Contacts of the helix formed by residues 95 - 110 (chain A) in PDB entry 1IAX
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 LEU 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ALA 5.4 0.4 - - - +
86A ILE* 4.4 20.6 - - + -
89A PHE* 3.6 37.6 - - + -
93A HIS 5.0 0.2 - - - +
94A GLY* 1.3 73.8 - - - +
96A PRO* 1.3 79.4 - - + +
97A GLU* 3.3 1.8 - - + +
98A PHE* 2.8 26.0 + - + +
99A ARG* 4.0 3.5 + - - +
312A THR* 3.5 26.7 - - + +
315A GLN* 2.9 21.3 + - + +
316A TYR* 3.6 31.2 - - + +
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Residues in contact with PRO 96 (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 PHE* 4.1 14.4 - - + -
94A GLY 3.4 4.6 - - - +
95A LEU* 1.3 90.2 - - + +
97A GLU* 1.3 61.4 + - + +
98A PHE 3.5 0.2 + - - -
99A ARG* 4.2 18.6 + - - +
100A LYS* 3.9 26.2 + - - +
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Residues in contact with GLU 97 (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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95A LEU* 3.3 2.3 - - + +
96A PRO* 1.3 79.2 - - + +
98A PHE* 1.3 64.3 + - - +
100A LYS* 3.7 28.2 + - - +
101A ALA* 3.0 24.1 + - - +
104A LYS* 4.8 8.5 + - - -
319A ALA* 4.0 18.4 - - + +
323A SER* 3.1 26.2 + - - +
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Residues in contact with PHE 98 (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 HIS 5.2 2.5 - - - -
95A LEU* 2.8 20.3 + - + +
97A GLU* 1.3 74.8 - - - +
99A ARG* 1.3 74.5 + - + +
101A ALA* 3.1 4.5 + - + +
102A ILE* 2.9 58.4 + - + +
121A VAL* 5.3 2.0 - - + -
123A MET* 3.6 39.5 - - + -
287A VAL* 4.0 15.9 - - + -
289A ILE* 4.5 6.5 - - + -
310A VAL* 4.7 3.6 - - + -
315A GLN* 3.9 44.9 - - + +
318A LEU* 4.3 21.8 - - + -
319A ALA* 4.2 9.2 - - - +
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Residues in contact with ARG 99 (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 HIS* 3.3 60.2 + - - +
94A GLY 5.3 1.2 + - - -
95A LEU 4.0 4.6 + - - +
96A PRO* 4.2 16.6 + - - +
97A GLU 3.6 0.2 - - - -
98A PHE* 1.3 82.7 - - + +
100A LYS* 1.3 65.1 + - + +
102A ILE* 3.4 2.9 + - - +
103A ALA* 3.0 23.9 + - - +
118A PRO* 3.0 30.8 + - + +
119A GLU* 3.0 45.8 + - - +
121A VAL* 3.8 31.8 - - + +
123A MET* 6.4 0.7 - - + -
302A ARG* 5.6 0.4 - - - +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PRO* 3.9 21.8 - - - +
97A GLU* 4.0 27.7 + - - +
98A PHE 3.2 0.6 - - - -
99A ARG* 1.3 79.1 - - + +
101A ALA* 1.3 58.2 + - - +
103A ALA* 3.4 2.9 + - - +
104A LYS* 2.9 38.5 + - + +
118A PRO* 3.5 25.8 - - + -
119A GLU* 5.9 2.9 - - - -
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Residues in contact with ALA 101 (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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97A GLU* 3.0 20.2 + - - +
98A PHE* 3.5 4.7 - - + +
100A LYS* 1.3 74.1 - - - +
102A ILE* 1.3 68.1 + - + +
104A LYS* 3.3 12.4 + - - +
105A PHE* 2.8 24.9 + - - +
318A LEU 4.7 0.4 - - - +
319A ALA* 4.1 16.2 - - - +
322A LEU* 3.9 28.4 - - + +
323A SER* 4.2 10.1 - - - +
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Residues in contact with ILE 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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98A PHE* 2.9 58.9 + - + +
99A ARG* 3.7 6.7 - - - +
101A ALA* 1.3 76.5 - - + +
103A ALA* 1.3 51.0 + - - +
105A PHE* 2.9 10.6 + - + +
106A MET* 2.6 58.4 + - + +
121A VAL* 4.2 9.9 - - + -
274A TYR* 5.1 4.7 - - + -
276A LEU* 4.8 8.3 - - + -
287A VAL* 4.5 11.4 - - + -
289A ILE* 4.1 22.0 - - + -
322A LEU* 4.2 17.5 - - + -
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Residues in contact with ALA 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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99A ARG 3.0 17.2 + - - +
100A LYS 3.7 4.0 - - - +
