Contacts of the helix formed by residues 109 - 120 (chain B) in PDB entry 1DXO
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ALA* 4.0 20.6 - - + +
42B TYR* 5.7 4.0 - - + +
101B PHE* 3.6 21.8 - - + -
102B PRO 3.8 9.0 - - - +
104B GLN* 3.7 26.9 - - - +
108B VAL* 1.3 91.9 - - + +
110B ALA* 1.3 60.9 + - - +
111B ILE* 4.1 18.6 - - + +
112B LEU* 3.1 6.9 + - + +
113B LYS* 2.8 24.4 + - - +
117D GLU* 3.3 10.8 - - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PRO* 4.0 1.4 - - - +
108B VAL 3.6 0.4 + - - -
109B PRO* 1.3 72.1 - - - +
111B ILE* 1.3 57.4 + - - +
113B LYS* 4.0 3.4 - - - -
114B GLY* 2.8 26.5 + - - -
48D PRO* 3.7 12.3 - - + +
49D ILE* 4.5 3.1 - - + -
110D ALA* 3.3 14.9 - - - +
113D LYS* 3.9 9.6 - - - +
114D GLY* 3.3 32.1 - - - +
117D GLU* 2.9 24.4 + - - +
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA* 4.1 22.0 - - + -
41B LEU* 3.5 45.0 - - + +
42B TYR* 4.1 25.8 - - + +
45B ASN* 5.5 1.1 - - - -
46B PHE* 3.9 24.2 - - + +
48B PRO* 4.0 7.6 - - + +
109B PRO* 4.1 6.3 - - + +
110B ALA* 1.3 78.9 - - - +
112B LEU* 1.3 59.6 + - - +
114B GLY* 3.7 1.0 + - - -
115B TRP* 3.2 18.5 + - - +
49D ILE* 3.7 37.4 - - + +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 4.6 4.9 - - + +
10B ALA* 4.0 19.5 - - + -
41B LEU* 3.7 11.4 - - + -
99B PHE* 4.2 14.4 - - + -
101B PHE* 3.8 25.1 - - + -
108B VAL* 3.4 31.2 - - + -
109B PRO* 3.1 9.3 + - + +
111B ILE* 1.3 77.2 - - - +
113B LYS* 1.3 66.4 + - - +
114B GLY 3.2 0.4 - - - -
115B TRP* 3.2 24.0 + - + -
116B PHE* 3.2 34.7 + - + -
144B LEU* 6.1 0.2 - - + -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 3.8 17.9 - - + +
109B PRO 2.8 13.1 + - - +
110B ALA* 3.1 11.9 + - - +
112B LEU* 1.3 77.0 - - - +
114B GLY* 1.3 57.5 + - - +
116B PHE* 3.3 11.3 + - + +
117B GLU* 2.7 54.3 + - + +
175B ILE* 5.0 4.9 - - + -
104D GLN 2.8 25.9 + - - -
105D TRP* 3.9 19.1 - - + -
107D GLY* 4.7 5.6 - - - -
108D VAL* 2.7 33.4 + - + +
110D ALA* 3.7 14.4 - - + -
113D LYS* 4.8 6.3 - - + -
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Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 4.1 3.8 - - - -
48B PRO* 3.1 26.2 - - - -
110B ALA 2.8 12.7 + - - -
111B ILE 4.0 0.9 - - - -
113B LYS* 1.3 76.2 - - - +
115B TRP* 1.3 56.9 + - - +
117B GLU* 3.8 4.2 - - - +
118B ARG* 3.0 36.6 + - - +
110D ALA* 3.2 10.5 - - - +
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Residues in contact with TRP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 4.9 3.1 - - + -
8B VAL* 4.1 24.9 - - + -
41B LEU* 3.7 25.2 - - + +
46B PHE* 3.4 34.3 - + + -
87B GLU* 2.9 36.0 + - + +
91B LEU* 3.9 38.6 - - + -
97B VAL* 5.4 0.2 - - + -
99B PHE* 3.5 23.6 - + - -
111B ILE 3.2 15.2 + - - +
112B LEU* 3.2 17.4 + - + +
114B GLY* 1.3 76.2 - - - +
116B PHE* 1.3 80.9 + + - +
119B VAL* 2.9 44.8 + - + +
120B PHE* 3.9 7.0 - + - -
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 3.5 44.4 - + - -
108B VAL* 4.7 8.3 - - + -
112B LEU* 3.2 40.7 + - + -
113B LYS* 3.5 11.4 - - + +
115B TRP* 1.3 85.8 - + - +
117B GLU* 1.3 62.1 + - - +
120B PHE* 2.9 64.5 + + + +
144B LEU* 5.7 1.6 - - + -
171B ILE* 5.1 4.7 - - + -
175B ILE* 3.7 36.1 - - + -
176B LEU* 4.3 5.2 - - + -
105D TRP* 3.4 15.7 + - + +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PRO 4.5 2.8 - - - +
50B ILE* 3.6 26.3 + - + +
67B TYR* 4.2 0.9 - - - -
113B LYS* 2.7 43.9 + - - +
114B GLY* 3.8 4.8 - - - +
116B PHE* 1.3 78.9 - - - +
118B ARG* 1.3 59.0 + - - +
120B PHE 4.6 2.4 + - - +
121B ILE* 3.8 13.3 - - - +
104D GLN* 2.8 31.8 + - - +
105D TRP* 3.9 19.5 - - + -
109D PRO* 3.4 4.3 - - - +
110D ALA* 3.1 27.6 + - - +
111D ILE 4.9 0.2 + - - -
301D FAD 3.9 15.5 - - + +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 4.2 12.3 - - + -
47B ASN* 2.7 43.2 + - - +
48B PRO 4.2 3.1 - - - +
49B ILE 3.5 15.0 - - - -
50B ILE* 3.4 17.0 - - + +
54B ASP* 2.3 45.5 + - - -
67B TYR* 4.1 3.1 - - - -
81B SER* 4.1 3.6 + - - -
83B ASP* 2.4 37.0 + - - -
84B ILE* 3.2 41.4 - - + +
114B GLY 3.0 17.4 + - - +
115B TRP 4.4 0.9 - - - +
117B GLU* 1.3 79.0 - - - +
119B VAL* 1.3 59.5 + - - +
120B PHE 3.7 0.2 - - - -
121B ILE* 3.1 22.2 - - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 4.5 7.2 - - + -
84B ILE* 4.4 13.9 - - - +
87B GLU* 3.5 28.3 - - + -
88B GLN* 3.2 23.9 + - + -
91B LEU* 3.3 34.1 - - + -
115B TRP* 2.9 39.1 + - + +
118B ARG* 1.3 76.2 - - - +
120B PHE* 1.3 61.1 + - + +
121B ILE 2.8 13.1 + - - -
124B PHE* 3.2 9.3 - - + -
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.7 25.4 - - + -
99B PHE* 4.9 1.8 - + - -
115B TRP* 3.9 13.9 - + - -
116B PHE* 2.9 52.3 + + - +
117B GLU 4.7 1.2 - - - +
119B VAL* 1.3 76.0 - - + +
121B ILE* 1.3 67.2 + - - +
125B ALA* 3.6 16.6 - - + -
126B TYR* 3.8 5.5 - - - -
137B PHE* 4.3 4.5 - + - -
175B ILE* 3.9 12.1 - - + -
176B LEU* 4.7 5.6 - - + -
179B CYS* 3.6 29.2 - - - -
181B PHE* 4.3 19.3 - + - -
105D TRP* 3.3 33.4 + + + -
301D FAD 5.9 0.7 - - - +
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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