Contacts of the helix formed by residues 113 - 130 (chain A) in PDB entry 1M4A
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 THR 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.3 51.6 + - + +
42A PHE 4.2 4.9 - - - -
43A LYS* 4.7 4.5 - - - -
44A PHE* 4.0 1.8 - - - -
112A ALA* 1.3 78.3 - - - +
114A ILE* 1.3 59.4 + - + +
115A VAL* 3.3 14.8 - - + +
116A GLU* 3.0 11.4 + - - +
117A PHE* 2.7 35.3 + - - +
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.5 31.0 - - + -
39A MET* 3.9 29.4 - - + +
40A LEU* 4.0 15.7 - - + -
42A PHE 4.3 1.4 + - - -
44A PHE* 3.4 31.2 - - + -
66A LEU* 3.7 29.4 - - + -
69A VAL* 4.3 6.1 - - + -
70A LEU* 3.8 19.7 - - + -
113A THR* 1.3 72.9 - - + +
115A VAL* 1.3 60.5 + - + +
117A PHE* 3.4 3.9 + - - +
118A LEU* 3.1 30.8 + - + +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.1 16.2 - - + +
28A ILE* 3.8 25.4 - - + -
29A ASN* 4.9 11.7 - - - +
36A LEU* 4.7 2.7 - - + -
40A LEU* 3.8 23.8 - - + -
113A THR* 3.0 8.2 - - + +
114A ILE* 1.3 83.6 - - + +
116A GLU* 1.3 58.7 + - + +
118A LEU* 3.2 4.2 + - - +
119A ASN* 3.0 41.2 + - - +
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A MET* 3.6 16.9 - - + +
112A ALA* 4.0 13.5 - - + -
113A THR* 3.0 15.8 + - - +
115A VAL* 1.3 79.9 - - + +
117A PHE* 1.3 60.6 + - - +
119A ASN* 4.0 12.8 - - - +
120A ARG* 3.0 29.7 + - - +
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 5.4 1.1 - - + -
44A PHE* 3.9 26.9 - + + -
45A TYR 4.4 8.1 - - - -
46A MET* 3.9 15.2 - - - -
59A LEU* 3.5 26.7 - - + -
62A GLU* 3.6 32.8 - - + -
66A LEU* 3.6 39.3 - - + -
113A THR 2.7 16.3 + - - +
114A ILE* 3.5 7.9 - - - +
115A VAL 3.2 0.2 - - - -
116A GLU* 1.3 78.6 - - - +
118A LEU* 1.3 75.3 + - + +
120A ARG* 3.7 0.5 + - - +
121A TRP* 3.0 49.6 + + - -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.0 26.9 - - + +
24A ILE* 3.8 17.5 - - + -
25A LEU* 3.6 46.2 - - + +
28A ILE* 4.0 11.7 - - + -
66A LEU* 4.6 9.4 - - + -
114A ILE* 3.1 20.8 + - + +
115A VAL 3.2 4.2 + - - +
117A PHE* 1.3 93.6 - - + +
119A ASN* 1.3 57.2 + - - +
120A ARG 3.1 1.3 - - - -
121A TRP* 2.9 6.0 + - - +
122A ILE* 2.7 42.6 + - + +
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Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.5 24.1 - - - +
29A ASN* 5.9 0.2 + - - -
115A VAL* 3.0 34.5 + - - +
116A GLU* 4.1 15.5 - - - +
118A LEU* 1.3 75.3 - - - +
120A ARG* 1.3 58.7 + - - +
122A ILE* 3.7 12.2 - - - +
123A THR* 2.8 35.9 + - - +
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A MET* 3.6 24.2 - - + +
47A PRO* 4.0 31.5 + - + +
48A LYS 4.8 4.4 + - - -
49A LYS* 4.7 0.8 - - - +
50A ALA* 3.5 41.2 + - + +
51A THR* 5.4 2.6 - - - +
116A GLU* 3.0 22.8 + - + +
117A PHE 3.9 4.0 - - - +
118A LEU 3.1 0.4 - - - -
119A ASN* 1.3 77.8 - - - +
121A TRP* 1.3 60.6 + - + +
123A THR* 3.7 9.0 - - - +
124A PHE* 3.3 21.3 + - - +
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Residues in contact with TRP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.8 21.5 - - + -
45A TYR 5.7 0.4 + - - -
46A MET* 5.7 0.6 - - - -
47A PRO* 3.8 33.8 - - + +
50A ALA* 4.4 7.6 - - + -
55A HIS 3.2 27.8 - - - -
56A LEU* 4.1 16.6 - - + -
58A CYS* 3.9 7.2 - - + -
59A LEU* 3.6 35.3 - - + +
117A PHE* 3.0 53.7 + + - +
