Contacts of the helix formed by residues 96 - 109 (chain A) in PDB entry 2IAG
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 PHE 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A GLU 6.1 0.7 - - - -
91A ARG* 4.2 19.7 - - + -
94A LEU 5.0 2.2 - - - -
95A ASP* 1.3 75.3 + - - +
97A HIS* 1.3 72.1 + - - +
98A ALA 3.5 1.7 + - - -
99A TYR* 3.6 8.6 + - - +
100A ALA* 3.4 21.0 + - + +
117A PRO* 3.9 30.5 - - + -
118A SER* 5.2 4.0 - - - -
121A LYS* 3.7 20.0 - - + -
358A THR 4.0 9.9 - - - +
359A ARG* 3.8 29.3 - - - +
438A HIS* 4.7 19.7 - - + -
439A ASN* 3.3 43.7 + - + +
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Residues in contact with HIS 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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91A ARG* 3.9 22.2 - - - +
95A ASP* 3.0 11.7 + - - +
96A PHE* 1.3 85.0 - - + +
98A ALA* 1.3 55.7 + - - +
100A ALA* 3.2 11.4 + - + +
101A ILE* 2.8 70.0 + - + +
104A MET* 5.5 1.1 - - - -
115A TYR* 3.2 45.4 + + - -
117A PRO* 3.7 34.5 - - + +
121A LYS* 6.2 0.2 - - - -
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Residues in contact with ALA 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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95A ASP* 3.2 20.2 + - - +
96A PHE 3.5 0.2 - - - -
97A HIS* 1.3 76.9 - - - +
99A TYR* 1.3 57.9 + - - +
101A ILE* 3.5 8.9 - - - +
102A PHE* 3.0 27.5 + - - +
360A GLU* 4.1 16.6 - - + -
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Residues in contact with TYR 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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95A ASP 6.0 0.2 - - - +
96A PHE* 3.6 8.5 + - - +
97A HIS 3.3 0.4 - - - -
98A ALA* 1.3 75.3 - - - +
100A ALA* 1.3 66.3 + - - +
102A PHE* 3.3 30.0 + + + +
103A LEU* 3.0 57.6 + - + +
218A ALA* 6.0 0.9 - - - +
356A PHE* 6.0 6.3 - + + -
358A THR* 4.1 28.0 - - + +
360A GLU* 4.4 13.7 - - + +
382A ARG* 3.5 39.1 + - - -
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Residues in contact with ALA 100 (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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96A PHE* 3.4 14.8 + - + +
97A HIS* 3.2 20.5 + - + +
99A TYR* 1.3 75.8 - - - +
101A ILE* 1.3 64.4 + - - +
103A LEU* 2.9 10.9 + - - +
104A MET* 2.9 33.4 + - + +
439A ASN* 5.9 3.1 - - - +
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Residues in contact with ILE 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 HIS* 2.8 58.7 + - + +
98A ALA* 3.5 9.0 - - - +
100A ALA* 1.3 72.7 - - - +
102A PHE* 1.3 64.0 + - - +
104A MET* 3.4 20.0 + - + +
105A GLU* 3.2 21.8 + - + +
110A VAL 4.7 0.7 - - - +
112A LEU* 5.7 5.8 - - + +
114A HIS* 6.4 3.4 - - + -
115A TYR* 4.6 10.8 - - + -
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Residues in contact with PHE 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 ALA 3.0 17.4 + - - +
99A TYR* 3.6 28.0 - + + +
100A ALA 3.2 0.4 - - - -
101A ILE* 1.3 78.1 - - - +
103A LEU* 1.3 79.8 + - + +
105A GLU* 3.6 10.4 + - - +
106A ARG* 3.0 77.2 + - + +
218A ALA 4.4 4.9 - - - -
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Residues in contact with LEU 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 TYR* 3.0 52.0 + - + +
100A ALA* 2.9 9.1 + - - +
102A PHE* 1.3 96.6 - - + +
104A MET* 1.3 65.1 + - - +
106A ARG* 5.6 0.2 - - + -
107A ILE* 2.9 53.9 + - + +
108A PHE* 4.4 2.1 - - - -
218A ALA* 4.4 11.0 - - + -
282A TRP* 6.5 1.6 - - + -
483A PHE* 5.2 10.8 - - + -
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Residues in contact with MET 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 HIS* 5.5 0.4 - - - -
100A ALA* 2.9 22.3 + - + +
101A ILE* 3.4 28.0 - - + +
103A LEU* 1.3 74.4 - - - +
105A GLU* 1.3 56.5 + - - +
108A PHE* 2.9 33.9 + - - +
109A ASP 3.1 6.8 + - - -
110A VAL* 3.2 36.3 + - + +
111A GLN* 5.2 0.2 - - - -
112A LEU* 4.0 26.0 - - + +
115A TYR* 4.3 18.4 - - + +
279A LEU* 3.7 28.9 - - + -
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Residues in contact with GLU 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 ILE* 3.2 13.5 + - + +
102A PHE* 4.0 12.0 - - - +
104A MET* 1.3 77.8 - - - +
106A ARG* 1.3 77.0 + - - +
109A ASP* 2.9 32.8 + - - +
110A VAL 3.3 17.6 + - - +
111A GLN* 5.2 11.4 - - + +
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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 PHE* 3.0 54.3 + - + +
103A LEU* 4.5 0.7 - - - +
105A GLU* 1.3 92.0 + - - +
107A ILE* 1.3 63.3 + - + +
109A ASP* 4.6 4.7 - - - +
217A LEU* 3.4 28.1 - - - +
218A ALA* 3.2 28.1 + - - +
219A ARG* 4.4 10.9 + - - +
220A GLY* 4.5 7.7 - - - +
234A LYS* 4.7 0.7 + - - -
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Residues in contact with ILE 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 LEU* 2.9 35.0 + - + +
106A ARG* 1.3 80.0 - - + +
108A PHE* 1.3 85.2 + - + +
109A ASP 3.6 0.7 - - - -
210A LEU* 4.7 2.5 - - + +
214A LEU* 3.8 26.2 - - + -
217A LEU* 4.1 16.4 - - + +
218A ALA* 3.8 38.6 - - + +
234A LYS* 2.9 28.6 + - - -
282A TRP* 6.2 2.5 - - + -
483A PHE* 4.2 13.9 - - + -
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Residues in contact with PHE 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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103A LEU 4.4 4.0 - - - -
104A MET* 2.9 14.5 + - - +
107A ILE* 1.3 104.9 - - + +
109A ASP* 1.3 74.8 + - - +
110A VAL* 3.2 19.2 + - + +
210A LEU* 4.1 22.9 - - + -
214A LEU* 4.2 6.7 - - + -
234A LYS* 4.8 2.0 - - - +
238A TRP* 3.7 16.1 + - - -
275A ARG* 4.3 4.7 - - - +
278A VAL* 3.9 16.6 - - + -
279A LEU* 3.7 31.9 - - + -
282A TRP* 3.4 57.4 - + + -
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Residues in contact with ASP 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 GLU* 2.9 25.8 + - - +
106A ARG 4.6 3.1 - - - +
108A PHE* 1.3 76.8 - - - +
110A VAL* 1.3 59.6 + - - +
111A GLN* 5.2 1.4 - - - +
234A LYS* 2.9 41.4 + - - +
238A TRP* 3.3 12.6 - - + -
272A MET* 3.7 5.4 - - - +
275A ARG* 3.0 38.7 + - - +
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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