Contacts of the helix formed by residues 113 - 131 (chain B) in PDB entry 1M4C
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LEU* 3.7 41.3 - - + +
42B PHE 4.1 6.3 - - - -
43B LYS* 4.0 12.8 - - - +
44B PHE* 4.3 0.7 - - - -
112B ALA* 1.3 76.8 - - - +
114B ILE* 1.3 54.4 + - - +
115B VAL* 3.8 3.3 + - - +
116B GLU* 2.8 44.1 + - - +
117B PHE* 2.6 35.5 + - - +
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Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.6 28.7 - - + -
36B LEU* 5.8 0.2 - - + -
39B MET* 4.4 26.2 + - + +
40B LEU* 4.4 9.6 - - + -
42B PHE 4.5 1.8 + - - -
44B PHE* 3.8 26.6 - - + -
66B LEU* 3.6 26.7 - - + -
69B VAL* 4.0 12.8 - - + -
70B LEU* 5.0 1.6 - - + -
113B THR* 1.3 71.7 - - - +
115B VAL* 1.3 76.5 + - + +
117B PHE* 3.0 7.6 + - + +
118B LEU* 2.7 51.3 + - + +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.2 20.5 - - + +
28B ILE* 4.5 9.6 - - + -
29B ASN* 4.5 18.6 - - - +
36B LEU* 4.9 3.6 - - + -
40B LEU* 3.8 21.5 - - + -
113B THR* 3.2 6.4 + - - +
114B ILE* 1.3 89.5 - - + +
116B GLU* 1.3 65.4 + - + +
118B LEU* 3.9 1.7 - - - +
119B ASN* 3.0 42.7 + - - +
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 5.5 0.2 + - - -
46B MET* 4.3 6.1 - - + +
111B THR 4.8 0.2 - - - +
112B ALA* 3.1 19.1 - - + +
113B THR* 2.8 43.9 + - - +
115B VAL* 1.3 79.5 - - + +
117B PHE* 1.3 65.0 + - - +
119B ASN* 3.1 9.0 + - - +
120B ARG* 2.9 24.6 + - - +
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 3.6 35.0 - + + -
45B TYR 4.1 14.4 - - - -
46B MET* 4.0 16.3 - - - -
58B CYS 5.3 1.1 - - - -
59B LEU* 3.8 14.4 - - + -
62B GLU* 3.7 33.9 - - + -
66B LEU* 4.0 22.9 - - + -
113B THR 2.6 17.6 + - - +
114B ILE* 3.3 11.7 - - - +
116B GLU* 1.3 75.2 - - - +
118B LEU* 1.3 78.8 + - + +
120B ARG* 3.3 14.6 + - - +
121B TRP* 3.4 44.2 + + - -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.9 37.1 - - + +
24B ILE* 4.2 15.7 - - + -
25B LEU* 4.3 24.9 - - + +
28B ILE* 3.8 18.4 - - + -
66B LEU* 4.1 21.3 - - + -
114B ILE* 2.7 41.1 + - + +
115B VAL 4.2 1.8 - - - +
117B PHE* 1.3 83.1 - - + +
119B ASN* 1.3 61.6 + - - +
121B TRP* 3.4 4.4 + - - +
122B ILE* 3.0 30.1 + - + +
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Residues in contact with ASN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 3.7 21.7 - - - +
115B VAL* 3.0 37.8 + - - +
116B GLU* 3.1 7.0 + - - +
118B LEU* 1.3 77.2 - - - +
120B ARG* 1.3 65.1 + - - +
122B ILE* 3.0 10.1 + - - +
123B THR* 3.0 26.3 + - - -
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B MET* 3.6 30.0 - - + +
47B PRO* 4.1 31.7 + - + +
48B LYS 4.5 6.3 + - - -
49B LYS* 4.8 0.2 - - - +
50B ALA* 4.1 36.0 + - - +
116B GLU 2.9 12.3 + - - +
117B PHE 3.3 10.8 - - - +
119B ASN* 1.3 77.6 - - - +
121B TRP* 1.3 62.0 + - + +
123B THR* 3.4 12.0 + - - +
124B PHE* 3.0 30.0 + - - +
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Residues in contact with TRP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.3 20.0 - - + -
45B TYR 5.3 0.8 + - - -
46B MET* 5.8 0.4 - - - -
47B PRO* 3.8 28.2 - - + +
50B ALA* 4.7 4.3 - - + -
55B HIS 3.7 23.1 - - - -
56B LEU* 4.3 9.9 - - + -
58B CYS* 3.6 15.9 - - + -
59B LEU* 3.5 36.9 - - + +
117B PHE* 3.4 56.1 + + - -
118B LEU 3.4 5.1 + - - +
119B ASN 3.3 0.4 - - - -
120B ARG* 1.3 81.7 - - + +
122B ILE* 1.3 64.7 + - - +
124B PHE* 3.3 44.4 - + + +
