Contacts of the helix formed by residues 119 - 132 (chain D) in PDB entry 1EJI
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 SER 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C TYR* 3.9 13.9 + - - -
305C HIS* 3.5 20.4 + - - -
117D PRO* 3.1 1.6 + - - +
118D TYR* 1.3 80.4 - - - +
120D GLY* 1.3 63.2 + - - +
122D PRO* 3.2 15.6 - - - +
123D ALA* 3.2 21.0 + - - +
256D HIS* 4.1 6.9 - - - -
263D ARG* 5.3 0.3 + - - -
264D ALA 3.7 10.2 + - - -
265D GLY* 3.8 9.5 - - - -
503D PLG 2.4 26.6 + - - -
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Residues in contact with GLY 120 (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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119D SER* 1.3 78.3 + - - +
121D SER* 1.3 66.3 + - - +
123D ALA* 3.0 17.4 + - - +
124D ASN* 3.2 14.4 + - - -
253D THR 4.8 2.2 - - - -
254D THR* 3.4 19.4 - - - +
264D ALA 4.1 0.4 + - - -
265D GLY* 4.8 0.9 - - - -
503D PLG 3.1 26.4 + - - -
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Residues in contact with SER 121 (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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300C LEU 3.7 20.6 - - - -
301C GLN 3.8 2.0 + - - -
302C GLY* 3.4 16.7 + - - -
120D GLY* 1.3 70.5 - - - -
122D PRO* 1.3 71.9 - - - +
124D ASN* 3.2 5.4 + - - +
125D PHE* 3.0 23.1 + - - +
148D HIS* 4.1 4.5 - - - -
150D THR* 3.2 33.5 - - - +
503D PLG 2.9 22.8 + - - -
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Residues in contact with PRO 122 (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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118C TYR* 3.8 28.0 - - + -
300C LEU 5.3 3.6 - - - +
301C GLN* 5.6 0.7 - - + -
117D PRO* 4.7 0.9 - - - -
118D TYR* 4.3 4.3 - - + +
119D SER* 3.2 32.1 - - - +
121D SER* 1.3 95.9 - - - +
123D ALA* 1.3 62.6 + - - +
125D PHE* 3.9 6.1 - - + +
126D ALA* 2.9 25.2 + - - +
300D LEU* 5.5 0.5 - - - +
301D GLN* 4.3 17.3 - - + +
503D PLG 4.1 0.4 - - - +
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Residues in contact with ALA 123 (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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117D PRO* 3.8 13.6 - - + +
119D SER 3.2 10.7 + - - +
120D GLY* 3.0 11.3 + - - +
122D PRO* 1.3 77.6 - - - +
124D ASN* 1.3 63.3 + - - +
126D ALA* 3.1 16.7 - - - +
127D VAL* 3.2 8.8 + - - +
252D THR* 4.5 7.6 - - - -
253D THR 4.9 1.6 - - - +
265D GLY* 4.7 0.2 - - - -
266D MSE 4.2 12.8 - - - +
267D ILE* 3.3 33.9 - - + +
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Residues in contact with ASN 124 (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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120D GLY 3.2 5.9 + - - +
121D SER 3.2 7.1 + - - +
123D ALA* 1.3 74.0 - - - +
125D PHE* 1.3 57.4 + - - +
127D VAL* 2.8 27.0 + - - +
128D TYR* 3.0 40.9 + - + +
150D THR* 3.0 27.3 + - - -
151D HIS* 4.5 0.4 - - - -
226D MSE 3.7 5.9 - - - +
228D ASP* 2.8 23.3 + - - +
252D THR* 2.7 29.8 + - - -
503D PLG 3.7 10.1 - - - -
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Residues in contact with PHE 125 (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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125C PHE* 4.3 13.2 - + - -
166C PHE* 3.9 13.2 - + - -
300C LEU* 4.7 8.5 - - + +
121D SER 3.0 12.4 + - - +
122D PRO* 3.9 6.5 - - + +
124D ASN* 1.3 79.4 - - - +
126D ALA* 1.3 56.8 + - - +
128D TYR* 3.4 12.7 + + - +
129D THR* 2.9 51.1 + - - -
150D THR* 5.9 0.2 - - - +
162D ALA* 4.0 23.6 - - + -
163D THR* 4.8 5.4 - - - -
166D PHE* 3.7 29.6 - + - -
167D PHE* 3.9 24.7 - + - -
