Contacts of the helix formed by residues 96 - 109 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A TRP* 5.9 1.8 - + - -
89B GLU 5.7 2.7 - - - -
91B ARG* 3.6 36.3 - - + -
94B LEU 3.7 4.8 + - - -
95B ASP* 1.3 74.0 + - - +
97B HIS* 1.3 69.8 + + + +
98B ALA 3.7 0.2 - - - -
99B TYR* 3.9 7.0 + - - +
100B ALA* 3.7 16.6 + - + +
117B PRO* 4.1 24.2 - - + -
118B SER* 5.2 4.5 - - - -
121B LYS* 5.0 10.8 - - + -
358B THR 4.4 4.5 - - - +
359B ARG* 3.7 23.6 - - - +
438B HIS* 3.8 37.9 - + + -
439B ASN* 3.1 46.5 + - - +
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Residues in contact with HIS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 3.4 26.9 - - - +
95B ASP* 3.0 1.8 + - - +
96B PHE* 1.3 87.4 - - + +
98B ALA* 1.3 63.0 + - - +
99B TYR 3.1 2.5 - - - -
100B ALA* 3.0 12.4 + - + +
101B ILE* 2.8 63.4 + - + +
104B MET* 5.2 2.0 - - - -
115B TYR* 3.3 45.9 + + - -
117B PRO* 3.4 29.5 - - + +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 4.5 1.2 - - - +
95B ASP* 3.3 26.4 + - + +
96B PHE 3.7 0.2 - - - -
97B HIS* 1.3 77.2 - - - +
99B TYR* 1.3 55.5 + - - +
101B ILE* 3.5 16.6 + - + +
102B PHE* 3.0 28.1 + - - +
360B GLU* 4.9 9.9 - - + -
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Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP 5.2 1.6 - - - +
96B PHE 3.9 9.9 + - - +
97B HIS 3.1 1.2 - - - -
98B ALA* 1.3 75.5 - - - +
100B ALA* 1.3 61.1 + - - +
102B PHE* 3.2 19.2 + + + +
103B LEU* 2.9 70.2 + - + +
356B PHE* 6.2 0.8 - + + -
358B THR* 3.5 36.6 - - + +
360B GLU* 4.0 20.0 - - + +
382B ARG* 3.2 42.9 + - - -
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PHE* 3.7 12.0 + - + +
97B HIS* 3.0 17.4 + - - +
99B TYR* 1.3 78.0 - - - +
101B ILE* 1.3 50.2 + - - +
103B LEU* 3.3 10.2 + - - +
104B MET* 2.7 50.6 + - + +
439B ASN* 5.7 4.5 - - - +
600B HEM 5.7 9.6 - - - +
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 5.6 0.4 - - - +
97B HIS* 2.8 59.0 + - + +
98B ALA* 3.5 15.7 - - + +
100B ALA* 1.3 71.0 - - - +
102B PHE* 1.3 67.0 + - - +
104B MET* 3.1 18.9 + - + +
105B GLU* 3.0 26.8 + - + +
110B VAL 5.0 0.2 - - - +
114B HIS* 6.6 0.2 - - + -
115B TYR* 6.0 1.3 - - + -
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA 3.0 11.7 + - - +
99B TYR* 3.4 23.6 - + + +
101B ILE* 1.3 79.7 - - - +
103B LEU* 1.3 71.2 + - + +
105B GLU* 3.8 5.1 - - + +
106B ARG* 3.0 64.7 + - + +
382B ARG* 5.6 2.7 - - - -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B TYR* 2.9 64.5 + - + +
100B ALA* 3.7 8.3 - - - +
102B PHE* 1.3 80.3 - - + +
104B MET* 1.3 66.2 + - - +
105B GLU 3.2 1.6 - - - -
106B ARG* 4.8 1.8 - - + -
107B ILE* 2.9 51.3 + - + +
108B PHE* 3.8 2.0 + - - -
218B ALA* 6.0 1.6 - - + -
600B HEM 5.9 2.9 - - - +
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Residues in contact with MET 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B HIS* 5.2 1.6 - - - -
100B ALA* 2.7 42.8 + - + +
101B ILE* 3.7 18.2 - - + +
103B LEU* 1.3 72.2 - - - +
105B GLU* 1.3 56.9 + - - +
108B PHE* 3.1 13.7 + - - +
109B ASP 3.0 21.3 + - - -
110B VAL* 3.1 38.2 + - + +
111B GLN* 5.6 0.2 - - - -
112B LEU* 3.7 24.5 - - + +
115B TYR* 4.1 17.5 - - + +
279B LEU* 4.0 24.0 - - + -
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Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ILE* 3.0 19.1 + - + +
102B PHE* 3.8 6.1 - - + +
104B MET* 1.3 75.8 - - - +
106B ARG* 1.3 69.2 + - - +
109B ASP* 3.0 30.0 + - - +
110B VAL 3.3 9.6 + - - +
111B GLN* 2.9 42.9 - - + +
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Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PHE* 3.0 51.2 + - + +
103B LEU* 4.3 1.8 - - - -
105B GLU* 1.3 85.2 - - + +
107B ILE* 1.3 82.3 + - + +
109B ASP* 4.2 5.8 - - - +
217B LEU* 3.1 37.6 + - - +
218B ALA* 3.7 21.9 + - - +
219B ARG 5.4 0.4 - - - -
220B GLY* 3.9 13.7 - - - +
234B LYS* 4.8 0.5 + - - -
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 2.9 46.9 + - + +
106B ARG* 1.3 110.0 - - + +
108B PHE* 1.3 76.2 + - + +
109B ASP 3.6 0.7 - - - -
214B LEU* 3.9 27.1 - - + +
217B LEU* 3.6 12.3 - - + +
218B ALA* 4.1 27.8 - - + +
230B MET* 5.8 0.4 - - + -
234B LYS* 2.8 31.0 + - - -
483B PHE* 6.1 1.6 - - + -
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Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU 4.6 4.3 - - - -
104B MET* 3.1 12.1 + - - +
107B ILE* 1.3 97.3 - - + +
109B ASP* 1.3 74.2 + - - +
110B VAL* 3.1 19.6 + - + +
210B LEU* 4.0 22.9 - - + -
214B LEU* 3.6 13.2 - - + -
234B LYS* 4.4 4.7 - - + +
238B TRP* 3.8 15.7 + - - -
275B ARG* 4.2 3.4 - - - +
278B VAL* 4.1 9.9 - - + -
279B LEU* 3.5 44.6 - - + -
282B TRP* 3.4 49.6 - + + -
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLU* 3.0 23.2 + - - +
106B ARG 4.2 6.4 - - - +
108B PHE* 1.3 77.4 - - - +
110B VAL* 1.3 61.0 + - - +
111B GLN* 5.1 2.9 - - - +
234B LYS* 2.8 39.9 + - - +
238B TRP* 3.7 12.2 - - + -
272B MET* 3.8 3.6 - - - +
275B ARG* 2.9 36.9 + - - +
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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