Contacts of the helix formed by residues 105 - 117 (chain F) in PDB entry 1DSX
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 PRO 105 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100F ARG* 3.7 7.0 - - - +
103F ASN 3.9 6.5 - - - +
104F VAL* 1.3 93.1 - - + +
106F LEU* 1.3 66.3 + - - +
107F ASP* 3.3 18.4 - - - +
108F ILE* 3.1 22.2 + - + +
109F PHE* 3.0 18.9 + - - +
99H ARG* 3.5 19.5 - - - +
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Residues in contact with LEU 106 (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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100F ARG* 3.3 36.2 - - + +
105F PRO* 1.3 71.8 - - - +
107F ASP* 1.3 57.1 + - - +
109F PHE* 4.6 4.0 - - + +
110F SER* 2.8 51.4 + - - +
113F ILE* 6.4 0.7 - - + -
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Residues in contact with ASP 107 (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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105F PRO* 3.3 8.1 - - - +
106F LEU* 1.3 74.1 - - - +
108F ILE* 1.3 66.8 + - - +
110F SER* 4.0 4.6 - - - -
111F GLU* 3.4 20.6 + - - +
97H ARG* 3.4 23.8 + - - +
99H ARG* 2.8 44.2 + - - -
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Residues in contact with ILE 108 (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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81F ASN* 3.7 37.5 - - + +
84F SER* 3.9 1.8 - - - +
104F VAL* 3.8 9.2 - - + -
105F PRO* 3.1 31.0 + - + +
107F ASP* 1.3 77.0 + - - +
109F PHE* 1.3 65.8 + - - +
111F GLU* 3.2 8.7 + - - +
112F GLU* 3.1 22.6 + - + +
90H TYR* 3.7 31.0 - - + +
97H ARG* 5.9 0.2 - - - +
99H ARG* 3.7 29.8 - - - +
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Residues in contact with PHE 109 (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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84F SER* 3.7 30.5 - - - -
87F ALA* 3.6 33.7 - - + -
88F ILE* 4.0 16.2 - - + -
98F LEU* 4.0 19.5 - - + -
99F ARG 3.8 4.5 - - - -
100F ARG* 3.7 36.1 - - + -
101F PRO* 3.7 13.0 - - + -
104F VAL* 4.1 6.1 - - + -
105F PRO 3.0 15.2 + - - +
106F LEU* 4.0 6.1 - - + +
108F ILE* 1.3 78.9 - - - +
110F SER* 1.3 56.2 + - - +
112F GLU* 3.1 4.2 + - + +
113F ILE* 2.9 54.5 + - + +
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Residues in contact with SER 110 (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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106F LEU* 2.8 43.9 + - - +
107F ASP* 4.0 5.8 - - - -
109F PHE* 1.3 72.9 - - - +
111F GLU* 1.3 57.5 + - - +
113F ILE* 3.3 15.3 + - - +
114F ARG* 3.0 27.4 + - - +
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Residues in contact with GLU 111 (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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80F ARG* 3.0 29.0 + - - +
107F ASP 3.4 10.1 + - - +
108F ILE* 3.2 9.7 + - - +
110F SER* 1.3 75.2 - - - +
112F GLU* 1.3 66.7 + - - +
114F ARG* 2.9 40.6 + - - +
115F PHE* 3.0 24.9 + - - +
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Residues in contact with GLU 112 (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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80F ARG* 2.9 47.2 + - - +
81F ASN* 3.5 28.3 + - + +
84F SER* 3.7 28.3 - - - +
88F ILE* 4.4 5.6 - - + -
108F ILE* 3.1 15.3 + - - +
109F PHE* 3.1 7.2 + - + +
111F GLU* 1.3 80.0 - - - +
113F ILE* 1.3 64.8 + - - +
115F PHE* 3.2 2.3 + - - -
116F TYR* 2.9 47.8 + - + -
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Residues in contact with ILE 113 (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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88F ILE* 4.5 9.6 - - + +
98F LEU* 3.6 27.4 - - + -
106F LEU* 6.4 0.7 - - + -
109F PHE* 2.9 47.3 + - + +
110F SER* 3.5 15.0 - - - +
112F GLU* 1.3 75.3 - - - +
114F ARG* 1.3 63.6 + - - +
116F TYR 3.5 0.3 + - - -
117F GLU* 3.1 16.8 + - - -
118F LEU* 3.4 26.1 + - + +
119F GLY* 4.4 10.8 + - - +
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Residues in contact with ARG 114 (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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80F ARG* 4.3 3.2 - - - +
110F SER 3.0 13.1 + - - +
111F GLU* 2.9 46.2 + - - +
113F ILE* 1.3 76.4 - - - +
115F PHE* 1.3 90.0 + - - +
117F GLU* 3.2 18.6 + - - +
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Residues in contact with PHE 115 (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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58F LEU* 3.6 30.9 - - + +
68F TYR* 3.5 33.9 - + - -
78F PHE* 3.6 24.7 - + - -
80F ARG* 3.5 57.0 - - + +
111F GLU 3.0 10.2 + - - +
112F GLU 3.2 3.6 + - - +
114F ARG* 1.3 95.5 - - - +
116F TYR* 1.3 77.3 + + - +
117F GLU* 3.2 8.1 + - - +
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Residues in contact with TYR 116 (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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39F ILE* 3.6 23.0 - - - +
57F THR* 3.7 5.5 - - - -
58F LEU* 3.2 23.4 + - + +
59F LEU* 4.2 21.3 + - + -
78F PHE* 4.3 12.4 - + - +
80F ARG* 3.7 17.0 - - - +
81F ASN 5.4 0.7 + - - -
84F SER* 6.1 0.7 - - - -
85F PHE* 3.6 19.4 - + - -
88F ILE* 3.9 33.2 - - + -
92F TYR* 4.6 2.3 + - - +
112F GLU* 2.9 46.6 + - + +
115F PHE* 1.3 98.0 - + - +
117F GLU* 1.3 69.6 + - - +
118F LEU* 3.3 20.7 + - + +
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Residues in contact with GLU 117 (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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56F GLU* 4.1 6.4 - - - +
57F THR* 3.4 18.3 - - - +
58F LEU* 4.0 16.0 - - + +
64F LYS* 2.8 43.1 + - - +
113F ILE 3.1 5.9 + - - -
114F ARG* 3.2 11.8 + - - +
115F PHE 3.2 14.4 - - - +
116F TYR* 1.3 77.9 - - - +
118F LEU* 1.3 62.0 - - - +
119F GLY 3.3 6.0 + - - +
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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