Contacts of the helix formed by residues 130 - 144 (chain B) in PDB entry 4EMX
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 ASN 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B ALA 3.1 5.3 + - - +
127B PHE 3.5 2.2 - - - -
129B ASP* 1.3 92.3 + - - +
131B GLU* 1.3 64.2 + - - +
132B GLU* 3.2 16.0 + - - +
133B THR* 3.1 34.4 + - + +
134B PHE* 3.0 24.3 + - - +
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Residues in contact with GLU 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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127B PHE* 3.0 57.4 + - + +
128B HIS* 4.8 5.5 + - - -
129B ASP 4.2 0.2 - - - -
130B ASN* 1.3 70.3 + - - +
132B GLU* 1.3 76.7 + - - +
134B PHE* 3.3 4.7 + - - +
135B LEU* 3.0 35.4 + - + +
162B LYS* 4.4 20.3 + - + +
166B THR* 5.1 2.2 + - - -
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Residues in contact with GLU 132 (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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130B ASN* 3.2 10.7 + - - +
131B GLU* 1.3 101.9 + - - +
133B THR* 1.3 61.5 + - - +
135B LEU* 3.5 4.5 + - - +
136B LYS* 3.1 37.3 + - - +
162B LYS* 5.2 6.6 + - - -
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Residues in contact with THR 133 (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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36B PHE* 3.8 20.9 - - + -
130B ASN* 3.1 29.4 + - - +
132B GLU* 1.3 73.0 - - - +
134B PHE* 1.3 62.3 + - - +
136B LYS* 3.3 12.4 + - - +
137B LYS* 2.9 28.7 + - + +
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Residues in contact with PHE 134 (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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123B MET* 3.6 25.6 - - + -
126B ALA* 3.7 16.2 - - + +
127B PHE* 3.5 37.2 - + - +
130B ASN 3.0 16.8 + - - +
131B GLU 3.6 4.3 - - - +
132B GLU 3.3 0.2 - - - -
133B THR* 1.3 78.1 - - - +
135B LEU* 1.3 64.6 + - + +
137B LYS* 3.5 8.7 + - + +
138B TYR* 3.4 17.3 + - - +
161B TYR* 3.5 39.2 + + - -
165B PHE* 3.7 33.2 - + - -
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Residues in contact with LEU 135 (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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127B PHE* 4.0 18.8 - - + -
131B GLU* 3.0 21.9 + - + +
132B GLU* 4.0 4.5 - - - +
134B PHE* 1.3 84.8 - - + +
136B LYS* 1.3 66.1 + - + +
138B TYR* 3.0 17.4 + - + +
139B LEU* 3.0 18.7 + - + +
158B ALA* 3.2 41.7 - - + +
161B TYR* 4.0 15.0 - - + -
162B LYS* 3.7 32.1 - - + -
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Residues in contact with LYS 136 (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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20B LYS* 3.7 36.2 - - - +
24B LEU* 3.5 20.6 - - + +
36B PHE* 3.6 14.1 - - + -
40B VAL* 4.6 22.7 - - + +
43B VAL* 5.8 6.3 - - - +
44B ASN* 4.0 13.7 + - - +
132B GLU* 3.1 30.5 + - - +
133B THR* 3.6 11.2 - - - +
135B LEU* 1.3 75.6 - - - +
137B LYS* 1.3 57.0 + - - +
139B LEU* 3.4 8.6 + - + +
140B TYR* 3.0 29.1 + - - +
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Residues in contact with LYS 137 (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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36B PHE* 3.7 21.7 - - + -
133B THR* 2.9 17.8 + - + +
134B PHE* 3.7 9.6 - - + +
135B LEU 3.2 0.4 - - - -
136B LYS* 1.3 74.3 - - - +
138B TYR* 1.3 61.3 + - - +
140B TYR* 3.8 2.4 - - + +
141B GLU* 2.9 42.5 + - + +
