Contacts of the helix formed by residues 144 - 150 (chain D) in PDB entry 3NJ4
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 144 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ILE 2.9 3.7 - - - +
140D HIS 4.5 8.7 - - - +
141D THR 4.5 4.3 - - - +
142D LYS* 3.3 12.8 - - - +
143D TYR* 1.3 88.7 - - - +
145D GLN* 1.3 73.7 + - + +
147D LEU* 2.8 40.6 + - + +
148D PRO* 3.5 4.3 - - - +
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Residues in contact with GLN 145 (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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119D TYR* 3.9 16.0 + - - -
142D LYS 3.9 4.2 - - - +
143D TYR* 3.6 34.2 - - - -
144D PRO* 1.3 79.7 - - + +
146D LEU* 1.3 64.8 + - + +
148D PRO* 3.5 16.3 - - - +
149D GLY* 4.8 0.3 + - - -
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Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LEU* 4.7 6.3 - - + -
119D TYR* 4.0 20.4 - - + +
124D PRO* 3.5 33.7 - - + -
125D LEU* 3.7 24.2 - - + +
139D ILE* 4.1 10.3 - - + -
143D TYR* 2.9 42.8 + - + +
145D GLN* 1.3 87.0 - - - +
147D LEU* 1.3 54.3 + - - +
149D GLY* 2.6 29.5 + - - -
150D ILE* 3.1 16.5 + - + +
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Residues in contact with LEU 147 (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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139D ILE* 3.1 43.0 - - + +
140D HIS* 3.8 28.7 - - + +
144D PRO* 2.8 30.6 + - + +
146D LEU* 1.3 68.6 - - - +
148D PRO* 1.3 69.7 - - + +
150D ILE* 2.9 30.7 + - + +
174D LYS* 3.4 44.9 - - + +
175D VAL* 4.7 6.4 - - + +
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Residues in contact with PRO 148 (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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144D PRO 3.5 4.9 - - - +
145D GLN* 3.5 15.7 - - - +
146D LEU 3.5 2.0 - - - -
147D LEU* 1.3 94.5 - - + +
149D GLY* 1.3 60.7 + - - +
150D ILE 3.3 4.1 - - - +
174D LYS 5.7 1.8 - - - +
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Residues in contact with GLY 149 (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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125D LEU 4.3 6.3 - - - -
126D ASN* 3.6 16.1 - - - +
145D GLN 4.8 0.4 + - - -
146D LEU* 2.6 19.2 + - - -
148D PRO* 1.3 79.2 - - - +
150D ILE* 1.3 57.3 + - - -
151D ARG* 3.6 3.5 + - - +
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Residues in contact with ILE 150 (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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125D LEU* 3.6 22.4 - - + +
126D ASN 3.4 13.0 - - - +
128D ILE* 3.8 20.0 - - + -
139D ILE* 3.6 47.6 - - + -
140D HIS* 6.3 0.4 - - + -
146D LEU* 3.6 13.9 - - + +
147D LEU* 2.9 18.7 + - + +
148D PRO 4.2 4.0 - - - +
149D GLY* 1.3 75.2 - - - +
151D ARG* 1.3 63.8 + - - +
152D GLY 3.6 22.0 - - - +
175D VAL* 3.5 20.9 - - + +
176D PRO* 5.1 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