125B CYS* 3.1 29.7 + - - -
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.7 21.0 - - + +
21B LEU* 3.7 23.3 - - + +
22B GLN* 3.5 44.4 - - + +
25B LEU* 3.8 24.7 - - + -
118B LEU 3.0 26.2 + - - +
119B ASN* 3.0 10.5 + - - +
121B TRP* 1.3 77.0 - - - +
123B THR* 1.3 62.0 + - - +
125B CYS 3.7 0.5 + - - -
126B GLN* 3.2 34.1 + - - +
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASN* 3.0 12.6 + - - +
120B ARG* 3.6 14.8 - - - +
122B ILE* 1.3 76.5 - - - +
124B PHE* 1.3 66.6 + - - +
126B GLN* 3.0 17.2 + - + +
127B SER* 2.9 27.0 + - - -
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 5.0 3.8 - - + -
50B ALA* 3.5 44.2 - - + -
51B THR 4.1 0.4 - - - -
52B GLU 3.5 26.9 - - - -
53B LEU* 4.5 2.0 - - + -
55B HIS* 4.5 1.3 - - + -
56B LEU* 3.6 35.7 - - + -
120B ARG* 3.0 19.4 + - + +
121B TRP* 3.3 33.4 - + + +
123B THR* 1.3 79.2 - - - +
125B CYS* 1.3 75.8 + - - +
127B SER* 3.1 5.8 + - - -
128B ILE* 3.1 48.6 + - + +
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Residues in contact with CYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 4.3 10.5 - - + +
17B LEU* 3.6 37.2 - - - -
18B LEU* 4.2 20.6 - - + -
21B LEU* 4.0 11.2 - - - -
56B LEU* 5.5 0.4 - - - -
59B LEU* 6.2 0.4 - - - -
121B TRP* 3.1 19.4 + - - +
122B ILE 4.0 4.3 - - - +
124B PHE* 1.3 91.2 - - - +
126B GLN* 1.3 57.2 + - - +
128B ILE* 3.5 4.6 + - - +
129B ILE* 3.0 37.3 + - + +
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Residues in contact with GLN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 4.2 19.8 - - + +
22B GLN* 4.6 8.7 - - - +
122B ILE* 3.2 28.0 + - - +
123B THR* 3.0 22.5 + - + +
125B CYS* 1.3 74.8 - - - +
127B SER* 1.3 65.7 + - - +
129B ILE* 3.5 6.5 + - - +
130B SER* 3.1 23.2 + - - -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA 6.1 0.9 - - - -
51B THR* 5.8 4.7 - - - +
123B THR* 2.9 17.6 + - - -
124B PHE* 3.5 10.5 - - - -
126B GLN* 1.3 77.0 - - - +
128B ILE* 1.3 66.0 + - - +
130B SER* 3.2 20.4 - - - -
131B THR* 3.3 14.6 - - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.6 25.6 - - + -
51B THR* 3.3 33.7 - - + +
52B GLU 4.7 3.8 - - - +
53B LEU* 4.1 18.6 - - + +
124B PHE* 3.1 41.7 + - + +
125B CYS 3.9 3.8 - - - +
127B SER* 1.3 78.4 - - - +
129B ILE* 1.3 65.6 + - - +
130B SER 3.0 2.0 - - - -
131B THR* 2.8 31.7 + - + +
132B LEU* 3.8 11.9 - - + +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLN* 4.0 26.1 + - + +
14B LEU* 3.7 31.4 - - + +
15B GLU* 3.7 33.7 - - + +
18B LEU* 4.1 18.4 - - + -
125B CYS 3.0 23.0 + - - +
126B GLN* 3.9 5.2 - - - +
128B ILE* 1.3 76.0 - - - +
130B SER* 1.3 62.8 + - - +
132B LEU* 3.4 27.1 + - - +
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 5.7 2.9 + - - -
126B GLN 3.1 14.2 + - - -
127B SER* 3.2 15.5 - - - -
128B ILE 3.0 0.2 - - - -
129B ILE* 1.3 74.9 - - - +
131B THR* 1.3 54.2 + - - +
132B LEU* 2.6 20.7 + - - +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 6.0 1.6 - - - -
123A THR* 3.5 32.3 - - + +
124A PHE* 5.7 0.5 - - - -
127A SER* 3.3 21.0 - - - -
127B SER* 3.3 20.4 - - - +
128B ILE* 2.8 24.0 + - + +
130B SER* 1.3 73.6 - - - +
132B LEU* 1.3 66.6 + - - +
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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
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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