Contacts of the helix formed by residues 136 - 153 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D LEU* 1.3 73.9 - - - +
137D PRO* 1.3 77.1 - - + +
138D GLU* 3.4 13.2 + - - +
139D THR* 2.7 40.3 + - - -
140D VAL* 3.0 20.8 + - - +
222D ARG* 3.2 39.4 + - + +
232D TYR* 4.0 2.6 - - - -
333D PRO* 3.7 6.7 - - + -
334D GLU* 3.2 21.1 + - + +
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Residues in contact with PRO 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D TYR* 3.6 22.4 - - + +
135D LEU 4.0 0.4 - - - +
136D ASP* 1.3 87.6 - - + +
138D GLU* 1.3 55.7 + - + +
140D VAL* 3.1 3.5 + - - +
141D ASP* 2.7 41.7 + - - +
314D TYR* 3.7 40.6 - - + +
333D PRO* 3.4 32.1 - - + +
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Residues in contact with GLU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ASP* 3.3 10.3 - - - +
137D PRO* 1.3 79.4 - - + +
139D THR* 1.3 53.9 + - - +
141D ASP* 3.0 11.1 + - - +
142D ASP* 2.7 37.7 + - - +
222D ARG* 3.2 32.0 + - - +
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Residues in contact with THR 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D LEU* 4.3 18.4 - - + -
136D ASP* 2.7 37.8 + - - -
138D GLU* 1.3 76.9 - - - +
140D VAL* 1.3 59.2 + - - +
142D ASP* 3.7 6.8 - - + +
143D ALA* 2.7 33.3 + - - +
146D ARG* 5.8 1.8 - - - +
215D LEU* 4.2 24.2 - - + -
222D ARG* 4.4 3.4 + - - +
232D TYR* 3.1 30.2 + - + +
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Residues in contact with VAL 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D TYR* 3.3 36.1 - - + -
132D THR* 4.1 7.9 - - + +
135D LEU* 3.3 33.0 - - + +
136D ASP 3.0 15.7 + - - +
137D PRO 3.5 0.4 - - - +
139D THR* 1.3 75.6 - - - +
141D ASP* 1.3 62.4 + - - +
143D ALA* 3.6 6.0 + - - +
144D PHE* 3.0 56.3 + - + -
173D PHE* 4.2 7.4 - - + -
397D LEU* 3.9 11.2 - - + -
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Residues in contact with ASP 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D TYR* 4.6 4.2 + - - -
128D ILE* 3.0 22.1 - - - +
131D TYR* 2.3 33.5 + - - -
137D PRO* 2.7 29.3 + - - +
138D GLU* 3.0 11.3 + - - +
140D VAL* 1.3 72.1 - - - +
142D ASP* 1.3 53.9 + - - +
144D PHE* 3.2 4.5 + - - +
145D ALA* 2.7 33.9 + - - +
161D ARG* 3.1 30.4 + - - +
314D TYR* 4.5 1.9 + - - -
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Residues in contact with ASP 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D GLU 2.7 19.6 + - - +
139D THR* 3.8 7.0 - - - +
141D ASP* 1.3 68.7 - - - +
143D ALA* 1.3 58.8 + - - +
145D ALA* 2.7 9.8 + - - +
146D ARG* 2.5 85.5 + - - +
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 5.6 0.9 - - + -
139D THR* 2.7 21.9 + - + +
140D VAL* 3.7 5.8 - - - +
142D ASP* 1.3 72.3 - - - +
144D PHE* 1.3 54.0 + - - +
146D ARG* 3.4 20.4 - - - +
147D ALA* 2.6 38.1 + - - +
215D LEU* 4.8 8.5 - - + -
397D LEU* 4.3 15.5 - - + -
398D PHE* 4.1 24.2 - - + +
401D ALA* 5.4 0.2 - - - -
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Residues in contact with PHE 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D TYR* 4.7 4.0 - - + -
128D ILE* 4.0 26.0 - - + -
140D VAL* 3.0 41.8 + - + -
141D ASP 3.5 6.1 - - - +
143D ALA* 1.3 78.6 - - - +
145D ALA* 1.3 60.9 + - - +
147D ALA* 3.4 4.4 - - - +
148D PHE* 2.9 33.2 + - - -
171D ILE* 3.3 31.4 - - + -
173D PHE* 3.7 24.5 - + - -
207D PHE* 3.3 32.5 - + - -
397D LEU* 3.9 9.0 - - + -
401D ALA* 3.7 7.9 - - + -
405D PHE* 3.4 20.2 - + + -
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TYR* 4.3 13.7 + - - +
141D ASP 2.7 18.4 + - - +
142D ASP* 2.7 18.5 + - - +
144D PHE* 1.3 69.8 - - - +
