Contacts of the helix formed by residues 134 - 153 (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 LEU 134 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L ASN* 4.8 6.3 - - - +
110L LEU* 3.9 37.7 - - + +
111L LEU* 4.6 14.1 - - + -
114L HIS* 4.2 7.9 - - + -
129L LEU* 2.9 20.5 + - + +
130L GLU* 3.9 29.6 + - + +
133L TYR* 1.3 75.7 - - + +
135L GLU* 1.3 62.0 + - - +
137L GLN* 3.5 5.8 + - - +
138L VAL* 3.3 26.5 + - - +
123T PRO* 3.8 30.5 - - + -
124T HIS* 3.5 19.2 - - + +
127T ASP* 6.1 0.7 - - + -
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Residues in contact with GLU 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L GLU 4.1 10.8 + - - +
131L SER 5.8 2.7 - - - +
133L TYR 3.5 0.4 - - - +
134L LEU* 1.3 75.0 - - - +
136L GLU* 1.3 68.0 + - - +
138L VAL* 3.3 2.5 + - - +
139L LYS* 3.0 30.0 + - + +
68T TYR* 5.4 0.7 - - - -
71T LYS* 2.8 33.1 + - - -
124T HIS* 3.0 33.9 + - + +
127T ASP* 5.1 7.4 + - - +
128T PHE* 5.7 3.5 - - - -
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Residues in contact with GLU 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L HIS* 5.1 15.7 - - + +
132L GLU 4.2 12.3 - - - +
133L TYR* 3.3 12.6 + - - +
134L LEU 3.3 0.4 - - - -
135L GLU* 1.3 80.6 - - - +
137L GLN* 1.3 57.6 + - + +
139L LYS* 3.5 7.3 - - - +
140L ASP* 3.1 34.7 + - - +
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Residues in contact with GLN 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L HIS* 5.1 1.6 - - - -
103L GLU* 3.0 47.9 + - - +
106L VAL* 3.9 9.5 - - - +
107L ASN* 3.6 22.8 - - - +
110L LEU* 3.7 20.2 - - + -
133L TYR* 3.0 19.2 + - + +
134L LEU 3.7 3.8 - - - +
135L GLU 3.2 0.2 - - - -
136L GLU* 1.3 76.5 - - + +
138L VAL* 1.3 61.5 + - - +
140L ASP* 3.3 3.1 + - - +
141L ILE* 2.9 34.3 + - - +
176L MG 3.4 16.6 - - - -
177L MG 2.7 20.5 - - - -
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Residues in contact with VAL 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L ASN* 5.0 11.2 - - - +
134L LEU 3.3 12.8 + - - +
135L GLU* 3.3 16.3 + - - +
137L GLN* 1.3 77.7 - - + +
139L LYS* 1.3 65.4 + - - +
141L ILE* 3.9 7.4 - - + +
142L LYS* 3.0 26.0 + - - +
71T LYS* 4.3 23.4 - - + +
72T ARG* 4.4 15.0 - - - +
124T HIS* 3.3 42.6 - - + +
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Residues in contact with LYS 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L GLU* 3.0 32.3 + - + +
136L GLU* 3.5 12.8 - - - +
138L VAL* 1.3 78.4 - - - +
140L ASP* 1.3 61.8 + - - +
142L LYS* 3.7 5.2 - - - +
143L ARG* 3.0 33.8 + - - +
71T LYS* 4.6 12.1 - - - +
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Residues in contact with ASP 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L HIS* 3.7 21.1 - - + -
57L GLU* 4.1 9.6 - - - +
61L HIS* 5.6 0.5 - - - -
103L GLU* 4.4 11.7 - - + +
136L GLU* 3.1 18.3 + - - +
137L GLN 3.7 3.6 - - - +
139L LYS* 1.3 80.3 - - - +
141L ILE* 1.3 64.2 + - - +
