Contacts of the helix formed by residues 105 - 119 (chain B) in PDB entry 2O25
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 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 3.5 16.2 - - - +
12B GLU* 3.4 24.9 - - + +
15B GLU* 3.6 21.2 + - - +
66B TYR* 5.3 0.7 - - - -
103B ALA 3.4 2.7 + - - +
104B MET* 1.3 78.2 - - - +
106B LEU* 1.3 66.5 + - - +
107B ARG* 3.4 10.7 + - - +
108B THR* 2.9 28.2 + - - +
109B VAL* 3.3 21.1 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.3 23.1 - - + +
12B GLU* 4.0 23.7 - - + +
13B PHE* 5.1 5.6 - - + +
16B VAL* 5.0 8.3 - - + -
29B VAL* 4.8 20.6 - - + -
39B LEU* 4.7 21.3 - - + -
60B ILE* 4.8 20.2 - - + -
62B ILE* 6.0 4.7 - - + -
66B TYR* 5.0 10.3 - - + +
71B PRO* 5.9 5.2 - - + -
105B THR* 1.3 74.0 - - - +
107B ARG* 1.3 57.2 + - - +
109B VAL* 3.1 9.0 + - + +
110B LEU* 2.9 41.5 + - + +
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Residues in contact with ARG 107 (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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12B GLU 5.2 1.0 + - - +
15B GLU* 3.8 31.0 - - - +
16B VAL* 4.5 18.1 - - + +
19B SER* 3.2 23.1 + - - -
20B GLU* 4.7 4.8 + - - -
21B GLU* 2.7 39.8 + - - -
27B ILE* 5.8 8.6 - - + +
105B THR* 3.4 10.1 - - - +
106B LEU* 1.3 78.2 - - - +
108B THR* 1.3 62.9 + - - +
110B LEU* 3.9 4.4 - - - +
111B LEU* 3.1 42.9 + - + +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 5.9 1.1 - - + -
104B MET* 4.3 28.1 - - + -
105B THR* 2.9 29.0 + - - +
106B LEU 3.2 0.6 - - - -
107B ARG* 1.3 78.6 - - - +
109B VAL* 1.3 57.6 + - - +
111B LEU* 3.7 5.7 - - - +
112B SER* 2.9 33.5 + - - -
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PRO* 5.5 9.0 - - + -
73B VAL* 5.4 10.3 - - + -
95B ILE* 4.8 11.7 - - + -
96B LEU* 4.5 21.5 - - + -
100B TRP* 4.9 13.0 - - + -
104B MET* 4.8 10.8 - - + -
105B THR 3.3 17.7 - - - +
106B LEU* 3.1 10.7 + - + +
108B THR* 1.3 73.2 - - + +
110B LEU* 1.3 67.5 + - + +
112B SER* 3.1 11.8 + - - +
113B LEU* 3.1 35.7 + - + +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 5.2 4.7 - - + -
27B ILE* 3.6 32.5 - - + -
28B LYS 3.4 26.5 - - - +
29B VAL* 4.7 10.8 - - + -
41B GLY* 4.5 11.4 - - - -
42B GLU 4.8 0.2 - - - +
43B ILE* 3.7 22.9 - - + +
58B LEU* 4.2 21.1 - - + -
60B ILE* 4.8 11.0 - - + -
106B LEU* 2.9 21.2 + - + +
107B ARG* 3.9 4.5 - - - +
109B VAL* 1.3 77.2 - - + +
111B LEU* 1.3 61.3 + - - +
113B LEU* 3.2 20.3 + - + +
114B GLN* 3.3 8.7 + - - +
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Residues in contact with LEU 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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21B GLU* 4.1 31.9 - - + +
26B GLN* 5.6 0.9 - - + -
27B ILE* 4.1 22.0 - - + +
107B ARG* 3.1 47.2 + - + +
108B THR* 3.9 4.5 - - - +
110B LEU* 1.3 76.5 - - - +
112B SER* 1.3 60.0 + - - +
114B GLN* 3.4 25.4 + - - +
115B ALA* 3.3 19.9 + - - +
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.5 25.7 - - - +
95B ILE* 3.5 17.7 - - - +
108B THR* 2.9 19.7 + - - -
109B VAL* 3.1 8.3 + - - -
110B LEU 3.2 0.4 - - - -
111B LEU* 1.3 75.1 - - - +
113B LEU* 1.3 66.8 + - - +
115B ALA* 3.6 6.9 + - - +
116B LEU* 3.1 21.7 + - - +
