Contacts of the helix formed by residues 136 - 153 (chain B) in PDB entry 1EAK
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 ASP 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B LEU* 1.3 73.2 - - - +
137B PRO* 1.3 76.1 - - + +
138B GLU* 2.9 16.8 + - - +
139B THR* 2.7 40.0 + - - -
140B VAL* 3.0 10.4 + - - +
222B ARG* 3.4 43.0 + - + +
232B TYR* 4.2 1.2 - - - -
333B PRO* 3.5 9.2 - - + +
334B GLU* 4.2 20.6 + - + +
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Residues in contact with PRO 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR* 3.3 19.7 - - + -
135B LEU 3.8 0.9 - - - +
136B ASP* 1.3 89.8 - - + +
138B GLU* 1.3 60.7 + - + +
141B ASP* 2.9 36.5 + - - +
314B TYR* 3.5 41.1 - - + +
333B PRO* 3.0 35.4 - - + +
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Residues in contact with GLU 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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136B ASP* 3.1 8.9 - - - +
137B PRO* 1.3 78.3 - - + +
139B THR* 1.3 67.2 + - - +
141B ASP* 3.5 7.2 - - - +
142B ASP* 2.9 26.0 + - - +
222B ARG* 2.7 35.6 + - - +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.1 27.8 - - + -
136B ASP* 2.7 32.7 + - - -
138B GLU* 1.3 78.1 - - - +
140B VAL* 1.3 64.2 + - - +
142B ASP* 3.3 6.2 + - - +
143B ALA* 3.0 21.0 + - + +
146B ARG* 5.8 0.2 + - - -
215B LEU* 4.5 17.0 - - + +
222B ARG* 4.5 3.1 + - - +
232B TYR* 2.3 39.3 + - + +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR* 3.7 28.7 - - + -
132B THR* 3.9 14.8 - - + +
135B LEU* 3.3 43.3 - - + +
136B ASP 3.0 5.2 + - - +
139B THR* 1.3 74.5 - - - +
141B ASP* 1.3 66.7 + - - +
143B ALA* 2.9 14.4 + - - +
144B PHE* 3.2 41.3 + - + -
173B PHE* 4.4 6.7 - - + -
397B LEU* 3.7 12.8 - - + -
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Residues in contact with ASP 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 4.7 4.0 + - - -
128B ILE* 4.0 7.3 - - - +
131B TYR* 2.4 34.6 + - - -
137B PRO 2.9 19.6 + - - +
138B GLU* 3.5 9.2 - - - +
140B VAL* 1.3 79.2 - - - +
142B ASP* 1.3 61.3 + - - +
144B PHE* 3.6 8.0 + - - +
145B ALA* 3.2 19.8 + - - +
161B ARG* 2.6 41.5 + - - +
314B TYR* 4.6 4.4 + - - -
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Residues in contact with ASP 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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138B GLU 2.9 17.6 + - - +
139B THR* 3.8 6.6 - - - +
141B ASP* 1.3 73.8 - - - +
143B ALA* 1.3 68.6 + - - +
145B ALA* 3.0 8.9 + - - +
146B ARG* 2.5 66.1 + - - +
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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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135B LEU* 5.6 0.7 - - + -
139B THR 3.0 13.2 + - - +
140B VAL 2.9 10.7 + - - +
142B ASP* 1.3 82.4 + - - +
144B PHE* 1.3 64.9 + - - +
146B ARG* 3.2 11.6 + - - +
147B ALA* 2.9 24.4 + - - +
215B LEU* 5.0 6.1 - - + -
397B LEU* 4.1 25.1 - - + -
398B PHE* 3.8 20.7 - - + +
401B ALA* 5.5 0.4 - - - -
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Residues in contact with PHE 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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126B TYR* 4.9 5.8 - - + -
128B ILE* 4.2 19.3 - - + -
140B VAL* 3.2 39.7 + - + -
141B ASP* 4.0 4.7 - - - +
143B ALA* 1.3 79.0 - - - +
145B ALA* 1.3 62.9 + - - +
147B ALA* 3.2 1.0 + - - -
148B PHE* 3.0 32.0 + - + -
171B ILE* 3.4 38.4 - - + -
173B PHE* 3.5 27.4 - + - -
207B PHE* 3.6 24.7 - + - -
397B LEU* 3.7 16.6 - - + -
401B ALA* 3.7 6.7 - - + -
405B PHE* 3.5 22.4 - + + -
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Residues in contact with ALA 145 (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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126B TYR* 4.0 16.5 + - - +
141B ASP 3.2 12.9 + - - +
142B ASP* 3.1 14.6 - - - +
144B PHE* 1.3 78.9 - - - +
