Contacts of the helix formed by residues 119 - 132 (chain A) in PDB entry 5XMA
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG* 3.6 32.3 - - - +
44A GLU* 5.8 0.9 - - - +
118A GLY* 1.3 83.6 - - - +
120A VAL* 1.3 69.5 + - + +
121A SER* 4.2 7.9 - - - +
122A TYR* 3.5 9.4 + - + -
123A LEU* 3.1 24.8 + - - +
173A ARG* 3.3 34.3 - - + +
174A LEU* 3.6 15.7 - - + -
23F A 5.1 0.9 - - - +
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Residues in contact with VAL 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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42A ARG* 6.4 0.4 - - - +
119A PRO* 1.3 72.6 - - + +
121A SER* 1.3 64.9 + - - +
123A LEU* 2.9 12.8 + - + +
124A ILE* 2.9 43.9 + - + +
1E T 4.2 13.9 - - + +
23F A 4.5 33.6 - - + +
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Residues in contact with SER 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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119A PRO* 4.2 7.1 - - - +
120A VAL* 1.3 77.0 - - - +
122A TYR* 1.3 62.4 + - - +
124A ILE* 3.2 13.1 + - - +
125A ARG* 3.1 38.1 + - - +
174A LEU* 2.8 25.0 + - - -
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Residues in contact with TYR 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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114A PHE* 3.9 28.9 - + - -
118A GLY 4.1 9.6 - - - -
119A PRO* 3.5 14.5 + - + -
120A VAL 3.3 0.6 - - - -
121A SER* 1.3 80.8 + - - +
123A LEU* 1.3 64.6 + - + +
125A ARG* 3.6 13.3 + - - +
126A ILE* 3.1 52.5 + - + +
160A ILE* 5.4 6.6 - - - +
165A PHE* 5.4 3.5 - - - +
166A THR 3.9 17.0 + - - -
168A ARG* 4.3 22.9 + - + +
173A ARG* 3.7 33.5 + - + +
174A LEU* 3.4 32.9 + - - +
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Residues in contact with LEU 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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114A PHE* 3.9 45.1 - - + +
115A HIS* 3.5 24.9 - - - +
118A GLY* 3.7 14.1 - - - +
119A PRO 3.1 19.0 + - - +
120A VAL* 2.9 11.8 + - + +
122A TYR* 1.3 76.7 - - + +
124A ILE* 1.3 65.6 + - + +
126A ILE* 3.4 4.8 + - - +
127A ARG* 2.9 45.8 + - - +
1E T 5.8 1.8 - - + +
23F A 4.1 26.2 - - + +
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Residues in contact with ILE 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 VAL* 2.9 35.8 + - + +
121A SER* 3.7 9.4 - - - +
123A LEU* 1.3 77.4 - - + +
125A ARG* 1.3 59.7 + - + +
127A ARG* 3.7 1.4 - - - +
128A ALA* 2.8 34.7 + - + +
1E T 4.0 64.1 - - + +
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Residues in contact with ARG 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 SER* 3.1 30.4 + - - +
122A TYR* 4.0 15.1 - - - +
124A ILE* 1.3 78.1 - - + +
126A ILE* 1.3 67.8 + - + +
128A ALA* 3.5 11.4 + - - +
129A ALA* 3.5 12.5 + - - +
168A ARG* 5.8 3.8 - - - +
174A LEU* 2.8 45.0 + - - +
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Residues in contact with ILE 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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114A PHE* 4.7 17.0 - - + -
122A TYR* 3.1 49.9 + - + +
123A LEU* 3.8 4.3 - - - +
124A ILE 3.3 0.4 - - - -
125A ARG* 1.3 81.1 - - + +
127A ARG* 1.3 63.4 + - + +
128A ALA 3.1 0.9 + - - -
129A ALA* 3.2 14.9 + - - +
130A LEU* 3.2 31.2 + - + +
137A LEU* 4.8 4.0 - - + -
163A LEU* 5.7 2.9 - - + -
165A PHE* 4.3 40.5 - - + -
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Residues in contact with ARG 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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114A PHE* 5.8 0.6 - - - -
115A HIS* 2.9 43.9 + - - +
123A LEU* 2.9 35.7 + - - +
124A ILE 4.0 2.2 - - - +
126A ILE* 1.3 74.7 - - - +
128A ALA* 1.3 57.1 + - - +
130A LEU* 3.8 9.2 - - - +
131A LYS* 2.9 29.6 + - - +
137A LEU* 3.4 47.8 + - + +
138A ASN* 3.5 22.2 - - - +
139A GLN* 5.6 0.2 + - - -
1E T 2.9 48.6 + - - +
2E G 3.2 21.5 + - - +
23F A 4.3 4.4 - - - -
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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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124A ILE* 2.8 25.7 + - + +
125A ARG* 3.6 9.9 - - - +
126A ILE 3.1 0.4 - - - -
127A ARG* 1.3 73.8 - - - +
129A ALA* 1.3 62.7 + - - +
131A LYS* 3.2 17.3 + - - +
132A LYS* 3.2 27.0 + - - +
1E T 4.9 8.9 + - - +
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Residues in contact with ALA 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 ARG 3.5 7.8 + - - +
126A ILE* 3.2 9.0 + - - +
128A ALA* 1.3 78.1 - - - +
130A LEU* 1.3 66.3 + - + +
132A LYS* 3.2 29.0 + - + +
133A LYS* 3.6 12.5 + - - +
165A PHE* 5.1 11.4 - - + -
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Residues in contact with LEU 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 ILE* 3.2 22.6 + - + +
127A ARG* 3.8 6.7 - - - +
128A ALA 3.2 0.8 - - - -
129A ALA* 1.3 75.0 - - - +
131A LYS* 1.3 60.7 + - - +
133A LYS* 3.0 19.9 + - + +
135A TYR* 3.1 42.6 + - + +
137A LEU* 3.8 40.2 - - + +
142A LEU* 5.3 5.2 - - + -
163A LEU* 4.9 14.8 - - + -
165A PHE* 3.7 30.3 - - + -
2E G 5.8 0.7 - - - +
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Residues in contact with LYS 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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127A ARG 2.9 18.6 + - - +
128A ALA* 3.2 8.7 + - - +
130A LEU* 1.3 75.5 - - - +
132A LYS* 1.3 61.1 + - + +
133A LYS 3.1 1.4 + - - -
134A ASN* 3.6 10.9 + - - +
135A TYR 3.6 11.1 + - - +
1E T 4.5 17.6 + - - +
2E G 3.1 30.7 + - - +
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Residues in contact with LYS 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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128A ALA* 3.4 24.2 - - - +
129A ALA* 3.2 16.7 + - + +
130A LEU 3.1 1.0 - - - -
131A LYS* 1.3 76.1 - - + +
133A LYS* 1.3 62.5 + - + +
134A ASN 3.6 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