Contacts of the strand formed by residues 45 - 49 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36K VAL* 3.4 4.2 - - - +
37K ARG* 2.8 43.2 + - - +
38K PRO 5.2 0.2 + - - -
39K ASP* 4.2 6.2 - - - +
44K GLY* 1.3 81.3 - - - +
46K VAL* 1.3 61.4 + - - +
47K ALA* 4.4 4.2 - - - +
255K ASP* 5.5 0.2 + - - -
257K HIS* 3.8 29.2 - - + +
258K VAL 3.5 12.6 - - - -
259K TYR* 3.6 28.0 - - + -
260K ARG* 3.7 12.6 - - - +
167L ARG* 4.0 11.5 + - - +
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Residues in contact with VAL 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ILE* 3.0 41.0 - - + +
31K ILE* 4.6 10.3 - - - +
34K GLY 3.4 23.3 - - - +
35K GLU 3.2 6.3 - - - +
36K VAL* 4.6 9.0 - - + +
45K THR* 1.3 73.6 - - - +
47K ALA* 1.3 60.9 + - - +
257K HIS* 3.3 1.2 - - - -
258K VAL* 3.0 42.0 + - + +
260K ARG* 5.4 3.6 - - - -
263K VAL* 5.0 8.7 - - + -
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Residues in contact with ALA 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ILE* 4.1 2.2 - - - -
34K GLY* 4.2 0.9 - - - -
35K GLU* 2.9 42.4 + - - +
37K ARG* 4.2 18.3 - - - +
45K THR* 4.4 2.7 - - - +
46K VAL* 1.3 76.7 - - - +
48K LEU* 1.3 69.7 + - - +
255K ASP* 3.7 13.7 - - - +
256K ALA 3.2 14.8 - - - +
257K HIS* 3.6 13.2 - - + -
194L PHE* 5.2 4.5 - - + -
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Residues in contact with LEU 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K LEU* 4.6 3.6 - - + -
29K ARG* 3.6 52.3 - - + +
30K ILE* 3.9 23.1 - - + +
33K VAL* 4.0 11.9 - - + +
34K GLY* 3.8 17.9 - - - +
35K GLU* 6.0 0.4 - - + -
47K ALA* 1.3 84.1 - - - +
49K PHE* 1.3 61.2 + - - +
51K PRO* 4.6 8.7 - - + -
254K GLY 3.6 0.2 - - - +
255K ASP 4.1 0.7 - - - -
256K ALA* 3.0 34.8 + - + +
194L PHE* 5.1 3.6 - - - -
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Residues in contact with PHE 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K LEU* 1.3 74.6 - - - +
50K ALA* 1.3 77.1 + - + +
51K PRO* 3.4 1.7 - - - +
254K GLY* 3.3 32.3 - - - -
255K ASP 4.1 0.4 - - - -
55L ARG* 3.8 9.2 + - - -
192L GLN* 3.5 37.9 - - + -
194L PHE* 3.4 58.1 - + + -
210L SER* 3.9 22.7 - - - -
211L CYS 4.2 0.4 - - - -
212L LEU* 3.6 29.6 - - + -
248L GLU* 5.4 1.2 - - - +
250L ILE* 4.2 6.5 - - + -
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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