143L ARG* 3.2 30.0 + - - +
144L ILE* 3.1 31.5 + - + +
177L MG 2.5 29.0 - - - -
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Residues in contact with ILE 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L LEU* 3.9 21.9 - - + +
103L GLU* 3.9 26.5 - - + +
104L LYS* 4.2 8.1 - - + -
107L ASN* 3.9 24.7 - - + +
137L GLN* 2.9 23.9 + - - +
138L VAL* 3.9 7.6 - - + +
140L ASP* 1.3 75.3 - - - +
142L LYS* 1.3 58.9 + - - +
144L ILE* 3.4 1.2 + - - -
145L GLY 2.9 24.9 + - - -
4T VAL* 3.5 35.3 - - + +
6T GLN* 3.9 22.0 - - + +
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Residues in contact with LYS 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L VAL 3.0 19.0 + - - +
139L LYS* 3.7 6.1 - - - +
141L ILE* 1.3 77.8 - - - +
143L ARG* 1.3 56.5 + - - +
145L GLY* 3.5 0.5 + - - -
146L ASP* 2.8 67.0 + - - +
38P ASP* 2.9 29.5 + - - -
40P ASP* 3.9 16.4 - - + +
45P HIS* 4.0 6.5 - - - -
4T VAL* 4.0 8.7 - - + +
67T LYS* 5.9 0.6 - - - +
70T ASN* 3.3 32.3 - - - +
71T LYS* 4.1 23.3 - - + +
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Residues in contact with ARG 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L PHE* 3.9 12.1 - - - -
54L HIS* 3.1 31.1 + - - -
57L GLU* 5.8 1.6 + - - -
139L LYS* 3.0 22.8 + - - +
140L ASP* 3.2 30.6 + - - +
141L ILE 3.2 0.2 - - - -
142L LYS* 1.3 75.4 - - - +
144L ILE* 1.3 61.5 + - + +
146L ASP* 3.4 11.8 + - + +
147L PHE* 3.0 57.9 + - + -
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Residues in contact with ILE 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 4.3 4.0 - - - +
50L PHE* 4.5 24.5 - - + -
54L HIS* 4.9 6.1 - - + -
96L MET* 3.4 37.9 - - - +
99L ALA* 4.1 15.0 - - + +
100L LEU* 3.9 16.8 - - + +
103L GLU* 3.9 28.5 - - + +
140L ASP 3.1 18.0 + - - +
141L ILE* 4.0 2.9 - - - +
143L ARG* 1.3 75.8 - - + +
145L GLY* 1.3 60.2 + - - +
147L PHE* 3.2 8.0 + - - +
148L ILE* 2.9 29.0 + - + +
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Residues in contact with GLY 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L LEU* 4.5 2.8 - - - +
141L ILE 2.9 17.8 + - - -
142L LYS 3.9 1.6 - - - -
144L ILE* 1.3 76.3 - - - +
146L ASP* 1.3 61.5 + - - +
148L ILE* 3.1 6.9 + - - +
149L THR* 3.0 20.3 + - - -
40P ASP* 4.3 3.4 - - - -
3T GLN* 3.2 28.4 + - - -
4T VAL* 4.0 11.0 - - - -
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Residues in contact with ASP 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142L LYS* 2.8 50.7 + - - +
143L ARG* 3.4 12.2 - - + +
145L GLY* 1.3 76.2 - - - +
147L PHE* 1.3 65.3 + - + +
149L THR* 3.4 1.9 + - - -
150L ASN* 3.0 31.1 + - - +
40P ASP* 3.3 17.7 - - - +
43P ALA* 3.8 15.4 - - + +
45P HIS* 3.0 27.3 + - + +
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Residues in contact with PHE 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L PHE* 3.7 32.1 - + - -
96L MET* 3.9 27.4 - - + -
143L ARG* 3.0 41.1 + - + -
144L ILE* 3.2 12.1 + - - +
