Contacts of the strand formed by residues 45 - 49 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167M ARG* 4.0 10.5 + - - +
36N VAL* 3.4 4.5 - - - +
37N ARG* 2.8 42.6 + - - +
39N ASP* 4.2 6.4 - - - +
44N GLY* 1.3 81.1 - - - +
46N VAL* 1.3 60.3 + - - +
47N ALA* 4.3 4.5 - - - +
255N ASP* 5.4 0.2 + - - -
257N HIS* 3.7 31.2 - - + +
258N VAL 3.4 11.0 - - - -
259N TYR* 3.6 28.9 - - + -
260N ARG* 3.7 12.8 - - - +
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Residues in contact with VAL 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N ILE* 3.0 42.7 - - + +
31N ILE* 4.6 11.0 - - - +
34N GLY 3.4 22.7 - - - +
35N GLU 3.2 6.5 - - - +
36N VAL* 4.5 9.0 - - + +
45N THR* 1.3 75.4 - - - +
47N ALA* 1.3 60.7 + - - +
257N HIS* 3.3 0.7 - - - -
258N VAL* 2.9 41.0 + - + +
260N ARG* 5.5 2.9 - - - -
263N VAL* 5.0 8.3 - - + -
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Residues in contact with ALA 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M PHE* 5.2 4.0 - - + -
30N ILE* 4.1 2.2 - - - -
34N GLY* 4.2 0.4 - - - -
35N GLU* 2.9 41.3 + - - +
37N ARG* 4.2 19.0 - - - +
45N THR* 4.3 2.5 - - - +
46N VAL* 1.3 77.7 - - - +
48N LEU* 1.3 70.4 + - - +
255N ASP* 3.7 13.5 - - - +
256N ALA 3.1 14.4 - - - +
257N HIS* 3.5 13.2 - - + -
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Residues in contact with LEU 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M PHE* 5.0 4.0 - - - -
26N LEU* 4.6 4.0 - - + -
29N ARG* 3.6 52.5 - - + +
30N ILE* 3.9 24.0 - - + +
33N VAL* 4.0 12.6 - - + +
34N GLY* 3.8 18.2 - - - +
35N GLU* 6.0 0.2 - - + -
47N ALA* 1.3 83.2 - - - +
49N PHE* 1.3 62.0 + - - +
51N PRO* 5.1 8.3 - - + -
254N GLY 3.6 0.2 - - - +
255N ASP* 4.1 0.7 - - - -
256N ALA* 2.9 35.9 + - + +
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Residues in contact with PHE 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M ARG* 3.9 9.0 + - - -
192M GLN* 3.5 37.5 - - + -
194M PHE* 3.4 56.9 - + + -
210M SER* 3.9 21.3 - - - -
211M CYS 4.2 2.0 - - - -
212M LEU* 3.6 30.1 - - + -
248M GLU* 5.5 0.8 - - - +
250M ILE* 4.3 5.2 - - + -
48N LEU* 1.3 75.9 - - - +
50N ALA* 1.3 75.8 + - + +
51N PRO* 3.4 1.2 - - - +
254N GLY* 3.3 32.1 - - - -
255N ASP 4.0 0.2 - - - -
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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