Contacts of the helix formed by residues 76 - 90 (chain F) in PDB entry 2I2X
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 ALA 76 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ILE* 3.8 19.4 - - + +
43F ILE* 3.9 35.8 - - + +
44F ALA* 4.6 4.0 - - - -
59F LEU* 5.0 1.1 - - + -
72F LEU* 2.7 29.7 + - + +
74F ASP 3.2 0.6 - - - -
75F ASP* 1.3 77.3 - - - +
77F LEU* 1.3 58.9 + - - +
78F MET 3.4 1.3 - - - -
79F VAL* 3.5 2.6 + - - +
80F GLY* 2.9 25.8 + - - -
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ILE* 3.8 10.8 - - + -
47F ILE* 3.6 28.8 - - + +
55F VAL* 3.6 18.8 - - + -
59F LEU* 4.1 14.1 - - + -
72F LEU 3.0 12.3 + - - +
73F ILE* 3.5 17.7 - - + +
76F ALA* 1.3 76.0 - - - +
78F MET* 1.3 59.3 + - - +
80F GLY* 3.6 1.2 + - - -
81F MET* 3.0 27.5 + - - +
105F MET* 4.1 20.7 - - + +
108F GLY* 3.5 31.4 - - - +
109F ILE* 3.6 20.9 - - + +
112F CYS* 4.7 1.3 - - - -
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Residues in contact with MET 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F ILE* 2.8 28.7 + - + +
74F ASP* 3.5 27.1 + - + +
77F LEU* 1.3 73.4 - - - +
79F VAL* 1.3 56.7 + - + +
81F MET* 3.7 3.3 - - - +
82F GLY* 2.8 28.3 + - - +
85F ILE* 5.6 1.3 - - + -
105F MET* 4.4 16.4 - - - +
109F ILE* 5.8 2.7 - - - -
148F ARG 4.9 1.8 - - - +
149F ALA 3.4 24.9 - - - +
150F ASN* 3.8 5.2 - - - +
151F GLY* 3.5 29.4 - - - +
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Residues in contact with VAL 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU 5.6 0.9 - - - +
35F PRO* 3.7 37.5 - - + -
74F ASP 3.5 16.7 + - - +
75F ASP* 3.7 15.0 - - - +
76F ALA 3.5 6.8 + - - +
77F LEU 3.4 0.2 - - - -
78F MET* 1.3 75.2 - - + +
80F GLY* 1.3 63.7 + - - +
82F GLY* 2.9 3.7 + - - +
83F VAL* 2.9 26.5 + - + +
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Residues in contact with GLY 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ALA* 3.9 24.8 - - - +
47F ILE* 3.4 16.8 - - - +
48F PHE* 5.3 0.2 - - - +
76F ALA 2.9 17.8 + - - -
77F LEU 3.8 2.0 - - - -
78F MET 3.4 0.2 - - - -
79F VAL* 1.3 76.4 - - - +
81F MET* 1.3 59.5 + - - +
83F VAL* 3.3 9.0 + - - +
84F VAL* 3.2 22.7 + - - +
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Residues in contact with MET 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE* 3.6 9.7 - - - +
77F LEU 3.0 16.8 + - - +
78F MET* 3.7 6.3 - - - +
80F GLY* 1.3 72.8 - - - +
82F GLY* 1.3 59.8 + - - +
84F VAL* 3.1 13.9 + - + +
85F ILE* 2.8 38.5 + - + +
98F VAL* 3.6 14.4 - - + +
101F SER* 3.7 24.2 - - - +
102F ALA* 3.4 32.5 - - + +
105F MET* 3.9 23.6 - - - +
149F ALA* 3.6 40.4 - - + +
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Residues in contact with GLY 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F MET* 2.8 17.6 + - - -
79F VAL* 2.9 6.6 + - - -
81F MET* 1.3 76.7 - - - +
83F VAL* 1.3 56.7 + - - +
85F ILE* 4.5 7.2 - - - +
86F ARG* 3.0 28.9 + - - +
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Residues in contact with VAL 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ALA* 4.1 15.9 - - + +
33F LEU* 3.9 39.9 - - + +
34F TYR* 4.2 21.3 - - + +
35F PRO* 4.7 4.3 - - + -
48F PHE* 4.6 3.6 - - + -
