Contacts of the strand formed by residues 5 - 12 (chain B) in PDB entry 1AO3
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 LEU 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLN 3.3 8.0 + - - +
4B PRO* 1.3 75.4 - - - +
6B ASP* 1.3 67.6 + - - +
7B VAL* 4.5 7.2 - - + -
32B PHE* 6.3 0.2 - - + -
42B LEU 3.0 5.7 + - - -
43B THR* 3.3 18.9 - - + +
44B GLN 2.8 27.5 + - - +
104B ARG* 3.3 6.1 + - - +
108B SER* 3.5 29.6 - - - +
109B LYS 4.7 0.2 - - - -
110B ALA* 4.2 17.5 - - + -
186B LEU* 4.1 29.4 - - + +
187B CYS* 3.9 29.6 - - + -
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Residues in contact with ASP 6 (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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5B LEU* 1.3 73.8 - - - +
7B VAL* 1.3 57.9 + - - +
44B GLN* 3.6 12.8 - - - +
60B TRP* 4.0 8.0 - - + -
96B LEU* 3.6 18.4 - - + +
102B GLY 5.3 0.2 - - - +
103B ALA* 3.5 8.4 - - - +
104B ARG* 2.8 53.4 + - - +
107B ALA* 3.8 4.9 - - - +
108B SER 2.8 14.9 + - - +
109B LYS* 2.7 28.0 + - + +
110B ALA 3.0 24.3 + - - +
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Residues in contact with VAL 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.5 10.8 - - + -
6B ASP* 1.3 74.5 - - - +
8B ILE* 1.3 68.2 + - - +
9B LEU* 4.0 20.0 - - + -
32B PHE* 4.1 15.7 - - + -
43B THR* 4.0 13.0 - - + -
44B GLN 2.9 16.9 + - - +
45B VAL* 3.4 24.7 - - + +
46B SER 3.1 23.7 + - - +
60B TRP* 3.8 2.1 - - - -
110B ALA* 3.3 19.1 - - + +
112B VAL* 4.2 13.9 - - + -
186B LEU* 4.5 3.4 - - + -
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Residues in contact with ILE 8 (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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7B VAL* 1.3 76.6 - - - +
9B LEU* 1.3 74.8 + - - +
10B LEU* 3.4 13.3 + - + +
46B SER* 3.4 9.9 - - - -
48B LEU* 4.1 19.7 - - + -
60B TRP* 3.8 16.2 - - + -
92B ALA* 3.4 32.3 - - + +
95B TYR* 3.9 22.7 - - + -
96B LEU* 3.9 15.5 - - + -
110B ALA 2.9 12.7 + - - +
111B VAL* 3.5 9.9 - - + -
112B VAL* 2.9 29.1 + - - +
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Residues in contact with LEU 9 (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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7B VAL* 4.0 11.2 - - + -
8B ILE* 1.3 76.5 - - - +
10B LEU* 1.3 58.2 + - - +
11B LEU* 3.7 8.7 + - + -
28B PHE* 4.4 14.4 - - + -
29B ALA* 3.8 34.5 - - + +
32B PHE* 3.9 39.3 - - + -
33B ILE* 4.7 0.4 - - + -
45B VAL* 3.9 19.7 - - + -
46B SER 2.9 10.8 + - - +
47B VAL* 3.4 14.7 - - + +
48B LEU 2.8 27.0 + - - +
112B VAL* 3.8 14.1 - - + -
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Residues in contact with LEU 10 (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 ILE* 3.4 9.1 + - + -
9B LEU* 1.3 71.4 - - - +
11B LEU* 1.3 63.2 + - - +
48B LEU* 3.4 31.9 - - + -
49B GLN 4.0 1.6 - - - +
50B TYR* 4.0 16.7 - - + -
54B THR* 4.0 17.7 - - + -
88B ALA* 3.8 25.8 - - + +
89B LEU* 4.3 2.2 - - - +
92B ALA* 4.0 11.7 - - + -
111B VAL* 4.2 9.2 - - + -
112B VAL 2.8 16.7 + - - +
113B ILE* 3.6 26.4 - - + +
114B LEU* 3.1 25.6 + - - +
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Residues in contact with LEU 11 (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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9B LEU* 4.3 17.0 - - + -
10B LEU* 1.3 75.6 - - - +
12B ASP* 1.3 60.4 + - - +
13B GLY 3.6 0.2 - - - -
22B PHE* 4.2 18.8 - - + -
25B MET* 3.9 34.8 - - + +
26B LYS* 4.4 4.7 - - + +
28B PHE* 4.6 8.1 - - + -
29B ALA* 4.6 5.6 - - + -
47B VAL* 4.1 11.2 - - + -
48B LEU 2.8 17.8 + - - +
49B GLN* 3.0 4.7 - - + -
50B TYR* 3.0 31.3 + - - -
76B MET* 4.2 20.6 - - + -
114B LEU* 3.7 22.7 - - + -
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Residues in contact with ASP 12 (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 LEU 3.9 1.4 + - - -
11B LEU* 1.3 70.3 - - - +
13B GLY* 1.3 58.1 + - - +
14B SER* 2.8 34.3 + - - +
22B PHE* 3.5 7.0 - - - -
25B MET* 3.4 36.4 - - + +
50B TYR* 3.1 28.0 + - - -
83B SER* 4.2 3.6 + - - -
114B LEU* 3.5 18.1 - - + +
116B THR* 2.9 34.5 + - + -
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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