146D ARG* 1.3 66.2 + - + +
147D ALA 3.0 0.9 - - - -
148D PHE* 2.8 18.0 + - - +
149D GLN* 3.2 13.2 + - - +
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Residues in contact with ARG 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D THR* 4.9 1.8 + - - +
142D ASP* 2.5 64.3 + - - +
143D ALA* 3.4 23.8 - - - +
145D ALA* 1.3 72.2 - - + +
147D ALA* 1.3 63.2 + - - +
149D GLN* 3.1 36.0 + - - +
150D VAL* 3.5 5.2 + - - +
215D LEU* 4.6 17.4 - - - +
398D PHE* 3.5 47.8 - - + +
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ALA 2.6 23.7 + - - +
144D PHE* 3.4 3.8 - - - +
145D ALA 3.0 0.2 + - - -
146D ARG* 1.3 76.1 - - - +
148D PHE* 1.3 60.8 + - - +
149D GLN 3.4 0.2 + - - -
150D VAL* 3.6 9.5 + - - +
151D TRP* 3.6 17.0 + - - -
398D PHE* 3.6 16.3 - - + -
401D ALA* 3.8 4.5 - - + -
402D ALA* 3.7 18.9 - - - +
405D PHE* 3.4 28.5 - - + -
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Residues in contact with PHE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TYR* 3.5 50.9 - + + -
144D PHE 2.9 23.4 + - - -
145D ALA* 2.8 12.1 + - - +
147D ALA* 1.3 70.9 - - - +
149D GLN* 1.3 66.2 + - - +
151D TRP* 3.1 13.4 + + - +
152D SER* 3.8 1.7 + - - -
159D PHE* 3.4 58.8 - + + -
169D ILE* 3.6 26.9 - - + -
171D ILE* 3.8 2.0 - - + -
405D PHE* 3.3 50.7 - + + -
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Residues in contact with GLN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ALA* 3.2 10.6 + - - +
146D ARG* 3.1 28.4 + - - +
148D PHE* 1.3 76.0 - - - +
150D VAL* 1.3 55.6 + - + +
151D TRP 2.6 13.0 + - - -
152D SER* 3.1 6.2 + - - -
153D ASP* 2.8 45.5 + - - +
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Residues in contact with VAL 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ARG 3.5 14.5 + - - +
147D ALA 4.0 6.7 - - - +
148D PHE 3.3 0.8 - - - -
149D GLN* 1.3 74.6 - - + +
151D TRP* 1.3 62.2 + - + +
153D ASP* 4.3 15.4 + - - +
154D VAL* 4.8 2.3 - - - +
398D PHE* 3.7 25.4 - - + -
402D ALA* 5.4 2.5 - - + -
420D LEU* 5.1 4.5 - - + -
431D PHE* 3.6 28.7 - - + -
433D LEU* 3.4 35.7 - - + +
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Residues in contact with TRP 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ALA 3.6 19.5 + - - -
148D PHE* 3.1 10.3 + - - +
149D GLN 2.6 8.1 + - - -
150D VAL* 1.3 82.8 - - + +
152D SER* 1.3 52.2 + - - +
153D ASP 3.4 0.2 - - - -
154D VAL* 3.3 8.4 - - - +
155D THR* 2.7 32.6 + - - +
157D LEU* 4.6 0.7 - - + -
159D PHE* 4.1 15.3 - + + -
402D ALA* 2.5 27.4 + - - +
405D PHE* 3.7 15.7 - - + +
406D GLY* 3.3 19.9 - - - +
409D MET* 4.9 3.6 - - + -
411D LEU* 3.3 35.4 - - + -
420D LEU* 3.2 33.4 - - + -
421D MET* 4.1 6.7 - - + -
433D LEU* 4.2 15.0 - - + -
437D ASP* 4.8 2.0 - - + -
441D ILE* 3.4 37.4 - - + +
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Residues in contact with SER 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PHE 3.8 5.0 + - - -
149D GLN* 3.6 8.0 + - - -
151D TRP* 1.3 68.4 - - - +
153D ASP* 1.3 58.3 + - - +
154D VAL 2.5 10.9 + - - -
155D THR* 2.3 53.0 + - - +
157D LEU* 2.6 36.1 + - - -
158D ARG* 4.8 2.1 - - - -
159D PHE* 4.4 5.3 - - - -
448D SER* 3.5 2.8 - - - -
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Residues in contact with ASP 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLN* 2.8 47.8 + - - +
150D VAL* 4.3 12.1 + - - +
151D TRP 3.4 0.4 - - - -
152D SER* 1.3 78.5 + - - +
154D VAL* 1.3 62.1 + - + +
448D SER* 3.0 14.7 + - - -
450D ASP* 4.0 4.7 - - - +
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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