Contacts of the helix formed by residues 101 - 115 (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 GLY 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A SER* 1.3 74.1 - - - +
102A GLU* 1.3 51.6 + - - -
103A THR* 2.6 19.7 + - - +
104A ILE* 2.6 22.8 + - - +
128A ASN* 2.8 18.9 - - - +
132A GLU* 3.3 25.7 - - - +
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Residues in contact with GLU 102 (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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99A LEU* 4.8 8.7 - - + +
100A SER 3.8 2.8 + - - -
101A GLY* 1.3 68.9 - - - -
103A THR* 1.3 62.5 + - - +
104A ILE 2.8 2.0 + - - -
105A LYS* 3.3 29.7 - - + +
106A ARG* 2.9 29.1 + - + +
128A ASN* 3.1 10.7 + - - -
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Residues in contact with THR 103 (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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89A TRP* 4.8 1.5 - - - -
90A GLN* 6.0 1.8 - - - +
97A ALA* 5.1 6.6 - - - +
98A THR 3.6 12.0 + - - +
99A LEU* 2.7 35.1 + - - +
100A SER* 3.6 4.0 - - - -
101A GLY 2.6 16.6 + - - +
102A GLU* 1.3 73.3 - - - +
104A ILE* 1.3 77.4 + - + +
106A ARG* 4.2 4.7 - - - +
107A ALA* 3.5 19.4 + - - +
135A ARG* 6.3 0.2 - - - +
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Residues in contact with ILE 104 (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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89A TRP* 3.4 23.1 - - + -
90A GLN* 4.0 3.1 - - - +
100A SER* 5.1 0.7 - - - -
101A GLY 2.6 33.5 + - - +
103A THR* 1.3 85.2 - - + +
105A LYS* 1.3 51.2 + - - +
106A ARG 2.5 6.6 + - - -
107A ALA* 2.4 30.2 + - - +
108A ALA* 2.4 23.1 + - + -
128A ASN* 3.7 17.0 - - + +
130A TRP* 3.5 30.3 - - + -
131A LEU* 3.4 38.1 - - + -
132A GLU* 4.6 3.6 - - + -
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Residues in contact with LYS 105 (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 GLU* 3.0 32.5 + - + +
104A ILE* 1.3 72.6 - - - +
106A ARG* 1.3 55.8 + - - +
108A ALA* 4.5 4.5 - - - -
109A ALA* 2.8 32.8 - - + +
125A ASN* 3.2 33.0 + - - +
126A PHE* 3.6 17.5 + - + +
127A SER* 4.4 11.7 - - - +
128A ASN* 3.0 31.5 - - - +
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Residues in contact with ARG 106 (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 GLU* 2.9 17.6 + - + +
103A THR* 4.2 5.2 - - - +
104A ILE 2.5 6.3 + - - -
105A LYS* 1.3 73.9 - - - +
107A ALA* 1.3 52.8 + - - +
109A ALA* 4.0 1.3 - - - +
110A ILE* 2.8 49.8 + - - +
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Residues in contact with ALA 107 (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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89A TRP* 3.4 33.4 - - + -
93A GLN* 4.4 11.0 + - + +
103A THR 3.5 10.9 + - - +
104A ILE 2.4 15.9 + - - +
106A ARG* 1.3 71.7 - - - +
108A ALA* 1.3 52.6 + - - +
110A ILE* 3.0 10.6 - - - +
111A LEU* 2.5 40.8 + - - +
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Residues in contact with ALA 108 (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* 4.9 2.5 - - + -
89A TRP* 4.8 2.9 - - + -
104A ILE* 2.4 41.5 + - + +
105A LYS* 4.5 1.1 - - - +
107A ALA* 1.3 70.4 - - - +
109A ALA* 1.3 61.5 + - - +
110A ILE 3.0 1.3 - - - -
111A LEU* 2.8 25.9 + - - +
112A TRP* 2.9 21.0 + - + +
123A VAL* 4.5 0.4 - - - +
126A PHE* 3.3 36.8 - - + -
130A TRP* 4.6 1.3 - - + -
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Residues in contact with ALA 109 (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 LYS* 2.8 25.7 + - + +
106A ARG* 4.2 2.5 - - - +
108A ALA* 1.3 78.9 - - - +
110A ILE* 1.3 56.8 + - - +
112A TRP* 5.3 0.2 - - - +
113A HIS* 3.1 33.0 + - + +
123A VAL* 5.1 7.9 - - - -
124A PRO 5.9 2.2 - - - +
126A PHE* 4.7 2.8 - - + -
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Residues in contact with ILE 110 (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 GLN* 5.8 2.7 - - - +
106A ARG* 2.8 37.6 + - - +
107A ALA* 3.0 18.2 - - - +
108A ALA 3.0 0.6 - - - -
109A ALA* 1.3 76.4 - - - +
111A LEU* 1.3 63.2 + - - +
112A TRP 3.5 0.7 - - - -
113A HIS* 3.9 6.5 - - + -
114A LYS* 3.2 56.7 + - + +
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Residues in contact with LEU 111 (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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89A TRP* 3.9 36.8 - - + -
93A GLN* 4.2 15.5 - - - +
107A ALA 2.5 24.2 + - - +
108A ALA* 2.8 6.5 + - - +
110A ILE* 1.3 77.6 - - - +
112A TRP* 1.3 86.9 + - + +
115A ILE* 3.0 38.2 + - + +
118A TYR* 3.2 42.0 - - + +
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Residues in contact with TRP 112 (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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82A LEU* 5.0 1.3 - - + -
85A ALA* 5.7 2.0 - - + -
86A LEU* 3.6 31.9 - - + -
108A ALA* 2.9 8.7 + - + +
109A ALA 5.3 0.4 - - - +
111A LEU* 1.3 91.1 - - + +
113A HIS* 1.3 63.1 + - - +
115A ILE 4.0 14.2 - - - +
116A PRO* 4.1 11.6 - - + +
118A TYR* 2.7 43.2 - + - -
119A GLN* 3.2 34.2 - - + +
120A ASP 4.7 1.6 - - - -
121A GLN* 3.1 31.7 + - + +
122A PRO* 4.4 9.3 - - + +
123A VAL* 3.3 42.8 - - + +
126A PHE* 3.3 30.1 - + - -
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Residues in contact with HIS 113 (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 ALA* 3.1 25.0 + - + +
110A ILE* 3.8 7.2 + - + -
111A LEU 3.4 0.2 - - - -
112A TRP* 1.3 81.5 - - - +
114A LYS* 1.3 61.8 + - + +
116A PRO* 5.0 4.9 - - - +
123A VAL 5.7 4.7 - - - -
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Residues in contact with LYS 114 (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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110A ILE* 3.2 50.1 + - + +
111A LEU 4.9 0.2 - - - +
113A HIS* 1.3 80.0 - - - +
115A ILE* 1.3 63.8 + - + +
116A PRO* 4.2 3.8 - - - +
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Residues in contact with ILE 115 (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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111A LEU* 3.0 30.2 + - + +
112A TRP* 4.0 5.5 - - - -
113A HIS 3.4 0.8 - - - -
114A LYS* 1.3 83.2 - - + +
116A PRO* 1.3 61.2 - - + +
117A GLU* 3.3 14.3 + - + +
118A TYR* 3.1 58.3 - - + +
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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