Contacts of the helix formed by residues 119 - 130 (chain A) in PDB entry 4Z5T
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 MET 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ARG* 3.5 37.7 - - - +
117A THR* 3.9 9.2 - - + +
118A ILE* 1.3 79.0 - - - +
120A PRO* 1.3 71.1 - - + +
121A LYS* 3.1 20.0 - - + +
122A ASP* 2.7 34.9 + - - +
123A ILE* 3.2 4.9 + - - +
47B SER* 4.0 12.1 - - - +
50B ILE* 3.3 9.6 - - - +
70I T 4.0 19.1 - - - +
71I G 3.6 24.7 - - - +
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Residues in contact with PRO 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 MET* 1.3 87.6 - - + +
121A LYS* 1.3 56.4 + - - +
123A ILE* 3.2 5.2 + - + +
124A GLN* 2.9 40.9 + - - +
47B SER* 4.1 5.4 - - - +
49B LEU* 3.6 47.1 - - + +
50B ILE* 3.9 13.0 - - + +
53B GLU* 4.0 26.2 - - + +
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Residues in contact with LYS 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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115A ARG* 3.6 25.7 - - - +
119A MET* 3.1 20.7 - - + -
120A PRO* 1.3 80.1 - - - +
122A ASP* 1.3 54.8 + - - +
124A GLN* 3.4 15.5 + - - +
125A LEU* 3.0 28.4 + - - +
112E HIS* 3.5 28.6 + - + +
114E LYS* 5.1 10.5 - - - +
71I G 4.7 7.7 + - - -
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Residues in contact with ASP 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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106A THR* 3.5 25.4 - - + +
109A CYS* 3.8 7.9 - - + +
110A ALA* 3.6 10.6 - - - +
115A ARG* 2.7 40.1 + - - -
118A ILE* 3.5 5.5 - - - -
119A MET* 2.7 30.4 + - - +
121A LYS* 1.3 75.3 - - - +
123A ILE* 1.3 59.3 + - - +
125A LEU* 3.2 3.7 + - - +
126A ALA* 2.9 29.3 + - - +
112E HIS* 2.9 20.2 + - - -
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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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102A LEU* 4.3 10.1 - - + -
103A LEU* 4.6 11.4 - - + -
106A THR* 3.4 29.8 - - + +
119A MET 3.2 6.0 + - - +
120A PRO* 3.2 7.7 + - + +
122A ASP* 1.3 76.8 - - - +
124A GLN* 1.3 59.0 + - - +
126A ALA* 3.3 1.5 + - - +
127A ARG* 2.9 50.5 + - + +
133A ARG* 6.1 0.2 - - - +
50B ILE* 3.7 20.9 - - + -
53B GLU* 4.2 19.1 - - + +
54B THR* 4.0 21.1 - - + +
57B VAL* 4.2 12.3 - - + -
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Residues in contact with GLN 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 PRO* 2.9 26.5 + - - +
121A LYS* 3.7 15.9 - - - +
122A ASP 3.2 0.2 - - - -
123A ILE* 1.3 75.2 - - + +
125A LEU* 1.3 58.2 + - - +
127A ARG* 3.3 2.4 + - - -
128A ARG* 2.9 29.6 + - - +
133A ARG* 3.2 38.5 - - - +
53B GLU* 3.5 28.4 + - - +
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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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109A CYS* 4.2 13.7 - - - -
121A LYS 3.0 17.1 + - - +
122A ASP* 3.2 5.4 + - - +
124A GLN* 1.3 77.9 - - - +
126A ALA* 1.3 63.0 + - - +
128A ARG* 3.2 7.0 + - + +
129A ILE* 2.9 45.5 + - + +
108E LEU* 4.2 30.3 - - + +
109E CYS* 4.6 12.1 - - - +
112E HIS* 3.3 46.4 - - + +
125E LEU* 5.5 2.0 - - + -
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Residues in contact with ALA 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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102A LEU* 4.1 12.3 - - + -
105A ASP* 4.0 26.5 - - + -
106A THR* 4.2 6.7 - - - +
109A CYS* 4.2 15.0 - - - -
122A ASP 2.9 16.7 + - - +
123A ILE 3.7 4.0 - - - +
125A LEU* 1.3 75.8 - - - +
127A ARG* 1.3 58.5 + - - +
129A ILE* 3.4 2.2 + - - +
130A ARG* 2.9 36.1 + - - +
129E ILE* 3.9 7.6 - - + +
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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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98A TYR* 4.2 1.6 + - - -
102A LEU* 3.7 21.8 - - + -
123A ILE* 2.9 26.0 + - - +
126A ALA* 1.3 73.6 - - - +
128A ARG* 1.3 62.7 + - - +
130A ARG* 3.8 5.7 + - - -
131A GLY 3.3 2.1 + - - -
132A GLU* 2.9 73.0 + - - +
133A ARG* 3.2 49.4 + - - +
53B GLU* 5.4 2.0 + - - -
57B VAL* 3.7 34.0 - - - +
60B VAL* 5.2 15.9 - - - +
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLN 2.9 17.1 + - - +
125A LEU* 3.2 6.9 + - + +
127A ARG* 1.3 74.2 - - - +
129A ILE* 1.3 70.4 + - + +
131A GLY* 3.1 13.7 + - - -
133A ARG* 3.7 29.7 - - + +
110C ASN* 6.1 0.8 - - - +
112C GLN* 5.4 5.8 + - - +
105E ASP* 4.9 4.8 - - - +
108E LEU* 3.5 40.1 - - + +
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Residues in contact with ILE 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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109A CYS* 6.1 0.4 - - - -
125A LEU* 2.9 39.9 + - + +
126A ALA* 4.8 0.2 - - - -
128A ARG* 1.3 78.2 - - - +
130A ARG* 1.3 63.8 + - - +
131A GLY* 3.1 1.7 + - - -
99C ARG* 5.3 3.1 + - - -
105E ASP* 3.6 50.0 - - + +
108E LEU* 4.6 5.4 - - + -
109E CYS* 4.5 9.2 - - - -
126E ALA* 3.7 17.7 - - + +
129E ILE* 3.6 35.7 - - + -
130E ARG* 4.0 20.0 + - + +
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Residues in contact with ARG 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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98A TYR* 3.4 23.2 + - - -
101A GLY* 3.1 30.3 - - - -
102A LEU* 3.1 20.2 - - - +
105A ASP* 2.8 26.9 + - - -
126A ALA 2.9 20.6 + - - +
127A ARG* 3.9 5.6 - - - +
129A ILE* 1.3 76.4 - - - +
131A GLY* 1.3 59.8 + - - +
132A GLU* 3.2 34.2 + - + +
95B ARG* 4.5 10.4 - - - +
99C ARG* 4.3 11.2 + - - -
129E ILE* 4.2 20.8 + - + +
130E ARG* 5.2 4.0 - - - +
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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