Contacts of the helix formed by residues 132 - 141 (chain A) in PDB entry 3CJR
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 GLY 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A THR* 2.8 26.5 + - - -
130A GLY 3.0 1.6 - - - -
131A SER* 1.3 77.6 - - - +
133A VAL* 1.3 64.9 + - - +
134A LEU 3.3 2.7 - - - -
135A ALA* 3.2 5.9 + - - +
136A ILE* 2.9 31.2 + - - +
158A ALA* 4.1 2.7 - - - -
171A PHE* 4.0 15.5 - - - -
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Residues in contact with VAL 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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77A VAL* 5.1 1.1 - - + -
91A LEU* 4.1 19.5 - - + +
93A ILE* 3.8 29.1 - - + +
100A GLY* 3.6 28.5 - - - +
102A GLY* 4.8 5.4 - - - -
107A THR* 3.7 26.9 - - + -
111A LEU* 4.5 8.7 - - + -
129A THR 4.1 0.4 + - - -
131A SER* 3.3 6.9 + - - +
132A GLY* 1.3 76.6 - - - +
134A LEU* 1.3 60.9 + - + +
136A ILE* 3.5 3.4 + - - +
137A ALA* 2.9 27.9 + - - +
255A SFG 4.0 11.9 - - - +
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Residues in contact with LEU 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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107A THR* 3.9 16.8 - - + +
110A ALA* 3.8 33.0 - - + -
111A LEU* 3.7 25.1 - - + +
114A LEU* 3.6 14.7 - - + +
126A ASP* 3.6 25.7 + - - +
129A THR 5.3 0.2 + - - -
132A GLY 3.3 0.6 - - - -
133A VAL* 1.3 76.3 - - + +
135A ALA* 1.3 61.3 + - - +
137A ALA* 4.3 2.2 - - - -
138A ALA* 2.9 28.8 + - - +
189A VAL* 3.8 17.3 - - + +
191A ASN* 4.4 8.7 - - + +
255A SFG 3.3 26.7 - - - +
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Residues in contact with ALA 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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124A VAL* 6.2 0.2 - - - -
126A ASP* 3.2 24.9 + - + +
129A THR* 3.9 7.9 - - - +
132A GLY 3.2 7.2 + - - +
134A LEU* 1.3 73.0 - - - +
136A ILE* 1.3 60.8 + - - +
138A ALA* 3.4 4.1 + - - +
139A GLU* 3.0 32.6 + - - +
145A ALA* 3.5 19.9 - - + +
147A GLY* 4.4 5.2 - - - -
169A PRO* 4.1 7.2 - - + -
171A PHE* 3.9 15.5 - - + -
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Residues in contact with ILE 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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91A LEU* 4.5 11.7 - - + -
93A ILE* 4.3 6.7 - - + -
132A GLY* 2.9 27.3 + - - +
133A VAL* 3.7 4.7 - - - +
135A ALA* 1.3 73.6 - - - +
137A ALA* 1.3 59.4 + - - +
139A GLU* 3.2 5.4 + - - +
140A LYS* 2.9 29.4 + - + +
158A ALA 4.2 4.5 - - - +
161A ASN* 3.6 19.7 - - + +
162A ALA* 3.5 34.8 - - + +
165A ASN* 3.6 34.3 - - + +
167A VAL* 3.8 12.9 - - + +
169A PRO* 4.3 9.4 - - + -
171A PHE* 4.5 1.3 - - + -
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Residues in contact with ALA 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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75A PHE* 3.7 15.9 - - + -
91A LEU* 3.8 16.3 - - + +
111A LEU* 3.4 28.3 - - + -
114A LEU* 4.3 4.3 - - + -
133A VAL 2.9 18.1 + - - +
134A LEU* 3.7 4.5 - - - +
136A ILE* 1.3 74.9 - - - +
138A ALA* 1.3 63.1 + - - +
140A LYS* 3.2 4.8 + - - +
141A LEU* 3.0 27.2 + - - +
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Residues in contact with ALA 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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114A LEU* 4.3 6.9 - - + +
118A LEU* 3.6 23.8 - - + +
124A VAL* 4.2 17.3 - - + -
134A LEU 2.9 18.9 + - - +
135A ALA* 3.5 6.5 - - - +
136A ILE 3.3 0.2 - - - -
137A ALA* 1.3 75.6 - - - +
139A GLU* 1.3 58.6 + - - +
141A LEU* 3.1 9.4 + - - -
142A GLY 3.4 0.2 + - - -
143A GLY* 2.8 25.4 + - - -
145A ALA* 4.0 14.4 - - + -
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Residues in contact with GLU 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 ALA 3.0 17.6 + - - +
136A ILE 3.5 8.1 - - - +
138A ALA* 1.3 75.4 - - - +
140A LYS* 1.3 58.1 + - - +
142A GLY* 3.0 18.7 + - - -
143A GLY 3.2 21.7 - - - +
144A LYS* 3.5 3.2 - - - -
145A ALA* 2.7 30.1 + - + +
167A VAL* 3.7 21.9 - - + +
168A ARG 4.1 9.7 + - - +
169A PRO* 3.6 35.0 - - + +
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Residues in contact with LYS 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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75A PHE* 4.4 3.1 - - + -
89A ILE* 4.0 27.3 - - + +
90A PRO* 3.9 23.3 + - - +
91A LEU* 4.0 14.8 - - + -
136A ILE* 2.9 18.0 + - + +
137A ALA* 3.2 12.3 + - - +
139A GLU* 1.3 75.3 - - - +
141A LEU* 1.3 61.4 + - - +
142A GLY 3.3 0.6 + - - -
165A ASN* 2.8 42.8 + - - +
167A VAL* 4.2 11.1 - - + +
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Residues in contact with LEU 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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74A PRO* 4.8 7.2 - - + -
75A PHE* 3.6 27.1 - - + -
89A ILE* 4.0 19.7 - - + -
114A LEU* 3.9 15.0 - - + +
115A ALA* 3.8 32.1 - - + +
118A LEU* 4.1 17.4 - - + +
119A ARG 4.8 1.4 - - - -
120A PRO* 4.0 20.4 - - - +
137A ALA 3.0 14.1 + - - +
138A ALA 3.1 7.6 + - - +
139A GLU 3.1 0.6 - - - -
140A LYS* 1.3 76.7 - - - +
142A GLY* 1.3 59.6 + - - +
143A GLY 3.3 1.5 + - - -
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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