Contacts of the helix formed by residues 95 - 110 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ALA 6.0 0.2 - - - -
86B ILE* 3.8 29.2 - - + -
89B PHE* 3.7 37.7 - - + -
94B GLY* 1.3 70.3 - - - -
96B PRO* 1.3 64.1 - - + +
97B GLU* 3.9 11.2 - - + +
98B PHE* 2.8 37.5 + - + +
99B ARG* 3.4 4.6 + - - +
312B THR* 4.4 5.2 - - + +
315B GLN* 2.9 21.6 + - + +
316B TYR* 3.9 33.0 - - + +
319B ALA* 5.6 2.7 - - + -
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Residues in contact with PRO 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 4.9 6.5 - - + -
94B GLY 3.4 6.5 - - - +
95B LEU* 1.3 83.9 - - + +
97B GLU* 1.3 80.1 + - - +
98B PHE 3.2 0.5 + - - -
99B ARG* 3.2 31.9 + - - +
100B LYS* 3.0 41.3 + - - +
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Residues in contact with GLU 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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95B LEU* 3.9 11.2 - - + +
96B PRO* 1.3 90.5 - - - +
98B PHE* 1.3 60.2 + - - +
100B LYS* 3.6 22.3 + - + +
101B ALA* 2.8 33.3 + - - +
319B ALA* 3.5 22.1 - - + +
323B SER* 5.2 0.7 + - - -
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Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B HIS 5.5 0.7 - - - -
95B LEU* 2.8 22.4 + - + +
97B GLU* 1.3 75.6 - - - +
99B ARG* 1.3 71.3 + - + +
101B ALA* 3.5 1.5 - - + +
102B ILE* 2.9 54.2 + - + +
121B VAL* 5.4 1.8 - - + -
123B MET* 3.8 31.4 - - + -
287B VAL* 3.6 20.4 - - + -
289B ILE* 4.3 5.6 - - + -
310B VAL* 4.6 4.0 - - + -
315B GLN* 3.8 50.0 - - + +
318B LEU* 3.4 31.4 - - + -
319B ALA* 3.9 8.7 - - - +
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B HIS* 3.3 62.3 + - - +
94B GLY 4.1 4.0 + - - -
95B LEU 3.4 1.5 + - - +
96B PRO* 3.2 42.1 + - - +
98B PHE* 1.3 82.7 - - + +
100B LYS* 1.3 57.4 - - - +
102B ILE 3.4 0.3 + - - -
103B ALA* 3.0 31.7 + - - +
118B PRO* 3.4 32.6 - - + +
119B GLU* 4.8 12.4 - - - +
121B VAL* 3.7 31.7 - - + +
123B MET* 6.5 0.4 - - + -
302B ARG* 4.8 2.1 - - - +
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PRO* 3.0 34.5 + - - +
97B GLU* 3.6 26.4 + - + +
99B ARG* 1.3 76.4 - - + +
101B ALA* 1.3 53.3 + - - +
103B ALA* 3.7 2.2 - - - +
104B LYS* 2.7 46.3 + - + +
118B PRO* 3.9 20.2 - - + -
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Residues in contact with ALA 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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97B GLU 2.8 21.4 + - - +
98B PHE* 3.5 3.8 - - + +
100B LYS* 1.3 71.3 - - - +
102B ILE* 1.3 55.6 + - + +
104B LYS* 3.2 8.0 + - - +
105B PHE* 2.6 38.1 + - - +
318B LEU 4.4 0.4 - - - +
319B ALA* 4.0 20.0 - - - +
322B LEU* 3.7 29.5 - - + +
323B SER* 4.4 7.6 - - - +
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Residues in contact with ILE 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 PHE* 2.9 61.4 + - + +
99B ARG 3.8 3.6 - - - +
101B ALA* 1.3 74.1 - - - +
103B ALA* 1.3 53.9 + - - +
105B PHE* 3.0 6.2 + - + +
106B MET* 2.6 55.7 + - + +
121B VAL* 4.1 15.0 - - + -
274B TYR* 4.9 5.6 - - + -
276B LEU* 4.2 17.7 - - + -
287B VAL* 4.6 2.9 - - + -
289B ILE* 4.0 21.3 - - + -
322B LEU* 3.9 18.6 - - + -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG 3.0 18.0 + - - +
100B LYS 3.7 3.4 - - - +
102B ILE* 1.3 76.2 - - - +
104B LYS* 1.3 64.5 + - - +
106B MET* 3.3 6.9 + - - +
107B GLU* 3.0 29.7 + - - +
116B PHE* 3.7 34.5 - - + +