146B ARG* 1.3 60.4 + - + +
148B PHE* 3.3 7.7 + - - +
149B GLN* 3.1 23.7 + - - +
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Residues in contact with ARG 146 (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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139B THR 5.8 0.2 + - - -
142B ASP* 2.5 49.6 + - - +
143B ALA* 3.9 6.9 - - - +
145B ALA* 1.3 73.5 - - + +
147B ALA* 1.3 63.7 + - - +
149B GLN* 3.3 19.4 - - - +
150B VAL* 3.2 18.0 + - - +
215B LEU* 4.3 19.8 - - - +
398B PHE* 3.2 49.8 - - + +
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Residues in contact with ALA 147 (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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143B ALA 2.9 16.6 + - - +
144B PHE 3.2 4.9 + - - +
146B ARG* 1.3 75.1 - - - +
148B PHE* 1.3 65.4 + - - +
150B VAL* 3.3 18.2 - - - +
151B TRP* 3.5 12.5 + - - -
398B PHE* 3.3 17.4 - - + +
401B ALA* 4.0 3.1 - - + -
402B ALA* 3.4 31.5 - - - +
405B PHE* 3.6 13.5 - - + -
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 3.5 52.0 - + + -
144B PHE 3.0 25.3 + - - -
145B ALA* 3.6 7.4 - - - +
147B ALA* 1.3 74.9 - - - +
149B GLN* 1.3 68.2 + - - +
151B TRP* 2.8 18.5 + + - +
152B SER* 3.1 12.5 + - - -
159B PHE* 3.3 45.4 - + + -
169B ILE* 3.6 25.1 - - + -
171B ILE* 3.8 2.9 - - + -
405B PHE* 3.3 49.8 - + + -
409B MET* 5.6 0.2 - - - -
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Residues in contact with GLN 149 (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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145B ALA 3.1 14.1 + - - +
146B ARG* 3.3 25.2 - - - +
148B PHE* 1.3 76.2 - - - +
150B VAL* 1.3 64.8 + - - +
151B TRP 2.8 0.3 + - - -
152B SER* 2.9 11.8 + - - +
153B ASP* 2.8 53.7 + - - +
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Residues in contact with VAL 150 (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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146B ARG 3.3 15.3 - - - +
147B ALA* 3.3 13.7 - - - +
148B PHE 3.1 0.2 + - - -
149B GLN* 1.3 77.4 - - - +
151B TRP* 1.3 63.1 + - + +
153B ASP* 3.9 16.5 + - - +
154B VAL* 4.4 4.0 + - - +
398B PHE* 3.4 26.2 - - + -
402B ALA* 4.4 3.6 - - + -
420B LEU* 4.5 6.5 - - + -
431B PHE* 3.7 19.5 - - + -
433B LEU* 3.5 40.2 - - + +
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Residues in contact with TRP 151 (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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147B ALA 3.5 15.9 + - - -
148B PHE* 2.8 10.2 + - - +
150B VAL* 1.3 81.1 - - + +
152B SER* 1.3 61.5 + - - +
153B ASP 3.1 2.6 + - - -
154B VAL* 3.4 5.3 + - - +
155B THR* 2.8 27.7 + - - +
157B LEU* 4.9 2.9 - - + -
159B PHE* 4.4 13.7 - + + -
402B ALA* 2.9 21.7 + - - +
405B PHE* 4.2 13.2 - - + -
406B GLY* 3.5 23.0 - - - +
409B MET* 5.1 3.8 - - + -
411B LEU* 3.0 21.5 - - + -
420B LEU* 3.7 24.1 - - + +
421B MET* 4.3 8.3 - - + -
433B LEU* 4.1 13.2 - - + -
437B ASP* 4.2 17.9 - - + -
441B ILE* 3.3 52.3 - - + -
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Residues in contact with SER 152 (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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148B PHE 3.1 5.3 + - - -
149B GLN* 3.1 29.6 + - - +
151B TRP* 1.3 72.8 - - - +
153B ASP* 1.3 64.9 + - - +
155B THR* 3.0 20.0 - - - +
157B LEU 3.3 24.3 - - - +
158B ARG* 5.1 1.6 - - - -
159B PHE* 4.0 17.0 - - - -
448B SER* 5.2 0.9 - - - -
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Residues in contact with ASP 153 (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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149B GLN* 2.8 50.6 + - - +
150B VAL* 3.9 11.6 + - - +
151B TRP 3.1 0.2 - - - -
152B SER* 1.3 78.2 + - - +
154B VAL* 1.3 64.3 + - + +
448B SER* 3.7 13.4 + - - -
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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