118A LEU 2.9 4.8 + - - +
120A ARG* 1.3 80.7 - - + +
122A ILE* 1.3 60.5 + - - +
123A THR 3.3 0.2 - - - -
124A PHE* 3.3 41.5 + + + +
125A CYS* 2.9 33.4 + - - -
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.7 14.5 - - + +
21A LEU* 3.7 23.1 - - + +
22A GLN* 3.5 39.0 - - + +
25A LEU* 3.9 23.8 - - + -
118A LEU* 2.7 22.7 + - + +
119A ASN* 3.7 9.9 - - - +
121A TRP* 1.3 74.9 - - - +
123A THR* 1.3 66.0 + - - +
125A CYS* 3.3 2.9 + - - +
126A GLN* 2.9 43.6 + - - +
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASN* 2.8 22.2 + - - +
120A ARG* 3.7 12.4 - - - +
122A ILE* 1.3 78.1 - - - +
124A PHE* 1.3 53.3 + - - +
126A GLN* 3.1 15.3 + - - +
127A SER* 2.7 42.7 + - - -
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.7 4.3 - - + -
50A ALA* 3.4 29.6 - - + +
51A THR* 4.5 0.4 - - - -
52A GLU 3.5 30.5 - - - -
53A LEU* 4.4 3.8 - - + -
55A HIS* 4.8 1.3 - - + -
56A LEU* 3.6 41.3 - - + -
120A ARG* 3.3 14.3 + - - +
121A TRP* 3.4 35.7 - + + +
122A ILE 3.2 0.2 - - - -
123A THR* 1.3 78.4 - - - +
125A CYS* 1.3 75.0 + - - +
127A SER* 3.2 6.9 + - - -
128A ILE* 2.9 53.6 + - + +
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Residues in contact with CYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.1 15.2 - - + +
17A LEU* 3.5 38.8 - - - -
18A LEU* 4.2 21.1 - - + -
21A LEU* 4.0 9.4 - - - -
121A TRP 2.9 21.4 + - - +
122A ILE 3.6 4.3 - - - +
123A THR 3.3 0.2 - - - -
124A PHE* 1.3 85.7 - - - +
126A GLN* 1.3 61.1 + - - +
128A ILE* 3.0 6.9 + - - +
129A ILE* 2.9 31.4 + - + +
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Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.7 19.9 - - + +
22A GLN* 4.1 10.2 + - - +
122A ILE* 2.9 38.1 + - - +
123A THR* 3.6 15.4 + - - +
125A CYS* 1.3 76.4 - - - +
127A SER* 1.3 58.0 + - - +
129A ILE* 3.3 10.8 + - - +
130A SER* 3.0 28.2 + - - -
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 5.6 7.1 - - - +
123A THR* 2.7 28.2 + - - -
124A PHE* 3.6 7.6 - - - -
125A CYS 3.2 0.2 - - - -
126A GLN* 1.3 73.8 - - - +
128A ILE* 1.3 61.5 + - - +
130A SER* 2.7 22.7 + - - -
131A THR* 3.3 13.3 - - - +
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Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.5 25.6 - - + -
51A THR* 3.4 32.5 - - - +
52A GLU* 4.4 5.4 - - - +
53A LEU* 4.6 14.6 - - + -
124A PHE* 2.9 42.0 + - + +
125A CYS* 3.0 5.6 + - - +
127A SER* 1.3 80.3 - - - +
129A ILE* 1.3 63.7 + - - +
130A SER 3.1 1.6 - - - -
131A THR* 2.5 28.2 + - + +
132A LEU* 3.4 15.4 - - + +
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 4.7 12.3 - - + +
14A LEU* 4.2 16.2 - - + +
15A GLU* 3.9 39.7 - - + +
18A LEU* 3.7 28.9 - - + -
125A CYS 2.9 18.1 + - - +
126A GLN* 3.3 8.5 + - - +
128A ILE* 1.3 77.2 - - - +
130A SER* 1.3 60.9 + - - +
131A THR 3.3 0.2 - - - -
132A LEU* 3.6 24.7 - - + -
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLN 3.0 12.5 + - - -
127A SER* 2.7 29.2 + - - -
129A ILE* 1.3 78.7 - - - +
131A THR* 1.3 62.0 + - - +
132A LEU 3.7 1.0 + - - -
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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
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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