Contacts of the strand formed by residues 45 - 49 (chain I) in PDB entry 2AAZ
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 45 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36I VAL* 3.4 4.3 - - - +
37I ARG* 2.8 43.0 + - - +
38I PRO 5.2 0.2 + - - -
39I ASP* 4.2 6.9 - - - +
44I GLY* 1.3 80.7 - - - +
46I VAL* 1.3 61.2 + - - +
47I ALA* 4.3 4.2 - - - +
255I ASP* 5.4 0.3 + - - -
257I HIS* 3.8 30.1 - - + +
258I VAL 3.5 12.1 - - - -
259I TYR* 3.6 27.6 - - + -
260I ARG* 3.7 12.7 - - - +
167J ARG* 4.0 11.2 + - - +
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Residues in contact with VAL 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ILE* 3.0 41.0 - - + +
31I ILE* 4.6 10.5 - - - +
34I GLY 3.4 23.3 - - - +
35I GLU 3.2 6.5 - - - +
36I VAL* 4.6 9.0 - - + +
45I THR* 1.3 73.6 - - - +
47I ALA* 1.3 60.3 + - - +
257I HIS* 3.3 1.0 - - - -
258I VAL* 3.0 41.9 + - + +
260I ARG* 5.5 3.6 - - - -
263I VAL* 5.0 8.3 - - + -
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Residues in contact with ALA 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ILE* 4.1 2.0 - - - -
34I GLY* 4.2 1.1 - - - -
35I GLU* 2.9 41.7 + - - +
37I ARG* 4.3 17.8 - - - +
45I THR* 4.3 2.9 - - - +
46I VAL* 1.3 76.8 - - - +
48I LEU* 1.3 69.5 + - - +
255I ASP* 3.6 14.6 - - - +
256I ALA 3.1 14.6 - - - +
257I HIS* 3.5 13.0 - - + -
194J PHE* 5.2 4.8 - - + -
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Residues in contact with LEU 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I LEU* 4.6 3.8 - - + -
29I ARG* 3.6 52.3 - - + +
30I ILE* 3.9 22.9 - - + -
33I VAL* 4.0 12.6 - - + +
34I GLY* 3.8 18.2 - - - +
35I GLU* 6.0 0.4 - - + -
47I ALA* 1.3 84.1 - - - +
49I PHE* 1.3 61.2 + - - +
51I PRO* 4.6 9.0 - - + -
254I GLY 3.5 0.9 - - - +
255I ASP* 4.0 0.7 - - - -
256I ALA* 3.0 34.3 + - + +
194J PHE* 5.0 3.6 - - - -
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Residues in contact with PHE 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I LEU* 1.3 74.8 - - - +
50I ALA* 1.3 78.4 + - + +
51I PRO* 3.4 2.0 - - - +
254I GLY* 3.3 31.2 - - - -
255I ASP 4.1 0.4 - - - -
55J ARG* 3.9 8.5 + - - -
192J GLN* 3.5 38.4 - - + -
194J PHE* 3.4 59.2 - + + -
210J SER* 3.9 21.8 - - - -
211J CYS 4.3 1.8 - - - -
212J LEU* 3.7 28.9 - - + -
248J GLU* 6.0 0.4 - - - -
250J ILE* 4.3 4.7 - - + -
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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