300D LEU* 3.8 25.4 - - + -
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Residues in contact with ALA 126 (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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117D PRO* 5.6 0.9 - - + -
122D PRO 2.9 13.6 + - - +
123D ALA* 3.1 12.1 - - - +
125D PHE* 1.3 79.5 - - - +
127D VAL* 1.3 58.2 + - - +
129D THR* 3.5 0.3 - - - -
130D ALA* 3.0 21.8 + - - +
267D ILE* 3.9 15.0 - - + -
292D ILE* 5.5 1.1 - - + -
295D ALA* 3.4 15.0 - - + +
296D VAL* 4.3 16.2 - - + -
300D LEU* 3.7 21.3 - - + +
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Residues in contact with VAL 127 (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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123D ALA 3.5 13.0 - - - +
124D ASN 2.8 13.1 + - - +
126D ALA* 1.3 70.2 - - - +
128D TYR* 1.3 61.4 + - - +
130D ALA* 3.0 5.6 + - - +
131D LEU* 2.7 53.9 + - + +
197D LEU* 4.2 8.5 - - + -
226D MSE 3.9 21.5 - - - -
250D VAL* 4.2 9.0 - - + -
252D THR* 3.8 12.6 - - + -
267D ILE* 3.7 30.7 - - + -
292D ILE* 4.6 6.5 - - + -
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Residues in contact with TYR 128 (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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124D ASN* 3.0 31.7 + - + +
125D PHE* 3.8 10.8 - + - +
127D VAL* 1.3 75.9 - - - +
129D THR* 1.3 59.5 + - - +
132D VAL* 2.7 32.8 + - - +
133D GLU 3.1 8.0 + - - -
138D ILE* 3.8 18.8 - - + -
150D THR* 2.7 30.9 + - - -
151D HIS* 3.9 1.0 - - - -
163D THR* 3.6 24.2 - - + -
167D PHE* 3.5 22.6 - + + -
197D LEU* 4.3 13.0 - - + -
199D ILE* 3.4 24.5 - - + +
226D MSE 3.6 31.1 - - + +
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Residues in contact with THR 129 (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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162C ALA* 5.8 0.4 - - + -
165C ILE* 4.9 14.4 - - + -
166C PHE* 3.4 22.0 - - + -
125D PHE* 2.9 46.5 + - - -
126D ALA 3.5 4.9 - - - -
128D TYR* 1.3 79.7 - - - +
130D ALA* 1.3 61.4 + - - +
133D GLU* 4.0 16.4 + - - +
134D PRO* 5.5 0.7 - - - +
167D PHE* 3.8 8.4 - - - -
295D ALA* 4.4 9.6 - - + -
299D GLY* 6.3 0.9 - - - -
300D LEU* 3.8 18.0 - - + +
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Residues in contact with ALA 130 (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 ALA 3.0 15.8 + - - +
127D VAL 3.0 4.7 + - - +
129D THR* 1.3 78.7 - - - +
131D LEU* 1.3 62.5 + - - +
133D GLU* 4.7 9.4 - - - +
291D LEU* 3.5 52.9 - - + +
292D ILE* 3.7 14.1 - - + +
295D ALA* 3.5 9.0 - - + -
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Residues in contact with LEU 131 (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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127D VAL* 2.7 39.1 + - + +
130D ALA* 1.3 81.7 - - + +
132D VAL* 1.3 61.4 + - - +
133D GLU* 4.5 3.8 - - - +
196D LYS* 3.6 20.3 + - - +
197D LEU* 4.6 11.0 - - + -
224D TYR* 4.1 35.9 - - + -
250D VAL* 4.1 12.6 - - + -
288D LEU* 3.6 34.1 - - + -
291D LEU* 4.0 24.9 - - + -
292D ILE* 4.4 9.2 - - + -
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Residues in contact with VAL 132 (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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128D TYR* 2.7 22.9 + - - +
131D LEU* 1.3 76.2 - - - +
133D GLU* 1.3 72.5 + - - +
136D GLY* 3.3 39.0 - - - +
137D ARG 4.0 3.6 - - - +
138D ILE* 3.8 26.5 - - + -
167D PHE* 3.7 9.9 - - + -
196D LYS* 3.2 24.4 + - + +
197D LEU* 3.8 30.3 - - + -
224D TYR* 6.5 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