146L ASP* 1.3 79.8 - - + +
148L ILE* 1.3 52.5 + - - +
150L ASN* 3.2 3.9 + - + +
151L LEU* 2.7 44.2 + - + +
166L PHE* 3.6 23.0 - + + -
170L SER* 3.5 33.0 - - - -
171L VAL* 4.3 9.4 - - + -
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Residues in contact with ILE 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93L LEU* 3.9 15.5 - - + -
96L MET* 3.7 35.7 - - + +
97L GLN* 4.0 17.9 - - + +
100L LEU* 3.7 33.4 - - + -
144L ILE 2.9 19.6 + - - +
145L GLY 3.1 6.0 + - - +
147L PHE* 1.3 74.4 - - - +
149L THR* 1.3 58.2 + - - +
151L LEU* 3.3 8.5 + - - +
152L LYS* 2.9 47.0 + - + +
3T GLN* 3.6 16.2 - - - +
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Residues in contact with THR 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L GLY 3.0 4.6 + - - -
146L ASP 3.6 5.4 - - - -
148L ILE* 1.3 77.1 - - - +
150L ASN* 1.3 59.8 + - - +
152L LYS* 3.4 9.6 + - - +
153L ARG* 3.0 45.1 + - - +
40P ASP 2.8 29.3 + - - +
41P ASP* 3.5 27.5 - - - +
43P ALA* 3.8 6.5 - - + -
3T GLN* 3.5 12.0 + - - -
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Residues in contact with ASN 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L ASP* 3.0 26.5 + - - +
147L PHE* 3.2 6.5 + - + +
149L THR* 1.3 75.2 - - - +
151L LEU* 1.3 64.8 + - - +
153L ARG* 3.3 21.3 + - - +
154L LEU* 3.1 30.1 + - - +
166L PHE* 4.6 6.5 - - + -
170L SER* 4.8 3.1 - - - +
43P ALA* 3.1 33.3 + - - +
44P LEU* 3.9 5.5 - - - +
45P HIS* 5.8 0.4 - - - -
164P TYR* 3.1 34.5 - - + -
168P LYS* 4.8 1.3 + - - -
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Residues in contact with LEU 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L THR* 4.1 9.4 - - + +
93L LEU* 3.9 17.7 - - + +
96L MET* 3.8 29.2 - - + -
147L PHE 2.7 28.8 + - - +
148L ILE* 3.6 7.6 - - - +
150L ASN* 1.3 74.5 - - - +
152L LYS* 1.3 59.0 + - - +
154L LEU* 3.3 9.7 + - + +
155L GLY 3.3 0.2 + - - -
156L LEU* 3.0 62.7 + - + +
166L PHE* 3.5 42.0 - - + -
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Residues in contact with LYS 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93L LEU* 4.3 17.3 - - + -
97L GLN* 4.1 14.4 + - - -
148L ILE* 2.9 39.4 + - + +
149L THR* 3.6 7.6 - - - +
151L LEU* 1.3 75.8 - - - +
153L ARG* 1.3 60.1 + - - +
155L GLY* 2.9 18.5 + - - +
156L LEU* 4.3 4.9 - - - +
157L PRO* 5.7 1.6 - - + -
3T GLN* 4.9 4.9 + - - -
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Residues in contact with ARG 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L THR* 3.0 28.6 + - - +
150L ASN* 3.3 34.0 + - - +
151L LEU 3.3 0.4 - - - -
152L LYS* 1.3 71.5 - - - +
154L LEU* 1.3 59.8 + - + +
155L GLY* 3.0 9.5 + - - -
41P ASP 5.5 0.4 + - - -
42P VAL* 2.5 31.9 + - - +
44P LEU* 3.4 28.9 - - - +
160P GLY* 3.3 52.8 - - - +
161P MET 3.6 0.9 + - - -
163P GLU* 3.4 21.4 + - - +
164P TYR* 4.0 14.6 - - - +
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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