Contacts of the helix formed by residues 122 - 128 (chain B) in PDB entry 2J3R
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 PRO 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B LYS 4.8 0.9 - - - +
121B GLU* 1.3 89.6 - - + +
123B LEU* 1.3 65.4 + - - +
124B ILE* 3.2 7.0 - - + -
125B ASN* 2.9 49.2 + - - +
126B ALA 4.6 0.9 + - - -
135B SER* 3.8 22.7 - - - +
136B THR 4.8 0.9 - - - +
167B GLY* 6.4 0.2 - - - -
168B THR* 3.7 18.2 - - + -
1177B NO3 3.4 22.4 - - - +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B TRP* 3.8 11.4 - - + +
98B PHE* 3.8 22.1 - - + -
119B GLU* 3.3 42.4 - - + +
121B GLU 4.1 0.9 - - - +
122B PRO* 1.3 70.8 - - - +
124B ILE* 1.3 61.7 + - - +
125B ASN 3.4 0.5 + - - -
126B ALA* 3.7 6.4 + - - +
127B TYR* 3.5 21.0 - - - -
139B CYS* 3.8 18.8 - - - +
140B ALA* 4.2 6.1 - - + -
143B THR* 3.4 36.1 - - + +
168B THR* 4.1 4.9 - - - +
170B LEU* 6.0 1.1 - - + -
1177B NO3 3.2 14.6 + - - +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 4.1 26.5 - - + -
30B ALA* 4.9 7.6 - - - +
33B PHE* 4.2 20.4 - - + -
122B PRO* 4.3 6.5 - - + -
123B LEU* 1.3 78.9 - - - +
125B ASN* 1.3 76.4 + - - +
127B TYR* 2.9 22.6 + - + -
128B ILE* 3.8 24.5 + - + +
136B THR* 5.9 2.7 - - - +
139B CYS* 4.1 10.2 - - + -
1177B NO3 3.6 18.0 + - - +
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Residues in contact with ASN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 5.3 0.7 + - - -
121B GLU* 4.3 14.7 + - + +
122B PRO* 2.9 44.4 + - - +
124B ILE* 1.3 85.3 - - - +
126B ALA* 1.3 58.8 + - - +
127B TYR 3.2 2.0 + - - -
128B ILE* 3.5 29.0 - - - +
131B PRO* 3.6 40.9 - - + +
132B LYS 4.3 2.1 + - - -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 3.3 30.8 + - - +
26B VAL* 3.2 14.2 - - - +
122B PRO 4.6 0.8 + - - -
123B LEU 3.7 5.4 + - - +
124B ILE 3.0 1.8 + - - -
125B ASN* 1.3 78.6 - - - +
127B TYR* 1.3 79.1 + - + +
128B ILE 3.6 0.7 - - - -
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A MET* 3.6 38.8 - - + +
18A LEU* 3.8 12.5 - - + +
26B VAL* 3.1 53.4 - - + +
27B SER* 4.7 1.6 + - - -
29B PHE* 3.8 25.1 - + + -
30B ALA* 3.5 14.1 - - + +
97B LEU 3.8 1.6 + - - -
98B PHE* 3.4 44.5 + + + +
123B LEU 3.5 23.8 - - - -
124B ILE* 2.9 10.9 + - + +
126B ALA* 1.3 92.1 - - + +
128B ILE* 1.3 64.6 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 5.1 0.9 - - - -
30B ALA* 4.1 15.5 - - + -
124B ILE* 3.9 30.1 - - + +
125B ASN* 3.5 34.3 - - - +
126B ALA 3.6 1.2 - - - -
127B TYR* 1.3 87.0 - - - +
129B SER* 1.3 69.2 + - - +
130B VAL* 3.7 23.4 - - - +
131B PRO* 3.9 5.0 - - + +
132B LYS* 4.1 10.3 - - + +
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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