Contacts of the helix formed by residues 130 - 143 (chain D) in PDB entry 5E6J
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 ALA 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D TYR 4.3 2.5 - - - +
73D TYR 4.2 10.8 - - - +
74D HIS* 3.8 13.4 + - + +
128D PHE* 3.5 1.7 - - - +
129D ASN* 1.3 78.1 - - - +
131D PRO* 1.3 71.1 - - + +
133D LEU* 3.0 30.1 + - + +
134D GLN* 3.0 13.0 + - - +
155D TYR* 4.0 20.6 - - - +
176D HIS* 3.9 7.8 + - + +
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Residues in contact with PRO 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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15A THR* 6.0 6.1 - - + -
71D GLU 3.7 21.1 - - - +
72D TYR* 3.4 32.5 - - + +
74D HIS* 4.0 7.0 - - - +
129D ASN 3.3 9.2 - - - +
130D ALA* 1.3 81.1 - - - +
132D ALA* 1.3 56.7 + - - +
134D GLN* 3.3 7.0 + - + +
135D GLU* 2.9 33.5 + - - +
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Residues in contact with ALA 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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72D TYR* 3.4 47.7 + - + +
73D TYR* 3.9 16.4 - - + -
130D ALA 3.2 0.8 - - - -
131D PRO* 1.3 77.4 - - - +
133D LEU* 1.3 59.2 + - - +
135D GLU* 3.9 1.3 - - - +
136D ALA* 2.8 33.4 + - - +
151D LEU* 3.5 14.4 - - + +
155D TYR* 4.4 5.8 - - - +
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Residues in contact with LEU 133 (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 PHE* 3.7 28.9 - - + -
130D ALA* 3.0 15.7 + - + +
132D ALA* 1.3 79.6 - - - +
134D GLN* 1.3 52.9 + - - +
136D ALA* 4.5 0.2 - - - -
137D TYR* 2.7 37.7 + - - +
148D PHE* 3.7 25.0 - - + -
151D LEU* 4.2 13.9 - - + -
152D ILE* 5.2 1.3 - - + +
155D TYR* 3.7 37.7 - - + -
173D LEU* 4.8 11.2 - - + +
176D HIS* 3.5 34.5 - - + -
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Residues in contact with GLN 134 (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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135A GLU* 6.0 0.9 - - - +
126D VAL 4.3 2.6 - - - +
127D LYS* 3.4 26.5 - - - +
128D PHE* 2.6 56.3 + - + +
130D ALA 3.0 8.7 + - - +
131D PRO* 3.7 9.9 - - + +
133D LEU* 1.3 76.4 - - - +
135D GLU* 1.3 58.0 + - - +
137D TYR* 3.3 7.9 + - - +
138D TYR* 2.9 79.7 + - + -
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Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 4.4 12.3 + - - -
134A GLN* 4.7 4.0 - - - +
138A TYR* 3.9 30.8 + - + -
15D THR* 5.5 1.4 + - - -
72D TYR* 3.3 25.7 + - - +
131D PRO 2.9 16.1 + - - +
132D ALA* 4.1 2.7 - - - +
134D GLN* 1.3 76.2 - - - +
136D ALA* 1.3 58.4 + - - +
138D TYR* 3.3 9.4 + - - +
139D ARG* 2.8 40.4 + - - +
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Residues in contact with ALA 136 (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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132D ALA 2.8 19.1 + - - +
135D GLU* 1.3 76.8 - - - +
137D TYR* 1.3 52.1 + - - +
139D ARG* 3.2 13.0 + - - +
140D ALA* 2.7 34.3 + - - +
145D ALA* 4.9 1.0 - - - -
147D ASN* 4.5 7.0 - - + -
148D PHE* 3.6 27.9 + - + +
151D LEU* 3.4 22.2 - - + -
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Residues in contact with TYR 137 (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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118D LEU* 6.1 1.6 - - + -
