Contacts of the helix formed by residues 119 - 125 (chain A) in PDB entry 1UJN
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 5.5 4.5 - - - +
93A GLY* 3.6 21.8 - - - +
94A GLY 4.1 1.9 + - - -
117A PRO 3.6 0.2 - - - -
118A THR* 1.3 86.3 - - - +
120A THR* 1.3 64.1 + - - +
121A LEU* 3.7 7.1 + - - +
122A ALA* 3.0 26.5 + - - +
123A ILE* 3.1 23.0 + - - +
159A LEU* 3.7 8.3 - - - -
162A LEU* 3.8 22.0 - - + -
166A THR* 4.8 10.5 - - + -
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Residues in contact with THR 120 (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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119A THR* 1.3 71.5 - - - +
121A LEU* 1.3 61.6 + - - +
123A ILE* 3.1 6.6 + - - +
124A VAL* 2.8 34.2 + - - +
159A LEU* 3.8 16.0 - - + +
162A LEU* 3.9 3.0 - - - +
166A THR 3.5 3.6 + - - -
167A PHE* 2.7 60.3 + - + +
170A GLY* 3.2 19.0 + - - -
171A LEU* 4.4 10.1 - - + -
203A LEU* 4.6 10.3 - - + -
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Residues in contact with LEU 121 (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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94A GLY* 6.1 6.3 - - - +
119A THR* 3.3 6.6 - - - +
120A THR* 1.3 83.4 + - - +
122A ALA* 1.3 57.1 + - - +
124A VAL* 4.9 0.9 - - - -
125A ASP* 2.8 50.2 + - + +
126A ALA 3.5 0.3 + - - -
166A THR* 5.2 2.9 + - + +
169A GLU* 4.8 19.7 - - + +
170A GLY* 3.6 15.9 - - - +
173A GLU* 3.4 34.5 - - + +
247A HIS* 4.6 19.3 - - + -
248A GLY* 5.3 1.8 - - - +
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Residues in contact with ALA 122 (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 GLY* 3.9 7.9 - - - -
94A GLY* 3.7 22.8 - - - +
97A THR* 5.0 2.5 - - + +
117A PRO* 3.6 24.2 - - + +
119A THR* 3.0 20.7 + - - +
121A LEU* 1.3 76.8 - - - +
123A ILE* 1.3 63.3 + - - +
126A ALA* 3.1 29.1 + - + +
127A SER* 3.2 11.1 + - - -
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Residues in contact with ILE 123 (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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14A ILE* 6.1 0.9 - - + -
16A VAL* 4.5 7.9 - - + -
117A PRO* 3.8 18.2 - - + +
119A THR 3.1 15.5 + - - +
120A THR* 3.1 7.9 + - - +
122A ALA* 1.3 77.8 - - - +
124A VAL* 1.3 57.9 + - + +
127A SER* 2.6 31.0 + - - -
154A ALA* 3.7 33.4 - - + -
155A GLU 5.8 0.7 - - - +
156A LEU* 4.4 3.8 - - + -
159A LEU* 4.0 30.7 - - + -
203A LEU* 4.2 26.2 - - + -
207A VAL* 3.4 19.1 - - + +
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Residues in contact with VAL 124 (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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120A THR 2.8 22.8 + - - +
121A LEU 4.4 1.1 - - - +
123A ILE* 1.3 75.6 - - + +
125A ASP* 1.3 58.2 + - - +
127A SER* 4.4 2.8 + - - -
170A GLY 4.1 14.8 - - - +
171A LEU* 5.8 0.2 - - + -
173A GLU* 3.9 9.0 - - + -
174A ALA* 3.8 23.8 - - + +
177A HIS* 3.4 36.4 - - + +
203A LEU* 3.7 28.0 - - + +
206A ALA* 4.0 14.4 - - + -
207A VAL* 4.3 9.0 - - - +
210A LYS* 4.1 7.8 - - - +
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Residues in contact with ASP 125 (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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121A LEU* 2.8 35.5 + - + +
124A VAL* 1.3 74.0 - - - +
126A ALA* 1.3 63.3 + - - +
127A SER 3.3 2.4 + - - -
128A VAL 3.3 4.4 + - - +
173A GLU* 4.1 23.2 - - + +
176A LYS* 4.8 6.2 + - - -
177A HIS* 4.9 1.9 + - - -
210A LYS* 2.7 48.9 + - - +
247A HIS* 5.5 3.1 + - - -
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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