Contacts of the helix formed by residues 129 - 138 (chain D) in PDB entry 4B94
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 ARG 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B LYS* 5.8 1.0 - - - +
168B LYS* 6.0 1.8 - - - +
125D PRO 4.6 0.2 + - - -
126D ASP 5.5 2.0 - - - +
127D ASP 3.5 1.3 - - - -
128D ALA* 1.4 74.8 - - - +
130D ASP* 1.3 79.4 + - - +
132D PHE* 3.1 8.5 + - - +
133D GLN* 3.0 65.5 + - - +
136D ARG* 5.0 2.4 - - - +
149D PHE* 4.0 18.2 - - + -
152D PHE* 3.8 19.9 - - + -
153D GLU* 3.8 19.6 + - - +
161D LYS* 4.8 15.4 - - - +
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Residues in contact with ASP 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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133B GLN* 4.1 10.9 + - - +
136B ARG* 2.6 35.4 + - - +
161B LYS* 3.8 21.5 + - - +
165B LEU* 5.1 0.2 - - - +
168B LYS* 3.2 23.2 + - - +
127D ASP 4.4 6.3 + - - +
128D ALA 3.3 0.8 - - - -
129D ARG* 1.3 101.4 + - - +
131D TYR* 1.4 61.8 + - + +
133D GLN* 3.5 2.9 + - - +
134D MET* 2.9 27.4 + - - +
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Residues in contact with TYR 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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133B GLN* 3.7 39.4 + - + -
134B MET* 4.3 2.7 - - + -
136B ARG* 4.4 5.2 + - - -
137B ALA* 3.2 22.2 + - + +
1199B MLI 2.5 38.1 + - + +
113D GLN 4.7 0.5 - - - +
116D PHE* 3.6 26.9 - + + -
117D ALA* 3.7 24.3 - - + +
120D LYS* 3.9 25.6 - - + -
124D GLU* 4.4 0.2 - - - -
127D ASP 3.6 20.6 - - - -
128D ALA 3.1 10.1 + - - +
130D ASP* 1.4 73.3 - - + +
132D PHE* 1.3 61.0 + - - +
134D MET* 3.3 11.6 + - + +
135D ALA* 3.0 26.7 + - - +
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Residues in contact with PHE 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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114D VAL* 4.8 2.9 - - + -
117D ALA* 3.6 38.1 - - + -
118D GLU* 3.9 14.4 - - + -
121D ALA* 4.2 3.8 - - + -
128D ALA* 3.4 21.7 + - + -
129D ARG* 3.1 4.6 + - - +
131D TYR* 1.3 77.3 - - - +
133D GLN* 1.3 57.1 + - - +
135D ALA* 3.4 6.6 + - + +
136D ARG* 2.9 28.1 + - - +
145D VAL* 5.0 1.9 - - - +
148D SER* 3.2 31.4 - - - -
149D PHE* 3.5 43.1 - - + +
152D PHE* 3.4 44.4 - + + -
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Residues in contact with GLN 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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129D ARG* 3.0 41.9 + - - +
130D ASP* 3.7 7.0 - - - +
131D TYR 3.3 0.2 - - - -
132D PHE* 1.3 76.0 - - - +
134D MET* 1.4 58.0 + - - +
136D ARG* 2.6 39.1 + - - -
137D ALA* 2.9 35.9 + - - +
149D PHE* 3.6 9.3 - - + -
1203D GOL 3.0 28.3 + - - -
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Residues in contact with MET 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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129B ARG* 6.4 0.2 - - - -
130B ASP* 3.6 18.8 - - - +
133B GLN* 3.4 41.3 - - - +
134B MET* 3.9 20.2 - - + -
95D ILE* 4.2 17.3 - - + -
113D GLN* 3.9 19.5 - - + +
116D PHE* 4.6 4.3 - - + -
130D ASP 2.9 18.3 + - - +
131D TYR* 3.6 18.4 - - + +
133D GLN* 1.4 74.9 - - - +
135D ALA* 1.4 56.9 + - - +
137D ALA* 3.9 4.0 - - - +
138D ASN* 3.0 49.6 + - - +
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Residues in contact with ALA 135 (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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110D ALA 5.2 0.4 - - - +
113D GLN* 3.8 40.4 - - + +
114D VAL* 4.3 8.1 - - + -
131D TYR 3.0 14.0 + - - +
132D PHE* 3.6 11.0 - - + +
133D GLN 3.3 0.2 - - - -
134D MET* 1.4 76.8 - - - +
136D ARG* 1.4 55.8 + - - +
138D ASN 3.4 0.5 + - - -
139D CYS* 2.9 29.7 + - + +
145D VAL* 3.6 20.9 - - + +
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Residues in contact with ARG 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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129D ARG* 5.0 3.0 - - - +
132D PHE 2.9 16.9 + - - +
133D GLN* 2.6 33.5 + - - +
135D ALA* 1.4 75.5 - - - +
137D ALA* 1.3 62.9 + - - +
140D LYS* 3.1 21.8 + - - +
145D VAL* 3.6 14.5 - - + +
146D HIS* 3.4 42.4 + - + +
149D PHE* 4.0 15.9 - - + -
161D LYS* 4.9 5.9 - - - +
165D LEU* 3.5 28.2 + - - +
168D LYS* 3.6 35.4 - - - +
172D ARG* 4.8 0.2 - - - +
1203D GOL 3.1 39.1 + - - +
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Residues in contact with ALA 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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129B ARG* 5.4 4.0 + - - +
133D GLN* 2.9 34.6 + - - +
134D MET* 3.9 5.4 - - - +
136D ARG* 1.3 74.3 - - - +
138D ASN* 1.4 65.8 + - - +
139D CYS 3.8 0.2 + - - -
140D LYS* 4.6 9.0 + - - +
1203D GOL 3.7 16.6 + - - +
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Residues in contact with ASN 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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129B ARG* 2.9 39.3 + - - +
130B ASP* 2.9 29.7 + - - -
100D PRO* 4.0 7.6 - - + +
104D GLY* 3.3 24.4 - - - +
109D PHE* 4.2 4.5 - - + -
113D GLN* 2.8 34.5 + - - +
134D MET* 3.0 22.1 + - - +
135D ALA 4.0 0.4 - - - +
137D ALA* 1.4 80.2 - - - +
139D CYS* 1.3 59.7 + - - +
140D LYS* 3.8 0.9 - - - -
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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