Contacts of the strand formed by residues 104 - 108 (chain B) in PDB entry 1AO5
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 MET 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B VAL 4.1 0.2 - - - +
53B LEU* 3.4 6.4 - - - +
54B THR* 3.0 37.6 + - + +
55B ALA 3.9 10.1 - - - +
56B ALA* 3.6 29.6 - - - +
58B CYS 4.4 2.9 - - - +
59B TYR* 4.7 11.4 - - + -
64B TYR* 3.7 29.6 - - - +
88B SER* 4.1 14.8 - - - +
89B PHE 3.4 8.7 - - - +
90B PRO* 3.5 35.7 - - + -
91B HIS 4.4 0.2 - - - +
95B MET* 5.9 0.9 - - - +
103B LEU* 1.3 79.9 - - - +
105B LEU* 1.3 69.7 + - - +
106B LEU* 4.2 6.1 - - + -
237B TRP* 4.6 1.3 - - - -
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Residues in contact with LEU 105 (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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47B LEU* 4.3 7.0 - - + -
51B TRP* 3.6 25.6 - - + -
52B VAL 3.6 13.9 - - - +
53B LEU* 3.9 18.8 - - + -
88B SER* 3.2 4.9 - - - -
89B PHE* 2.7 43.8 + - + +
104B MET* 1.3 74.3 - - - +
106B LEU* 1.3 60.9 + - - +
107B ARG 4.2 0.2 - - - -
237B TRP* 4.4 11.4 - - + -
238B ILE* 4.1 22.9 - - + +
241B THR* 3.6 33.2 - - + +
242B MET* 4.3 20.0 - - + -
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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
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33B VAL* 4.5 13.2 - - + -
50B ASN 3.5 2.9 - - - +
51B TRP* 3.6 4.5 - - - -
52B VAL* 3.0 44.5 + - + +
54B THR* 3.9 27.6 - - + -
64B TYR* 3.9 31.9 - - + -
66B VAL* 4.5 14.1 - - + -
85B VAL* 3.8 17.7 - - + -
87B LYS 3.6 1.3 - - - -
88B SER* 3.4 30.3 - - - -
104B MET* 4.2 7.2 - - - -
105B LEU* 1.3 76.4 - - - +
107B ARG* 1.3 61.4 + - - +
108B LEU* 3.7 1.3 + - + +
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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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50B ASN* 3.2 16.6 - - + +
51B TRP* 3.7 26.2 - - + -
85B VAL* 3.6 2.8 - - - -
86B SER* 2.8 54.4 + - - +
87B LYS* 2.9 30.5 + - - +
89B PHE* 3.2 30.2 - - + -
106B LEU* 1.3 71.3 - - - +
108B LEU* 1.3 64.8 + - - +
245B ASN* 3.3 38.1 + - - +
246B ALA* 4.8 14.3 - - - +
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Residues in contact with LEU 108 (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 LEU* 4.8 2.2 - - + -
49B ARG 3.4 22.7 - - - +
50B ASN* 2.9 30.5 + - - +
52B VAL* 3.9 22.7 - - + -
66B VAL* 3.6 28.5 - - + -
68B LEU* 4.5 6.3 - - + -
83B ARG* 4.0 22.7 - - + -
84B LEU 3.5 7.0 - - - +
85B VAL* 4.2 13.5 - - + -
86B SER* 4.0 1.0 + - - -
106B LEU 4.7 1.3 - - - +
107B ARG* 1.3 82.8 - - - +
109B SER* 1.3 65.4 + - - +
110B LYS 3.5 11.6 + - - +
112B ALA* 4.2 10.1 - - + -
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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