 3.1 30.2 + - - -
4R VAL* 4.0 10.8 - - - -
100S LEU* 4.5 2.8 - - - +
141S ILE 2.9 17.8 + - - -
142S LYS 3.9 1.3 - - - -
144S ILE* 1.3 75.2 - - - +
146S ASP* 1.3 61.8 + - - +
148S ILE* 3.1 5.7 + - - +
149S THR* 3.0 19.9 + - - -
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Residues in contact with ASP 146 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N ASP* 3.3 17.3 - - - -
43N ALA* 3.7 15.7 - - + +
45N HIS* 3.0 28.3 + - + +
142S LYS* 2.8 51.0 + - - +
143S ARG* 3.4 13.0 - - + +
145S GLY* 1.3 75.7 - - - +
147S PHE* 1.3 65.1 + - + +
149S THR* 3.4 1.9 + - - -
150S ASN* 3.0 31.0 + - - +
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Residues in contact with PHE 147 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S PHE* 3.7 32.5 - + - -
96S MET* 3.9 27.6 - - + -
143S ARG* 3.0 40.1 + - + -
144S ILE* 3.2 12.1 + - - +
146S ASP* 1.3 80.5 - - + +
148S ILE* 1.3 51.8 + - - +
150S ASN* 3.2 3.9 + - + +
151S LEU* 2.7 43.0 + - + +
166S PHE* 3.6 24.0 - + + -
170S SER* 3.5 32.5 - - - -
171S VAL* 4.3 9.2 - - + -
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Residues in contact with ILE 148 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R GLN* 3.6 16.6 - - - +
93S LEU* 3.9 15.3 - - + -
96S MET* 3.7 35.0 - - + +
97S GLN* 4.0 17.3 - - + +
100S LEU* 3.7 33.0 - - + -
144S ILE* 2.9 19.4 + - + +
145S GLY* 3.1 6.3 + - - +
147S PHE* 1.3 73.9 - - - +
149S THR* 1.3 57.0 + - - +
151S LEU* 3.3 8.5 + - - +
152S LYS* 2.9 48.5 + - + +
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Residues in contact with THR 149 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N ASP 2.8 28.3 + - - +
41N ASP* 3.4 28.9 - - - +
42N VAL 3.8 2.5 - - - +
43N ALA* 3.9 4.0 - - + -
3R GLN* 3.5 11.3 + - - -
145S GLY 3.0 5.2 + - - -
146S ASP 3.6 5.8 - - - -
148S ILE* 1.3 75.9 - - - +
150S ASN* 1.3 58.5 + - - +
152S LYS* 3.4 9.9 + - - +
153S ARG* 3.0 44.6 + - - +
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Residues in contact with ASN 150 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N ALA* 3.1 33.5 + - - +
44N LEU* 3.9 6.1 - - - +
164N TYR* 3.1 34.6 - - + -
168N LYS* 4.8 1.4 + - - -
146S ASP* 3.0 26.3 + - - +
147S PHE* 3.7 6.5 - - + +
149S THR* 1.3 73.6 - - - +
151S LEU* 1.3 65.0 + - - +
153S ARG* 3.3 22.2 + - - +
154S LEU* 3.1 30.2 + - - +
166S PHE* 4.6 6.5 - - + -
170S SER* 4.8 2.5 - - - +
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Residues in contact with LEU 151 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92S THR* 4.1 9.0 - - + +
93S LEU* 3.9 16.8 - - + +
96S MET* 3.8 29.2 - - + -
147S PHE 2.7 30.4 + - - +
148S ILE* 3.5 7.2 - - - +
150S ASN* 1.3 74.3 - - - +
152S LYS* 1.3 59.3 + - - +
154S LEU* 3.3 9.3 + - - +
155S GLY 3.3 0.2 + - - -
156S LEU* 3.0 62.2 + - + +
166S PHE* 3.5 42.4 - - + -
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Residues in contact with LYS 152 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R GLN* 4.9 4.4 + - - -
93S LEU* 4.3 17.7 - - + -
97S GLN* 4.1 14.6 + - - -
148S ILE* 2.9 39.4 + - + +
149S THR* 3.6 8.3 - - - +
151S LEU* 1.3 74.6 - - - +
153S ARG* 1.3 58.8 + - - +
155S GLY* 2.9 18.8 + - - +
156S LEU* 4.3 4.5 - - - +
157S PRO* 5.7 1.6 - - + -
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Residues in contact with ARG 153 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N ASP 5.5 0.4 + - - -
42N VAL* 2.5 32.5 + - - +
44N LEU* 3.4 29.1 - - - +
160N GLY* 3.2 54.1 + - - +
161N MET 3.6 0.7 + - - -
163N GLU* 3.4 20.9 + - - +
164N TYR* 4.0 13.7 - - - +
149S THR* 3.0 29.5 + - - +
150S ASN* 3.3 33.8 + - - +
151S LEU 3.3 0.2 - - - -
152S LYS* 1.3 71.8 - - - +
154S LEU* 1.3 59.3 + - + +
155S GLY 3.0 8.6 + - - -
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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