121D LEU* 2.9 41.4 + - + -
122D GLN* 4.4 4.3 - - + -
124D LEU 3.6 8.1 + - - -
126D VAL* 4.0 22.7 - - + +
128D PHE* 4.1 20.0 - + + -
133D LEU 2.7 24.9 + - - +
134D GLN* 3.5 15.0 - - - +
136D ALA* 1.3 69.6 - - - +
138D TYR* 1.3 64.9 + + - +
140D ALA* 2.9 7.6 + - + +
141D ARG* 2.8 80.9 + - + +
148D PHE* 3.5 28.2 - + + -
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Residues in contact with TYR 138 (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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135A GLU* 3.5 39.5 + - + -
138A TYR* 4.0 24.7 - + + +
139A ARG* 3.8 41.0 + - + +
142A ALA* 4.7 1.0 - - - +
127D LYS* 4.2 11.7 + - - +
134D GLN* 2.9 47.9 + - + +
135D GLU* 3.6 7.6 - - - +
137D TYR* 1.3 83.7 - + - +
139D ARG* 1.3 61.4 + - - +
141D ARG* 3.5 24.3 + - - +
142D ALA* 3.4 19.8 + - - +
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Residues in contact with ARG 139 (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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138A TYR* 3.5 45.6 + - + -
135D GLU* 2.8 28.0 + - - +
136D ALA* 3.4 12.3 - - - +
138D TYR* 1.3 74.8 - - - +
140D ALA* 1.3 61.5 + - - +
142D ALA* 3.3 8.8 + - - +
143D GLY 3.3 5.2 + - - -
144D ASP* 2.8 56.7 + - + +
145D ALA 4.0 2.7 - - - +
147D ASN* 3.2 40.9 + - + +
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Residues in contact with ALA 140 (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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103D THR* 3.1 18.2 + - - +
118D LEU* 4.4 10.5 - - + -
122D GLN* 4.7 0.7 - - - -
136D ALA 2.7 17.5 + - - +
137D TYR* 2.9 15.9 + - + +
139D ARG* 1.3 70.8 - - - +
141D ARG* 1.3 58.2 + - + +
142D ALA 3.0 4.3 - - - -
143D GLY* 2.9 17.7 + - - -
145D ALA* 3.5 29.4 - - + +
148D PHE* 4.1 15.3 - - + -
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Residues in contact with ARG 141 (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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142A ALA* 4.0 26.3 - - + +
98D GLN* 5.0 2.4 + - - +
103D THR* 4.0 5.9 + - - -
122D GLN* 3.2 45.2 + - + +
123D GLN* 5.3 1.0 - - - +
124D LEU 4.8 7.1 + - - -
126D VAL 5.7 0.4 + - - -
137D TYR* 2.8 66.8 + - + +
138D TYR* 3.9 21.4 - - - +
139D ARG 3.4 0.2 - - - -
140D ALA* 1.3 75.4 - - - +
142D ALA* 1.3 59.5 + - - +
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Residues in contact with ALA 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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138A TYR* 4.4 5.8 - - + +
141A ARG* 4.0 33.1 - - + +
142A ALA* 4.1 10.7 - - - +
98D GLN* 3.9 8.2 + - - -
138D TYR 3.4 10.3 + - - +
139D ARG* 3.3 13.9 + - - +
140D ALA 3.0 0.6 - - - -
141D ARG* 1.3 80.4 - - - +
143D GLY* 1.3 55.8 + - - +
144D ASP* 4.8 1.6 - - + +
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Residues in contact with GLY 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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96D PHE* 3.6 21.1 - - - +
98D GLN* 3.4 20.9 - - - -
103D THR* 3.5 9.6 - - - -
140D ALA 2.9 6.0 + - - -
141D ARG 3.4 0.2 - - - -
142D ALA* 1.3 79.6 - - - +
144D ASP* 1.3 65.0 + - - +
145D ALA 4.0 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