79F VAL* 2.9 21.7 + - + +
80F GLY* 3.4 9.4 - - - +
82F GLY* 1.3 75.9 - - - +
84F VAL* 1.3 63.3 + - + +
86F ARG* 3.3 7.3 + - - +
87F LEU* 3.0 43.2 + - + +
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Residues in contact with VAL 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE* 3.9 3.6 - - + -
48F PHE* 3.7 26.9 - - + -
80F GLY 3.2 13.9 + - - +
81F MET* 3.1 17.8 + - + +
83F VAL* 1.3 76.4 - - - +
85F ILE* 1.3 64.3 + - - +
87F LEU* 3.1 3.3 + - - -
88F TYR* 2.9 20.6 + - - +
93F ILE* 3.5 23.3 - - + +
98F VAL* 4.0 17.7 - - + -
101F SER* 3.5 36.6 - - - +
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Residues in contact with ILE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F MET* 5.6 1.1 - - + -
81F MET* 2.8 31.3 + - + +
82F GLY* 4.5 5.8 - - - +
84F VAL* 1.3 74.8 - - + +
86F ARG* 1.3 61.7 + - - +
88F TYR* 3.4 9.0 + - + +
89F ASP* 3.0 36.0 + - - +
98F VAL* 5.3 5.6 - - + -
146F LEU* 4.4 16.6 - - + -
149F ALA* 3.1 47.3 - - + +
150F ASN* 4.1 26.0 - - - +
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Residues in contact with ARG 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 3.4 43.7 - - + +
82F GLY 3.0 19.6 + - - +
83F VAL* 3.3 5.4 - - - +
84F VAL 3.2 0.4 - - - -
85F ILE* 1.3 79.5 - - - +
87F LEU* 1.3 57.8 + - - +
89F ASP* 3.3 8.7 + - - +
90F GLU* 3.1 52.3 + - - +
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Residues in contact with LEU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F PRO 4.6 0.2 - - - +
29F ALA* 4.0 15.3 - - + -
30F ALA* 3.8 11.9 - - - +
33F LEU* 3.8 20.2 - - + -
48F PHE* 3.5 30.5 - - + -
83F VAL* 3.0 35.3 + - + +
84F VAL 3.8 2.9 - - - +
86F ARG* 1.3 74.1 - - - +
88F TYR* 1.3 61.4 + - - +
89F ASP 3.1 0.2 - - - -
90F GLU* 3.0 13.2 + - - +
91F GLY 2.8 24.3 + - - -
92F VAL* 2.9 43.1 + - + -
93F ILE* 3.8 9.0 - - + -
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Residues in contact with TYR 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E LYS* 3.1 51.1 + - + +
237E ASN* 2.7 22.6 + - - -
84F VAL 2.9 12.9 + - - +
85F ILE* 3.8 8.7 - - + +
87F LEU* 1.3 75.3 - - - +
89F ASP* 1.3 63.2 + - - +
91F GLY* 3.0 16.5 + - - -
93F ILE* 3.4 23.8 - - + +
94F PHE 3.8 9.9 - - - -
95F LEU* 3.7 19.5 - - + +
98F VAL* 3.6 25.4 - - + -
142F ILE* 5.0 5.2 - - + +
146F LEU* 4.4 27.6 - - + -
230F GLU* 4.8 7.4 + - - -
231F ALA* 6.1 0.2 - - - +
232F ALA* 5.3 10.3 - - + -
500F B13 5.6 1.0 + - - -
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Residues in contact with ASP 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E LYS* 3.2 20.5 + - - +
85F ILE* 3.0 28.5 + - - +
86F ARG* 3.4 11.0 - - - +
88F TYR* 1.3 78.7 - - - +
90F GLU* 1.3 58.8 + - + +
91F GLY 3.0 4.7 - - - -
146F LEU* 5.5 1.6 - - - +
232F ALA* 4.8 18.1 - - - +
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Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LYS* 4.0 35.1 + - - +
33F LEU* 4.7 1.4 - - - +
86F ARG* 3.1 48.8 + - - +
87F LEU* 3.0 21.9 + - - +
89F ASP* 1.3 74.4 - - + +
91F GLY* 1.3 60.1 + - - +
92F VAL* 3.2 14.4 + - + +
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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