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Residues in contact with LEU 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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43B ILE* 3.8 13.0 - - + -
58B LEU* 3.9 31.9 - - + -
60B ILE* 6.2 0.9 - - + -
73B VAL* 4.6 9.9 - - + -
75B PHE* 4.5 7.0 - - + -
91B ILE* 3.8 30.7 - - + -
93B LEU* 4.1 18.8 - - + -
96B LEU* 5.7 1.6 - - + -
109B VAL* 3.1 31.8 + - + +
110B LEU* 3.2 12.1 + - + +
112B SER* 1.3 75.4 + - - +
114B GLN* 1.3 65.6 + - - +
116B LEU* 3.2 13.0 + - + +
117B LEU* 3.2 26.3 + - - +
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN* 3.0 51.1 + - - +
27B ILE* 4.7 5.6 - - + -
43B ILE* 4.1 14.1 - - + +
44B ALA 2.9 29.8 + - - +
46B PRO* 3.2 26.3 - - + +
110B LEU 3.3 8.4 + - - +
111B LEU* 3.5 27.6 - - - +
112B SER 3.2 0.4 - - - -
113B LEU* 1.3 79.1 - - - +
115B ALA* 1.3 57.0 + - - +
117B LEU* 3.2 6.6 + - - +
118B ALA* 3.1 20.0 + - - -
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Residues in contact with ALA 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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111B LEU 3.3 11.0 + - - +
112B SER* 4.0 8.5 - - - +
114B GLN* 1.3 74.6 - - - +
116B LEU* 1.3 55.7 + - - +
118B ALA* 2.9 13.1 + - + +
119B ALA* 2.7 37.2 + - - +
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Residues in contact with LEU 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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81B HIS* 3.0 32.3 - - + +
83B ASN* 4.2 24.9 - - + +
84B ILE* 5.0 9.2 - - + -
91B ILE* 4.2 15.0 - - + -
92B CYS 4.9 1.6 - - - +
93B LEU* 4.0 38.1 - - + -
112B SER 3.1 15.1 + - - +
113B LEU* 3.2 19.9 + - + +
115B ALA* 1.3 74.0 - - - +
117B LEU* 1.3 62.2 + - + +
119B ALA 3.1 25.2 - - - +
121B GLU* 5.1 4.7 - - + +
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Residues in contact with LEU 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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43B ILE* 4.5 13.2 - - + -
44B ALA 5.2 0.9 - - - +
45B GLY* 4.9 0.4 - - - -
46B PRO* 3.7 24.0 - - + -
49B THR* 3.3 15.6 - - - +
51B TYR* 3.3 19.9 - - + -
56B TYR* 4.4 17.7 - - + -
75B PHE* 4.3 8.1 - - + -
79B ILE* 3.7 33.0 - - + -
81B HIS* 3.8 12.7 - - - +
84B ILE* 3.9 19.3 - - + -
113B LEU 3.2 14.1 + - - +
114B GLN* 3.2 7.5 + - - +
115B ALA 3.1 0.2 - - - -
116B LEU* 1.3 81.1 - - + +
118B ALA* 1.3 60.2 + - - +
119B ALA* 3.1 1.1 + - - -
120B ALA* 4.5 1.7 + - - +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 3.5 26.4 - - + +
47B PRO 5.6 0.4 - - - +
49B THR* 4.1 12.8 + - - +
114B GLN 3.1 7.3 + - - +
115B ALA* 2.9 15.8 + - + +
117B LEU* 1.3 74.5 - - - +
119B ALA* 1.3 60.8 + - + +
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Residues in contact with ALA 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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115B ALA* 2.7 11.0 + - + +
116B LEU* 3.1 17.9 - - - +
117B LEU 3.1 2.0 - - - -
118B ALA* 1.3 83.1 - - + +
120B ALA* 1.3 67.6 + - - +
121B GLU* 4.7 5.0 - - - +
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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