Contacts of the helix formed by residues 127 - 139 (chain A) in PDB entry 1D02
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 THR 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A CYS 4.0 0.4 + - - -
124A LYS 2.9 21.0 + - - +
126A PHE* 1.3 78.8 - - - +
128A PRO* 1.3 71.1 - - - +
130A LEU* 3.3 20.6 + - - +
131A LEU* 2.9 21.1 + - - +
123B CYS* 3.5 30.1 - - + -
126B PHE* 3.8 17.5 - - + -
169B TRP* 3.4 32.2 + - + -
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Residues in contact with PRO 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE 3.4 2.6 - - - +
127A THR* 1.3 83.5 - - - +
129A GLY* 1.3 59.1 + - - +
131A LEU* 3.8 10.4 - - + +
132A LYS* 3.0 28.2 + - - +
126B PHE* 3.4 22.9 - - + -
146B LEU* 5.5 0.2 - - + -
169B TRP 3.3 16.8 - - - +
170B TYR* 3.6 17.9 - - - +
171B ASP* 3.8 15.3 - - + +
172B HIS* 5.0 3.1 - - + -
173B TYR* 3.8 23.6 - - + -
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO* 1.3 79.3 - - - +
130A LEU* 1.3 56.5 + - - +
132A LYS* 3.4 4.1 + - - +
133A ALA 3.0 21.5 + - - -
168B PHE* 3.3 43.1 - - - -
169B TRP 2.9 12.0 + - - -
171B ASP* 3.9 10.9 - - - +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 4.1 16.2 - - + -
53A TYR* 3.9 15.0 - - - +
80A VAL* 4.6 5.4 - - + -
124A LYS* 3.3 44.9 - - + +
125A LEU* 4.4 12.6 - - + -
127A THR* 3.2 13.8 + - - +
129A GLY* 1.3 73.1 - - - +
131A LEU* 1.3 62.0 + - - +
133A ALA* 4.3 2.2 - - + -
134A TYR* 2.8 53.4 + - + -
168B PHE* 3.9 14.6 - - + -
169B TRP* 3.7 26.0 - - + +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU 3.4 21.3 + - - +
126A PHE* 3.4 25.6 - - + +
127A THR 2.9 13.1 + - - +
128A PRO* 3.8 9.0 - - + +
130A LEU* 1.3 75.7 - - - +
132A LYS* 1.3 57.6 + - - +
134A TYR* 3.7 4.2 - - - +
135A ARG* 2.9 43.3 + - + +
146A LEU* 4.2 14.6 - - + -
147A PRO* 3.7 28.0 - - + -
148A PHE* 4.1 8.3 - - + -
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Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO* 3.0 17.3 + - - +
129A GLY* 3.6 5.2 - - - +
131A LEU* 1.3 78.8 - - - +
133A ALA* 1.3 61.4 + - - +
135A ARG* 3.5 6.0 + - - +
136A THR* 3.0 33.6 + - - +
171B ASP* 2.7 37.6 + - - +
172B HIS* 4.5 6.7 + - - -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.2 9.6 - - + -
52A LEU* 4.1 19.1 - - + -
129A GLY 3.0 17.4 + - - +
130A LEU* 3.3 5.8 + - - +
132A LYS* 1.3 75.2 - - - +
134A TYR* 1.3 59.3 + - + +
136A THR* 3.4 4.7 + - - -
137A ILE* 2.9 37.6 + - + +
168B PHE* 3.9 21.5 - - + -
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.5 28.7 - - + +
80A VAL* 4.2 9.3 - - + +
82A PRO* 3.7 18.5 - - - +
96A PHE* 3.4 36.2 - + + -
98A GLU* 3.8 7.3 + - - -
125A LEU* 3.2 30.6 - - + +
130A LEU* 2.8 44.8 + - + +
133A ALA* 1.3 74.3 - - + +
135A ARG* 1.3 58.3 + - - +
138A GLY* 2.7 32.7 + - - +
140A ILE 5.1 0.2 + - - -
147A PRO* 3.6 33.8 - - + +
148A PHE* 3.9 20.9 - + + -
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 2.9 27.3 + - - +
132A LYS* 3.9 5.4 - - - +
134A TYR* 1.3 75.6 - - - +
136A THR* 1.3 59.0 + - - +
139A GLY* 2.9 30.8 + - - +
140A ILE* 2.8 32.8 + - - +
141A ASN* 3.6 26.7 + - - +
142A ASP 3.0 21.9 + - - -
143A GLU* 3.6 35.3 + - - +
145A ILE 2.9 25.0 + - - -
146A LEU* 4.0 14.1 - - - +
147A PRO* 3.8 21.9 - - + +
173A TYR* 5.6 0.6 + - - -
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS* 3.0 24.9 + - - +
133A ALA* 3.7 5.6 - - - -
135A ARG* 1.3 79.0 - - - +
137A ILE* 1.3 69.9 + - + +
139A GLY* 4.0 4.7 + - - -
141A ASN* 5.2 1.6 - - - +
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS* 3.6 45.1 - - + +
49A LEU* 3.4 28.3 - - + -
52A LEU* 4.3 15.9 - - + -
92A HIS 5.2 1.9 - - - +
94A ILE* 4.7 7.1 - - - +
96A PHE* 4.1 7.6 - - + -
133A ALA* 2.9 15.1 + - + +
134A TYR 4.3 0.2 - - - +
136A THR* 1.3 84.8 - - + +
138A GLY* 1.3 61.6 + - - +
139A GLY 3.7 0.2 + - - -
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A HIS 4.3 2.3 - - - +
93A LYS* 3.2 9.5 - - - +
94A ILE* 2.8 45.3 + - - +
96A PHE* 3.9 12.0 - - - -
134A TYR 2.7 20.5 + - - -
137A ILE* 1.3 75.6 - - - +
139A GLY* 1.3 58.3 + - - +
140A ILE* 3.4 4.5 + - - -
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Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LYS* 3.5 27.4 + - - -
135A ARG 2.9 15.3 + - - -
136A THR 4.0 3.7 + - - -
137A ILE 3.4 2.0 - - - -
138A GLY* 1.3 78.1 - - - +
140A ILE* 1.3 61.0 + - - +
141A ASN* 3.1 18.0 + - - -
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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