102A ILE* 1.3 74.2 - - - +
104A LYS* 1.3 65.6 + - - +
106A MET* 3.1 6.4 + - - +
107A GLU* 2.9 30.8 + - - +
116A PHE* 3.8 32.9 - - + +
118A PRO* 4.0 17.3 - - + -
121A VAL* 4.5 5.8 - - + +
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Residues in contact with LYS 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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97A GLU* 4.8 8.5 + - - -
100A LYS* 2.9 28.2 + - + +
101A ALA* 3.8 5.8 - - - +
103A ALA* 1.3 71.8 - - + +
105A PHE* 1.3 58.1 + - - +
107A GLU* 3.3 17.0 + - - +
108A LYS* 3.0 32.9 + - + +
322A LEU 4.7 12.1 + - - +
323A SER* 4.4 27.7 + - - +
325A GLU* 4.8 19.6 + - - +
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Residues in contact with PHE 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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101A ALA 2.8 14.6 + - - +
102A ILE* 3.2 10.1 - - + +
104A LYS* 1.3 76.4 - - - +
106A MET* 1.3 64.9 + - - +
108A LYS* 3.5 2.9 + - - +
109A THR* 3.0 30.7 + - - -
242A ALA* 5.1 1.3 - - + -
274A TYR* 3.3 30.3 - + - -
276A LEU* 3.9 25.4 - - + -
279A ASP* 4.2 4.9 - - - -
280A MET* 3.2 36.6 - - + -
322A LEU* 3.6 26.9 + - + +
328A VAL* 3.8 28.7 - - + -
332A LEU* 4.0 22.2 - - + -
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Residues in contact with MET 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 ILE* 2.6 42.9 + - + +
103A ALA* 3.1 7.4 + - - +
105A PHE* 1.3 73.4 - - - +
107A GLU* 1.3 60.4 + - - +
109A THR* 3.3 1.0 - - - -
110A ARG* 2.8 61.1 + - - +
116A PHE* 3.5 40.7 - - + -
121A VAL* 5.0 5.8 - - - -
272A ILE* 4.3 12.3 - - + -
274A TYR* 4.0 29.6 - - + -
289A ILE* 4.3 10.1 - - + -
291A TYR* 4.5 7.6 - - + -
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Residues in contact with GLU 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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103A ALA 2.9 24.5 + - - +
104A LYS* 3.5 18.9 - - - +
105A PHE 3.1 0.2 - - - -
106A MET* 1.3 74.8 - - - +
108A LYS* 1.3 68.7 + - - +
109A THR 2.8 2.2 + - - -
110A ARG* 3.0 9.0 + - - -
112A GLY* 2.7 30.7 + - - -
114A VAL 3.7 16.6 - - - +
115A ARG* 2.9 31.5 + - - -
116A PHE* 2.9 37.4 + - + +
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Residues in contact with LYS 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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104A LYS* 3.0 19.3 + - + +
105A PHE 4.0 3.8 - - - +
107A GLU* 1.3 76.0 - - + +
109A THR* 1.3 63.4 + - - +
111A GLY* 3.4 11.5 + - - +
112A GLY* 4.3 6.7 - - - +
325A GLU* 3.8 30.1 + - - +
328A VAL* 4.1 16.8 - - + -
329A ASP* 3.0 32.1 + - - +
332A LEU* 3.8 23.6 - - + +
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Residues in contact with THR 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 PHE* 3.0 27.0 + - - -
106A MET 3.3 5.4 - - - -
107A GLU 2.8 0.2 + - - -
108A LYS* 1.3 75.2 - - - +
110A ARG* 1.3 78.1 + - + +
111A GLY 2.9 9.9 + - - -
241A ALA* 3.3 42.0 - - + +
242A ALA* 4.0 13.5 - - - +
250A PHE* 4.5 6.7 - - + +
274A TYR* 3.7 12.7 + - - +
332A LEU* 4.5 7.8 - - - +
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Residues in contact with ARG 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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106A MET* 2.8 43.3 + - - +
107A GLU 3.0 3.9 + - - +
109A THR* 1.3 98.1 - - - +
111A GLY* 1.3 54.1 + - - -
112A GLY 3.2 8.9 + - - -
113A ARG* 3.8 9.5 + - - +
114A VAL* 4.0 12.3 - - + +
116A PHE* 3.6 18.6 - - - -
238A GLU* 2.7 43.2 + - - +
241A ALA* 3.8 5.1 - - - +
249A GLN* 5.3 1.6 - - - -
250A PHE* 3.4 16.8 - - + -
252A SER* 3.1 31.9 - - - -
255A GLU* 3.3 26.4 - - - +
272A ILE* 4.9 1.2 - - - +
274A TYR* 3.3 33.1 - - - -
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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