Contacts of the helix formed by residues 104 - 114 (chain O) in PDB entry 2D2I
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 THR 104 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102O PHE* 5.4 0.3 - - - -
103O VAL* 1.3 84.9 + - + +
105O ALA* 1.3 65.0 + - - +
106O GLU* 3.8 7.1 + - - +
107O GLY* 2.9 23.2 + - - -
108O ALA* 2.9 24.9 + - - +
121O ILE* 4.8 0.2 - - - -
126O LYS* 3.3 28.5 - - + +
127O ALA* 4.9 6.3 - - + -
130O VAL* 4.6 1.8 - - - -
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Residues in contact with ALA 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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104O THR* 1.3 72.6 - - - +
106O GLU* 1.3 57.8 + - - +
109O SER* 2.7 35.0 + - - +
126O LYS 4.1 2.4 + - - -
127O ALA* 5.5 0.6 - - - +
128O GLU 3.6 21.9 + - - +
129O GLY* 3.9 22.4 - - - +
130O VAL* 4.0 11.6 - - + +
149O VAL* 3.8 14.6 - - + +
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Residues in contact with GLU 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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104O THR* 3.2 6.9 + - - +
105O ALA* 1.3 77.8 - - - +
107O GLY* 1.3 59.6 + - - +
109O SER* 2.8 29.4 + - - -
110O LYS* 3.4 11.0 + - - +
113O GLN* 4.5 5.0 - - - +
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Residues in contact with GLY 107 (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 PHE* 4.0 21.1 - - - +
104O THR* 2.9 19.0 + - - -
106O GLU* 1.3 79.8 + - - +
108O ALA* 1.3 62.0 + - - +
110O LYS* 3.0 41.5 + - - +
111O HIS* 4.9 1.2 - - - -
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Residues in contact with ALA 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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97O GLU* 5.1 0.4 - - + -
102O PHE* 3.6 23.2 + - - +
104O THR 2.9 21.7 + - - +
107O GLY* 1.3 71.3 - - - -
109O SER* 1.3 61.7 + - - +
110O LYS 3.1 0.2 - - - -
111O HIS* 3.2 27.2 + - - +
119O VAL* 3.4 31.1 - - + +
121O ILE* 4.0 2.9 - - + -
149O VAL* 3.8 17.5 - - + -
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Residues in contact with SER 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105O ALA* 2.7 19.9 + - - +
106O GLU* 2.8 18.3 + - - -
108O ALA* 1.3 72.5 - - - +
110O LYS* 1.3 66.8 + - - +
111O HIS 2.9 2.7 - - - -
112O ILE* 2.8 17.3 + - - +
113O GLN* 2.8 38.0 + - - +
148O ALA* 5.8 0.2 - - - +
149O VAL* 3.9 10.1 - - - +
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Residues in contact with LYS 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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81O ASN* 4.7 2.3 - - - +
82O PRO* 3.6 20.3 - - + +
83O LEU* 3.4 48.3 - - + +
102O PHE* 4.2 22.9 - - + -
106O GLU* 3.4 8.3 + - - +
107O GLY* 3.0 29.3 + - - +
109O SER* 1.3 77.7 - - - +
111O HIS* 1.3 56.7 + - - +
113O GLN* 3.9 8.0 + - - +
114O ALA* 3.1 27.4 + - - +
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Residues in contact with HIS 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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8O ASN* 3.3 32.3 + - + +
82O PRO* 3.7 15.8 - - + +
85O LEU* 3.5 15.9 - - + +
87O TRP* 2.9 29.7 + - + -
95O VAL* 3.9 29.0 - - + +
97O GLU* 2.7 27.9 + - - -
102O PHE* 4.7 0.9 - - + -
107O GLY 4.9 0.4 - - - -
108O ALA* 3.2 26.4 + - - +
109O SER 2.9 0.6 - - - -
110O LYS* 1.3 76.6 - - - +
112O ILE* 1.3 61.0 + - - +
114O ALA* 3.3 2.2 + - - -
115O GLY 3.2 5.9 + - - -
116O ALA* 2.9 23.3 + - - +
119O VAL* 4.0 7.2 - - + -
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Residues in contact with ILE 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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109O SER* 2.8 15.3 + - - +
111O HIS* 1.3 72.3 - - - +
113O GLN* 1.3 68.7 + - + +
114O ALA 3.0 1.3 - - - -
115O GLY* 3.0 12.5 + - - -
116O ALA 3.1 23.5 - - - +
117O LYS* 4.1 10.3 - - - +
119O VAL* 3.6 19.3 - - + -
148O ALA* 3.1 47.3 - - + +
149O VAL* 4.3 6.7 - - + -
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Residues in contact with GLN 113 (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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83O LEU* 4.1 13.6 - - + +
106O GLU* 4.5 4.5 - - - +
109O SER* 2.8 29.9 + - - +
110O LYS* 3.5 20.5 + - - +
112O ILE* 1.3 80.7 - - + +
114O ALA* 1.3 57.1 + - - +
115O GLY 3.6 0.3 + - - -
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Residues in contact with ALA 114 (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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82O PRO 3.3 26.7 - - - +
83O LEU* 4.0 11.7 - - - +
85O LEU 3.6 19.7 - - - +
87O TRP* 4.1 7.9 - - + -
88O LYS* 3.1 22.8 + - - +
89O GLU* 4.7 1.0 - - - +
110O LYS 3.1 12.0 + - - +
111O HIS 3.6 7.2 - - - +
112O ILE 3.0 0.6 - - - -
113O GLN* 1.3 76.5 - - - +
115O GLY* 1.3 57.4 + - - +
116O ALA 3.9 0.2 - - - -
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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