Contacts of the helix formed by residues 128 - 138 (chain A) in PDB entry 1IUF
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 ASN 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLY* 2.8 44.2 - - - +
102A GLU* 3.1 5.0 + - - +
104A ILE* 3.7 16.5 - - + +
105A LYS* 3.0 42.5 - - - +
126A PHE* 3.9 4.6 + - - -
127A SER* 1.3 83.6 + - - +
129A GLY* 1.3 61.7 + - - +
130A TRP* 3.1 9.8 - - - -
131A LEU* 2.8 22.7 + - - +
132A GLU* 3.1 12.6 + - - +
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Residues in contact with GLY 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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127A SER* 3.7 6.3 - - - -
128A ASN* 1.3 77.9 - - - +
130A TRP* 1.3 51.5 + - - +
132A GLU* 3.7 16.9 + - - +
133A GLY* 2.6 35.0 + - - -
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Residues in contact with TRP 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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79A TYR* 4.0 34.9 - + + +
82A LEU* 4.4 2.9 - - + -
83A GLU* 3.1 46.4 - - + +
86A LEU* 2.9 52.3 - - + -
104A ILE* 3.5 19.1 - - + -
126A PHE* 3.3 35.9 - + - +
127A SER* 2.6 43.6 + - - +
128A ASN* 4.2 0.7 - - - -
129A GLY* 1.3 76.2 - - - +
131A LEU* 1.3 104.4 + - + +
134A PHE* 3.3 6.4 + - - -
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Residues in contact with LEU 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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86A LEU 3.5 6.5 - - - +
89A TRP* 2.9 46.7 - - + +
90A GLN* 3.3 32.8 - - + +
104A ILE* 3.4 21.3 - - + -
128A ASN 2.8 10.7 + - - +
130A TRP* 1.3 94.9 - - + +
132A GLU* 1.3 56.6 + - + +
133A GLY 3.0 1.1 - - - -
134A PHE* 2.9 27.2 + - + -
135A ARG* 2.7 43.8 + - + +
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Residues in contact with GLU 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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100A SER* 2.7 32.1 + - - -
101A GLY* 3.3 34.1 + - - +
104A ILE* 4.6 4.3 - - + -
128A ASN* 3.1 8.4 + - - +
129A GLY* 3.7 21.4 + - - +
131A LEU* 1.3 76.1 - - + +
133A GLY* 1.3 55.2 + - - +
135A ARG* 3.9 9.1 - - - +
136A LYS* 2.7 42.3 + - + +
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Residues in contact with GLY 133 (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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83A GLU* 4.1 9.6 - - - -
129A GLY 2.6 21.4 + - - -
130A TRP 3.7 2.9 - - - -
131A LEU 3.0 0.4 - - - -
132A GLU* 1.3 73.1 - - - +
134A PHE* 1.3 56.6 + - - +
136A LYS* 4.0 1.8 - - - +
137A ARG* 2.8 37.6 + - - +
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Residues in contact with PHE 134 (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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83A GLU* 3.6 29.9 + - + +
86A LEU* 3.7 2.9 - - + -
87A PHE* 3.2 57.9 - + + -
90A GLN* 3.6 12.8 - - + -
91A VAL* 5.6 0.2 - - + -
130A TRP 3.3 8.9 + - - +
131A LEU* 2.9 53.4 + - + -
133A GLY* 1.3 68.1 - - - -
135A ARG* 1.3 90.0 + - + +
136A LYS 3.0 2.2 - - - -
137A ARG* 4.1 4.9 - - - +
138A HIS* 2.6 48.7 + - + +
139A ILE* 4.0 6.1 - - + -
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Residues in contact with ARG 135 (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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90A GLN* 4.1 15.8 + - + -
98A THR* 5.4 6.3 - - - +
99A LEU 5.4 3.4 - - - +
100A SER* 4.2 26.9 - - - +
131A LEU* 2.7 33.8 + - + +
132A GLU* 3.9 10.0 - - - +
134A PHE* 1.3 88.2 - - + +
136A LYS* 1.3 53.1 + - + +
139A ILE* 3.0 47.0 - - + +
140A LEU 2.7 28.2 + - - +
141A HIS 2.7 32.8 + - - -
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Residues in contact with LYS 136 (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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132A GLU* 2.7 22.1 + - + +
133A GLY* 4.0 2.5 - - - +
135A ARG* 1.3 78.8 - - + +
137A ARG* 1.3 62.6 + - + +
138A HIS 3.2 7.1 + - - -
140A LEU* 4.0 24.6 + - - +
141A HIS* 4.7 23.6 - - - +
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Residues in contact with ARG 137 (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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5A LYS* 5.8 0.6 - - - +
75A ARG* 3.1 35.7 - - - +
133A GLY* 2.8 24.0 + - - +
134A PHE* 3.2 3.1 - - - +
136A LYS* 1.3 80.7 + - + +
138A HIS* 1.3 78.0 + - + +
140A LEU* 6.2 0.4 - - - -
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Residues in contact with HIS 138 (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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87A PHE* 5.3 6.4 - + + -
134A PHE* 2.6 29.0 + - + +
136A LYS 3.2 2.8 + - - -
137A ARG* 1.3 89.1 - - + +
139A ILE* 1.3 67.2 + - + +
140A LEU* 3.2 15.2 + - - +
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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