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Residues in contact with TYR 138 (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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134B PHE 3.4 4.0 + - - +
135B LEU* 3.0 11.6 + - + +
137B LYS* 1.3 76.9 - - - +
139B LEU* 1.3 68.5 + - - +
141B GLU* 4.0 3.8 - - - +
142B ILE* 3.2 51.3 + - + +
154B LEU* 4.3 12.7 - - + +
157B PHE* 3.7 20.4 + - - +
158B ALA* 3.7 37.2 - - + -
161B TYR* 3.4 59.7 - + + +
185B LEU* 4.3 13.8 + - + +
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Residues in contact with LEU 139 (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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21B ALA* 3.7 38.4 - - + +
24B LEU* 3.8 14.8 - - + -
25B ILE* 4.2 11.0 - - + -
135B LEU* 3.0 13.0 + - + +
136B LYS* 3.5 13.7 - - + +
138B TYR* 1.3 81.8 - - + +
140B TYR* 1.3 56.9 + - - +
142B ILE* 3.5 2.1 + - - +
143B ALA* 3.0 32.4 + - - +
154B LEU* 3.8 35.7 - - + +
155B LEU* 5.0 2.5 - - + -
158B ALA* 3.8 27.1 - - + -
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Residues in contact with TYR 140 (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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24B LEU* 4.3 10.5 - - + -
28B ALA* 3.8 15.5 - - + -
31B LEU 5.5 0.2 - - - -
34B CYS 2.7 19.8 + - - -
35B PRO* 3.3 10.0 - - - +
36B PHE* 3.6 41.1 - + + -
39B HIS* 3.4 34.5 - + - -
136B LYS 3.0 17.4 + - - +
137B LYS* 3.8 4.0 - - + +
139B LEU* 1.3 77.8 - - - +
141B GLU* 1.3 85.3 + - - +
143B ALA* 4.0 0.6 - - - +
144B ARG* 3.1 67.5 + - + +
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Residues in contact with GLU 141 (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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115B LEU* 3.8 26.7 - - + -
137B LYS* 2.9 29.8 + - + +
138B TYR* 4.0 4.9 - - + +
140B TYR* 1.3 96.0 - - - +
142B ILE* 1.3 63.5 + - + +
144B ARG* 3.4 14.8 + - - +
145B ARG* 2.7 65.0 + - - +
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Residues in contact with ILE 142 (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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115B LEU* 5.0 11.0 - - + -
138B TYR* 3.2 46.2 + - + +
139B LEU 4.0 2.9 - - - +
141B GLU* 1.3 82.4 - - + +
143B ALA* 1.3 60.1 + - - +
145B ARG* 3.1 3.0 + - - -
146B HIS* 2.9 41.8 + - + +
149B PHE* 3.6 35.9 - - + -
154B LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 143 (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 ILE* 4.1 19.1 - - + -
28B ALA* 3.8 20.9 - - + -
29B GLN* 3.3 26.1 - - + +
139B LEU 3.0 18.8 + - - +
142B ILE* 1.3 74.9 - - - +
144B ARG* 1.3 61.9 + - - +
146B HIS 3.2 24.5 - - - +
147B PRO* 3.4 1.9 - - - +
154B LEU* 4.4 6.9 - - + +
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Residues in contact with ARG 144 (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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28B ALA* 3.6 22.9 + - + +
32B GLN* 2.9 53.7 + - - +
33B GLN* 4.1 12.3 + - - +
34B CYS 4.6 0.6 + - - -
35B PRO* 5.5 1.0 - - - +
110B PRO* 3.6 6.6 - - - +
112B LEU* 3.0 44.0 - - + +
113B PRO* 5.7 3.0 - - - +
140B TYR* 3.1 62.5 + - + +
141B GLU* 3.4 28.2 + - - +
143B ALA* 1.3 75.9 - - - +
145B ARG* 1.3 64.4 + - - +
146B HIS 3.4 0.2 - - - -
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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
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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