Contacts of the strand formed by residues 24 - 28 (chain I) in PDB entry 2AJQ
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 24 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ASP 5.0 0.3 - - - +
22I ALA* 4.1 2.7 - - - -
23I ILE* 1.3 84.6 - - - +
25I VAL* 1.3 75.6 + - - +
52I LYS 5.1 0.4 - - - +
53I LEU* 4.0 9.2 - - + -
54I THR 2.3 46.9 + - - +
55I VAL* 2.9 33.0 - - + -
56I ALA 3.3 0.2 + - - -
78I LEU* 5.7 6.1 - - + -
79I LEU 2.5 22.2 - - - +
80I LEU* 3.3 40.4 - - + -
99I LEU* 6.3 1.1 - - + -
102I PHE* 5.9 2.7 - - + -
103I LEU* 4.5 13.7 - - + -
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Residues in contact with VAL 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I LEU* 3.4 19.3 - - + -
12I PHE* 5.1 0.9 - - + -
15I ASP 5.2 1.6 - - - +
16I VAL* 4.3 24.0 - - + -
24I LEU* 1.3 86.6 - - - +
26I ASP* 1.3 60.8 + - - +
27I PHE* 4.1 16.2 - - + -
55I VAL* 3.2 6.8 - - - +
56I ALA* 3.1 34.3 - - + +
58I LEU* 5.9 0.4 - - + -
77I THR 3.0 2.1 - - - +
78I LEU* 3.0 27.5 - - - +
79I LEU* 3.2 29.9 + - + +
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Residues in contact with ASP 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I VAL* 1.3 69.1 - - - +
27I PHE* 1.3 63.3 + - - +
28I TRP* 3.6 13.0 + - - +
38I ILE* 4.7 3.4 - - - +
42I LEU* 4.1 20.4 - - + +
55I VAL* 4.5 2.0 - - + -
56I ALA 2.3 28.1 + - - +
57I LYS* 3.4 25.7 - - + -
58I LEU 2.7 32.6 + - - +
76I PRO* 3.7 24.6 - - - +
77I THR 3.2 4.2 - - - +
78I LEU* 3.7 15.0 - - + +
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Residues in contact with PHE 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PHE* 4.5 5.4 - + - -
25I VAL* 4.2 17.0 - - + -
26I ASP* 1.3 72.1 + - - +
28I TRP* 1.3 60.2 + - - +
58I LEU* 3.2 47.6 - - + -
60I ILE* 4.0 19.7 - - + -
66I THR* 4.5 2.2 - - + -
67I ALA* 4.6 7.6 - - + -
70I TYR* 4.1 29.2 - + - -
72I ILE* 3.6 22.9 - - + -
75I ILE* 3.7 9.3 - - + +
76I PRO* 3.4 8.1 - - - +
77I THR* 2.9 34.1 + - - +
79I LEU* 3.3 36.3 - - + -
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Residues in contact with TRP 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I HIS* 3.3 22.8 + + - -
26I ASP* 3.7 15.9 - - - +
27I PHE* 1.3 74.2 - - - +
29I ALA* 1.3 79.7 + - - +
30I GLU* 3.6 39.7 - - + -
35I CYS* 3.4 27.8 - - + +
36I LYS* 5.7 4.7 - - + -
57I LYS* 3.3 36.3 - - + +
58I LEU 3.1 17.4 + - - -
59I ASN* 3.3 26.6 - - + +
60I ILE* 3.2 28.1 + - - +
62I GLN* 5.7 0.7 - - - -
75I ILE* 4.5 1.8 - - - -
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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
------------------------------------------------------------
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