Contacts of the helix formed by residues 104 - 114 (chain I) in PDB entry 1O1F
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 GLY 104 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102I VAL 3.4 1.6 + - - -
103I MET* 1.3 71.9 - - - +
105I ALA* 1.3 60.8 + - - +
106I GLU 3.1 0.5 + - - -
107I LEU* 3.1 13.2 + - - +
108I ARG* 3.2 25.3 + - - +
131I GLU* 3.1 26.0 - - - -
135I GLY* 2.9 13.7 + - - -
137I ILE* 3.6 10.6 - - - +
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Residues in contact with ALA 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731G ALA* 5.5 1.8 - - + -
103I MET* 3.2 1.8 + - + +
104I GLY* 1.3 72.7 - - - +
106I GLU* 1.3 63.8 + - + +
108I ARG* 3.7 26.3 - - - +
109I HIS* 3.0 51.9 + - + +
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Residues in contact with GLU 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728G ASN* 4.0 2.2 - - - +
749G GLY* 6.0 5.5 - - - -
94I PHE* 3.8 32.7 - - + +
95I ASP* 5.1 3.6 - - - +
96I LYS* 5.8 1.8 + - - -
102I VAL* 3.8 5.8 - - + +
103I MET* 2.9 55.8 + - + +
105I ALA* 1.3 76.7 - - + +
107I LEU* 1.3 58.6 + - - +
109I HIS* 4.0 1.2 - - - -
110I VAL* 3.0 34.2 + - - +
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Residues in contact with LEU 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I LEU* 4.7 14.1 - - + -
94I PHE* 4.4 4.9 - - + -
102I VAL* 3.6 30.5 - - + -
103I MET 3.5 0.6 + - - -
104I GLY 3.1 1.8 + - - -
106I GLU* 1.3 77.6 - - - +
108I ARG* 1.3 57.8 + - - +
110I VAL* 3.8 3.8 - - + +
111I LEU* 2.9 46.0 + - + +
123I VAL* 5.4 0.2 - - + -
127I MET* 3.9 22.0 - - + -
137I ILE* 3.8 27.6 - - + -
139I TYR* 5.6 0.2 - - + -
142I PHE* 3.9 29.4 - - + -
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Residues in contact with ARG 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I GLY* 3.2 14.8 + - - +
105I ALA* 3.7 32.5 - - - +
106I GLU 3.3 0.2 - - - -
107I LEU* 1.3 78.7 - - + +
109I HIS* 1.3 68.5 + - + +
111I LEU* 3.9 1.9 - - - +
112I ALA* 3.1 24.4 + - - +
120I GLU* 3.7 25.2 + - - +
123I VAL* 3.6 20.4 - - + +
124I GLU* 5.3 7.9 - - - +
127I MET* 4.4 17.3 - - + -
131I GLU* 3.5 25.4 + - - +
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Residues in contact with HIS 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728G ASN* 2.4 41.1 + - - +
730G SER* 1.7 43.6 + - - +
731G ALA* 2.9 25.7 - - + +
734G GLU* 4.4 10.3 + - - -
105I ALA* 3.0 37.7 + - + +
108I ARG* 1.3 83.2 + - + +
110I VAL* 1.3 53.4 + - - +
112I ALA* 3.3 3.8 + - + -
113I THR* 2.8 26.4 + - + +
120I GLU* 5.1 7.2 - - - -
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Residues in contact with VAL 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728G ASN* 3.0 17.7 - - - +
750G GLY* 3.6 24.5 - - - -
751G GLY 4.1 2.9 - - - +
94I PHE* 3.7 19.5 - - + -
106I GLU* 3.0 19.5 + - - +
107I LEU* 3.9 4.9 - - + +
109I HIS* 1.3 75.4 - - - +
111I LEU* 1.3 57.3 + - + +
114I LEU* 2.9 50.7 + - + +
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Residues in contact with LEU 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791G GLN* 5.3 11.6 + - + +
794G CYS* 5.6 12.1 - - + -
107I LEU* 2.9 32.6 + - + +
108I ARG 3.9 3.1 - - - +
110I VAL* 1.3 78.7 - - + +
112I ALA* 1.3 59.3 + - - +
114I LEU 4.9 1.8 + - - +
116I GLU 4.0 4.3 - - - +
118I MET* 3.2 45.0 + - + +
123I VAL* 3.8 28.5 - - + -
126I LEU* 4.2 25.6 - - + -
127I MET* 5.3 1.3 - - - -
142I PHE* 5.9 2.5 - - + -
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Residues in contact with ALA 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I ARG 3.1 15.9 + - - +
109I HIS* 4.0 4.0 - - + +
111I LEU* 1.3 80.9 - - - +
113I THR* 1.3 66.8 + - + +
114I LEU 3.8 0.2 - - - -
117I LYS* 3.3 29.9 - - - +
118I MET 3.1 19.4 + - - +
120I GLU* 3.7 19.1 - - + +
123I VAL* 4.4 1.6 - - + -
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Residues in contact with THR 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726G VAL 4.0 4.5 - - - +
727G LEU* 2.0 39.2 + - - +
728G ASN* 2.2 40.8 + - - -
729G ALA* 3.7 18.6 - - + +
730G SER* 5.2 1.3 - - - +
109I HIS* 3.0 10.3 + - - +
112I ALA* 1.3 87.1 - - + +
114I LEU* 1.3 63.4 + - - +
115I GLY 3.7 2.4 + - - -
117I LYS* 3.2 25.9 + - - +
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Residues in contact with LEU 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727G LEU* 3.3 37.7 - - + +
728G ASN* 3.5 16.6 - - + +
750G GLY 3.6 2.9 - - - -
751G GLY* 2.6 47.6 - - - +
752G ASP 5.5 1.1 - - - +
787G ILE* 4.6 12.1 - - + +
791G GLN* 3.8 11.1 + - - -
110I VAL* 2.9 36.3 + - + +
111I LEU* 4.8 0.9 - - - +
112I ALA 3.8 0.8 - - - -
113I THR* 1.3 77.7 - - - +
115I GLY* 1.3 62.3 + - - +
116I GLU 3.7 4.2 + - - +
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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