Contacts of the helix formed by residues 102 - 112 (chain O) in PDB entry 2DFS
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 102 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100O ILE 4.0 0.2 + - - -
101O SER* 1.3 71.9 - - - +
103O ALA* 1.4 56.1 + - - +
105O LEU* 3.8 11.4 - - + +
106O ARG* 3.1 32.6 + - - +
121O VAL* 5.7 0.9 - - - +
125O ILE* 5.9 9.6 - - + -
130O ILE* 4.0 18.9 - - + +
134O GLY* 3.0 20.1 + - - +
136O VAL* 5.5 0.2 - - - -
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Residues in contact with ALA 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N ASP 4.9 1.1 - - - +
23N GLY* 4.5 18.6 - - - +
101O SER* 3.2 12.0 + - - +
102O ALA* 1.4 73.6 - - - +
104O GLU* 1.3 58.3 + - - +
106O ARG* 3.4 8.4 + - - +
107O HIS* 3.0 31.4 + - - +
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Residues in contact with GLU 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N LYS 3.5 2.2 - - - +
22N ASP* 3.0 36.8 - - - +
23N GLY* 4.3 7.6 - - - -
92O PHE* 3.2 30.8 - - + +
100O ILE* 2.9 32.2 - - + +
101O SER* 2.6 35.7 + - - +
103O ALA* 1.3 74.4 - - - +
105O LEU* 1.3 59.7 + - - +
107O HIS* 3.0 4.3 + - - +
108O VAL* 2.8 34.1 + - - +
135O GLN* 4.2 4.7 + - - -
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Residues in contact with LEU 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90O ARG* 3.9 17.5 - - - +
100O ILE* 4.3 10.8 - - + -
101O SER 3.1 13.2 + - - +
102O ALA* 3.8 9.4 - - - +
103O ALA 3.4 0.2 - - - -
104O GLU* 1.3 79.5 - - - +
106O ARG* 1.3 61.2 + - - +
108O VAL* 3.4 6.8 + - - +
109O MET* 3.1 47.5 + - + +
121O VAL* 5.2 7.0 - - + -
124O MET* 6.2 0.4 - - + -
125O ILE* 4.8 17.7 - - + -
136O VAL* 4.2 17.0 - - + -
141O PHE* 3.6 42.2 - - + -
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Residues in contact with ARG 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O ALA* 3.1 19.5 + - - +
103O ALA* 3.6 7.4 - - - +
105O LEU* 1.3 75.9 - - - +
107O HIS* 1.3 57.0 + - - +
109O MET* 3.3 1.8 + - - -
110O THR* 2.8 44.1 + - + +
118O ASP* 2.7 47.0 + - - +
121O VAL* 3.9 26.3 - - + +
122O ASP* 2.6 46.0 + - - -
125O ILE* 3.6 18.4 - - - +
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Residues in contact with HIS 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N LYS* 4.9 13.1 + - - -
17N SER* 3.0 24.7 + - - +
20N ASP* 3.6 23.0 + - - +
23N GLY* 4.4 12.5 + - - -
25N GLY* 6.3 0.4 - - - -
92O PHE* 4.9 6.7 - - + -
103O ALA 3.0 15.8 + - - +
104O GLU* 3.5 11.0 - - - +
106O ARG* 1.3 77.4 - - - +
108O VAL* 1.3 61.1 + - - +
110O THR* 4.4 4.5 + - - -
111O ASN* 3.1 49.1 + - - +
112O LEU* 3.8 2.4 + - - +
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Residues in contact with VAL 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794M ALA* 4.9 9.1 - - + +
798M GLN* 3.7 5.5 + - - -
90O ARG* 3.6 33.2 - - + +
92O PHE* 3.2 36.7 - - + -
100O ILE* 5.7 0.2 - - + -
104O GLU 2.8 27.9 + - - +
105O LEU* 3.6 4.9 - - - +
107O HIS* 1.3 71.8 - - - +
109O MET* 1.3 73.1 + - + +
112O LEU* 3.2 45.3 + - + +
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Residues in contact with MET 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794M ALA* 4.5 4.3 - - - +
797M ILE* 4.0 10.3 - - + -
798M GLN* 2.8 39.8 + - + +
801M VAL* 4.1 15.7 - - - -
90O ARG* 3.4 28.5 - - - +
105O LEU* 3.1 32.9 + - + +
106O ARG 3.9 0.2 - - - +
108O VAL* 1.3 90.8 - - + +
110O THR* 1.3 59.9 + - - +
111O ASN 3.6 0.2 - - - -
115O LYS* 3.7 0.3 - - - -
116O LEU* 2.9 37.3 + - + +
121O VAL* 3.8 23.6 - - + -
141O PHE* 6.2 0.7 - - - -
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Residues in contact with THR 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O ARG* 2.8 41.4 + - + +
107O HIS* 4.4 4.0 + - - -
109O MET* 1.3 72.0 - - - +
111O ASN* 1.3 66.7 + - - +
115O LYS* 3.4 22.2 - - - +
116O LEU 3.4 21.1 - - - +
117O THR 4.0 9.2 - - - +
118O ASP* 4.1 13.6 + - - +
121O VAL* 3.8 24.2 - - + -
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Residues in contact with ASN 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791M ARG* 4.2 0.3 + - - -
13N LYS* 4.9 18.3 - - - +
14N GLU* 3.6 23.1 + - - +
17N SER* 3.1 28.5 + - - +
107O HIS* 3.1 45.3 + - - +
110O THR* 1.3 83.4 + - - +
112O LEU* 1.3 60.5 + - - +
115O LYS* 3.5 24.1 - - - +
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Residues in contact with LEU 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791M ARG* 3.9 4.5 - - + +
794M ALA* 4.6 10.5 - - + -
798M GLN* 2.9 19.1 + - - -
14N GLU 3.4 25.6 - - - +
17N SER* 3.4 29.2 - - - +
18N LEU* 3.5 26.0 - - + +
92O PHE* 3.9 14.4 - - + -
107O HIS 3.8 1.3 - - - +
108O VAL* 3.2 41.9 + - + +
111O ASN* 1.3 82.9 - - - +
113O GLY* 1.4 66.4 + - - +
115O LYS* 3.4 10.5 + - - +
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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