Contacts of the helix formed by residues 134 - 145 (chain A) in PDB entry 3R9X
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 VAL 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ALA* 4.8 1.1 - - + -
122A ILE* 4.0 36.6 - - + -
125A ILE* 4.3 9.4 - - + -
128A ILE* 3.7 21.9 - - + +
131A ALA* 3.2 14.2 + - - +
133A ASN* 1.3 79.3 - - - +
135A LEU* 1.3 73.3 + - + +
136A PRO 3.3 0.2 - - - -
137A LEU* 3.2 12.8 + - + +
138A ILE* 3.1 33.4 + - + +
153A PRO* 4.6 11.9 - - + -
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Residues in contact with LEU 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 ALA 4.9 1.1 - - - +
132A LYS* 3.4 27.8 - - + +
134A VAL* 1.3 83.5 - - + +
136A PRO* 1.3 63.3 - - + +
138A ILE* 3.1 19.9 + - + +
139A ASP* 2.8 32.3 + - - +
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Residues in contact with PRO 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 3.7 4.0 - - - +
133A ASN* 3.1 22.0 - - - +
134A VAL 3.4 0.4 - - - -
135A LEU* 1.3 95.8 - - + +
137A LEU* 1.3 55.8 + - - +
139A ASP* 3.3 7.8 + - + +
140A GLU* 2.8 29.3 + - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 4.2 5.6 - - + -
95A ALA* 4.5 11.0 - - - +
98A GLY* 3.9 17.3 - - - -
99A TRP 3.8 21.8 - - - +
122A ILE* 3.8 37.7 - - + -
133A ASN 4.9 1.1 + - - +
134A VAL* 3.2 14.1 + - + +
135A LEU 3.2 0.6 - - - -
136A PRO* 1.3 77.0 - - - +
138A ILE* 1.3 66.9 + - - +
140A GLU* 3.2 24.0 + - - +
141A ILE* 3.0 32.9 + - + +
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Residues in contact with ILE 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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122A ILE* 3.7 20.9 - - + -
134A VAL* 3.1 25.3 + - + +
135A LEU* 3.5 19.5 - - + +
137A LEU* 1.3 75.6 - - - +
139A ASP* 1.3 64.3 + - - +
141A ILE* 3.2 16.1 + - - +
142A HIS* 3.2 34.6 + - + +
151A ILE* 4.1 18.9 - - + +
153A PRO* 4.0 27.1 - - + -
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Residues in contact with ASP 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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135A LEU 2.8 20.6 + - - +
136A PRO* 3.4 8.5 - - + +
138A ILE* 1.3 74.8 - - - +
140A GLU* 1.3 62.0 + - - +
142A HIS* 3.1 10.7 + - - +
143A LYS* 3.0 61.7 + - - +
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Residues in contact with GLU 140 (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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99A TRP* 4.8 10.7 + - + +
136A PRO 2.8 13.7 + - - +
137A LEU* 3.2 30.7 + - + +
139A ASP* 1.3 77.6 + - - +
141A ILE* 1.3 57.6 + - + +
143A LYS* 3.4 7.8 - - - +
144A LYS* 2.8 54.5 + - + +
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Residues in contact with ILE 141 (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 ILE* 3.8 20.2 - - + -
99A TRP* 3.6 33.7 - - + -
120A VAL* 4.2 12.1 - - + -
122A ILE* 4.3 8.7 - - + -
137A LEU* 3.0 27.3 + - + +
138A ILE 3.2 6.5 + - - +
140A GLU* 1.3 74.1 - - + +
142A HIS* 1.3 57.4 + - - +
144A LYS* 4.3 5.6 - - - +
145A HIS* 2.7 33.9 + - + +
148A LEU* 4.1 26.2 - - + -
151A ILE* 3.4 24.7 - - + -
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Residues in contact with HIS 142 (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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138A ILE* 3.2 27.5 + - + +
139A ASP* 3.1 10.6 + - - +
141A ILE* 1.3 71.4 - - - +
143A LYS* 1.3 73.7 + - + +
145A HIS 4.6 2.9 - - - -
146A PRO* 3.2 30.4 + - + +
148A LEU 3.3 24.7 + - - -
149A THR* 4.3 13.2 - - - -
151A ILE* 3.5 22.8 - - + +
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Residues in contact with LYS 143 (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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139A ASP* 3.0 47.4 + - - +
140A GLU* 3.4 11.7 - - - +
142A HIS* 1.3 82.2 - - + +
144A LYS* 1.3 63.3 + - - +
146A PRO* 3.7 9.4 - - - +
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Residues in contact with LYS 144 (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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99A TRP* 3.8 30.4 + - + +
104A GLU* 3.9 9.4 - - - +
140A GLU* 2.8 46.4 + - - +
141A ILE* 3.9 4.5 - - - +
143A LYS* 1.3 77.6 - - - +
145A HIS* 1.3 94.3 + - + +
146A PRO* 3.4 5.0 - - - +
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Residues in contact with HIS 145 (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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99A TRP* 3.5 28.8 - + - -
104A GLU* 2.7 27.5 + - - -
107A TYR* 3.8 12.0 - + - -
108A GLN* 3.4 26.0 - - - -
112A LYS* 4.6 6.5 + - - -
141A ILE* 2.7 18.2 + - + +
144A LYS* 1.3 99.2 + - + +
146A PRO* 1.3 58.7 - - - +
147A GLU* 3.1 16.4 + - - +
148A LEU* 2.9 42.5 + - + +
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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