Contacts of the helix formed by residues 121 - 132 (chain A) in PDB entry 4UPG
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 ASP 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A VAL* 1.3 75.6 - - - +
122A PRO* 1.3 71.4 - - + +
123A GLN* 2.8 25.8 - - - +
124A GLU* 2.8 45.1 + - - +
125A LEU* 2.8 24.4 + - - +
152A GLY 3.8 9.2 - - - +
153A LYS* 5.7 1.1 - - + -
154A ILE* 4.1 2.9 - - - -
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Residues in contact with PRO 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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121A ASP* 1.3 88.3 - - + +
123A GLN* 1.3 72.4 + - - +
125A LEU* 3.6 8.7 - - + +
126A GLN* 3.1 27.5 + - - +
141A VAL* 5.0 4.2 - - - +
145A ALA* 4.2 22.6 - - + +
149A SER* 4.9 5.2 - - - +
152A GLY* 3.3 20.9 - - - +
154A ILE* 3.9 16.4 - - + -
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Residues in contact with GLN 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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121A ASP* 2.8 35.1 - - - +
122A PRO* 1.3 86.1 - - - +
124A GLU* 1.3 67.0 + - + +
126A GLN* 3.4 9.0 + - - +
127A LYS* 3.2 22.0 + - - +
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Residues in contact with GLU 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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112A PHE* 2.9 45.1 - - + +
119A THR 4.9 0.5 - - - +
120A VAL* 3.4 21.0 - - + -
121A ASP* 2.8 51.6 + - - +
123A GLN* 1.3 77.7 - - + +
125A LEU* 1.3 51.4 + - - +
127A LYS* 3.3 3.4 + - - +
128A ALA* 2.8 36.5 + - - +
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Residues in contact with LEU 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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120A VAL* 4.2 15.5 - - + +
121A ASP 2.8 15.4 + - - +
122A PRO* 3.6 9.9 - - + +
124A GLU* 1.3 70.1 - - - +
126A GLN* 1.3 60.5 + - - +
128A ALA* 3.5 3.6 - - - +
129A LEU* 2.8 54.4 + - + +
141A VAL* 5.5 3.6 - - + +
144A ILE* 4.2 22.9 - - + +
145A ALA* 4.4 13.7 - - + -
148A TYR* 5.7 1.3 - - + -
154A ILE* 4.0 31.9 - - + -
159A TYR* 3.9 30.7 - - + -
162A CYS* 5.2 4.7 - - + -
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Residues in contact with GLN 126 (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 PRO 3.1 15.7 + - - +
123A GLN* 3.6 12.3 - - - +
124A GLU 3.4 0.2 - - - -
125A LEU* 1.3 74.6 - - - +
127A LYS* 1.3 59.2 + - + +
129A LEU* 3.2 4.7 + - - +
130A THR* 2.6 55.4 + - - +
136A LEU* 4.9 4.8 + - - +
138A PRO* 5.4 6.1 - - - +
141A VAL* 3.6 43.6 - - + +
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Residues in contact with LYS 127 (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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112A PHE* 3.8 28.2 - - + -
123A GLN 3.2 13.6 + - - +
124A GLU* 4.8 0.7 - - - -
126A GLN* 1.3 84.2 - - + +
128A ALA* 1.3 55.4 + - - +
130A THR* 3.8 6.3 - - - -
131A THR* 2.8 48.0 + - + +
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Residues in contact with ALA 128 (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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108A HIS* 3.0 23.1 - - - +
109A PHE* 5.9 1.8 - - + -
112A PHE* 3.6 29.1 - - + -
120A VAL* 6.1 2.5 - - + -
124A GLU 2.8 19.6 + - - +
125A LEU* 3.5 8.7 - - - +
127A LYS* 1.3 76.8 - - - +
129A LEU* 1.3 61.3 + - - +
131A THR* 3.3 3.2 + - - -
132A MET* 3.1 20.0 + - + +
159A TYR* 4.4 12.3 - - + -
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Residues in contact with LEU 129 (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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125A LEU* 2.8 48.1 + - + +
126A GLN* 3.8 5.8 - - - +
128A ALA* 1.3 71.9 - - - +
130A THR* 1.3 65.4 + - - +
132A MET* 3.3 17.3 + - + +
134A PHE* 3.3 26.6 + - + +
136A LEU* 3.9 28.9 - - + -
141A VAL* 5.3 7.4 - - + -
144A ILE* 4.3 17.5 - - + -
162A CYS* 4.5 3.4 - - - -
163A CYS* 4.0 23.8 - - - -
166A LEU* 3.9 22.7 - - + -
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Residues in contact with THR 130 (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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126A GLN* 2.6 40.3 + - - +
127A LYS* 3.8 7.8 - - - -
129A LEU* 1.3 77.4 - - - +
131A THR* 1.3 65.2 + - + +
133A GLY* 3.3 6.4 + - - -
134A PHE 3.7 9.6 - - - +
135A ARG* 2.9 38.4 + - - +
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Residues in contact with THR 131 (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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108A HIS* 3.0 32.0 + - - -
112A PHE* 4.1 4.5 - - + -
127A LYS* 2.8 41.5 + - + +
128A ALA* 3.8 0.7 - - - -
130A THR* 1.3 82.4 - - + +
132A MET* 1.3 57.0 + - - +
133A GLY 3.2 3.4 + - - -
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Residues in contact with MET 132 (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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105A TRP* 4.1 21.9 + - + +
108A HIS* 3.5 17.7 - - + +
128A ALA 3.1 24.8 + - - +
129A LEU* 3.3 15.7 + - + +
130A THR 3.2 1.2 - - - -
131A THR* 1.3 78.3 - - - +
133A GLY* 1.3 56.6 + - - +
134A PHE* 3.6 19.0 + - + -
159A TYR* 3.0 42.0 - - + +
163A CYS* 3.7 21.5 - - - -
167A ARG* 4.0 13.7 + - - -
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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