118B PRO* 4.0 18.6 - - + -
121B VAL* 4.2 6.6 - - + +
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Residues in contact with LYS 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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100B LYS* 2.7 35.1 + - + +
101B ALA* 3.4 8.3 - - - +
103B ALA* 1.3 74.0 - - + +
105B PHE* 1.3 63.0 + - - +
107B GLU* 3.0 31.1 + - - +
108B LYS* 3.2 31.3 + - - +
322B LEU 5.1 6.5 - - - +
325B GLU* 5.8 6.5 - - - +
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA 2.6 20.1 + - - +
102B ILE* 3.5 4.3 - - + +
104B LYS* 1.3 73.1 - - - +
106B MET* 1.3 64.7 + - - +
108B LYS* 3.5 2.5 + - - +
109B THR* 3.1 37.3 + - - -
242B ALA* 4.8 0.9 - - + -
274B TYR* 3.0 31.4 - + - -
276B LEU* 4.1 20.9 - - + -
279B ASP* 4.0 9.4 - - - -
280B MET* 4.0 24.2 - - + -
322B LEU* 3.8 29.3 + - + -
328B VAL* 3.3 33.9 - - + -
331B PHE* 5.0 0.9 - + - -
332B LEU* 3.9 25.1 - - + -
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Residues in contact with MET 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 ILE* 2.6 38.4 + - + +
103B ALA* 3.7 7.0 - - - +
105B PHE* 1.3 73.6 - - + +
107B GLU* 1.3 65.2 + - - +
109B THR* 3.3 7.1 + - - -
110B ARG* 3.0 51.8 + - - +
116B PHE* 3.9 37.0 - - + -
121B VAL* 5.7 1.6 - - - -
272B ILE* 4.3 13.9 - - + -
274B TYR* 4.0 36.1 - - + -
289B ILE* 4.6 8.5 - - - -
291B TYR* 4.7 13.0 - - + -
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Residues in contact with GLU 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 ALA* 3.0 18.2 + - - +
104B LYS* 3.0 31.5 + - - +
106B MET* 1.3 73.3 - - - +
108B LYS* 1.3 70.0 + - + +
110B ARG* 2.8 15.3 + - - +
111B GLY 3.3 0.2 + - - -
112B GLY* 3.0 22.0 + - - -
114B VAL 3.7 16.4 - - - +
115B ARG* 3.0 37.5 + - - +
116B PHE* 3.6 21.2 + - + +
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Residues in contact with LYS 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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104B LYS* 3.2 24.4 + - - +
105B PHE 4.1 4.3 - - - +
107B GLU* 1.3 79.0 - - + +
109B THR* 1.3 63.6 + - - +
111B GLY* 3.1 13.2 + - - -
112B GLY* 4.3 5.8 - - - +
325B GLU* 3.8 25.3 + - - +
328B VAL* 4.1 18.6 - - + +
329B ASP* 3.0 41.5 - - - +
332B LEU* 4.0 18.3 - - + +
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Residues in contact with THR 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 PHE* 3.1 34.7 + - - -
106B MET* 3.3 11.0 - - - -
107B GLU 3.0 0.6 - - - -
108B LYS* 1.3 79.3 - - - +
110B ARG* 1.3 68.9 + - - +
111B GLY 3.2 2.6 + - - -
241B ALA* 3.2 37.6 - - + +
242B ALA* 3.9 20.7 - - + +
250B PHE* 4.4 8.6 - - + +
274B TYR* 4.1 2.6 + - - +
332B LEU* 4.2 7.3 - - - +
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MET* 3.0 44.3 + - - +
107B GLU 2.8 7.5 + - - +
109B THR* 1.3 86.4 - - - +
111B GLY* 1.3 63.3 + - - +
112B GLY 3.3 1.8 - - - -
113B ARG* 3.1 24.0 + - - +
114B VAL* 4.1 11.7 - - + -
116B PHE* 3.8 16.8 - - - -
238B GLU* 2.4 38.0 + - - +
241B ALA* 3.7 20.7 - - - +
250B PHE* 3.5 14.2 - - + -
252B SER* 3.2 31.9 + - - -
255B GLU* 3.4 12.5 - - - +
272B ILE* 4.6 1.6 - - - +
274B TYR* 3.7 22.8 - - - -
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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
------------------------------------------------------------
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