Contacts of the strand formed by residues 45 - 49 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ARG* 3.2 30.5 + - - +
36B VAL* 3.4 3.3 - - - -
37B ARG* 2.8 41.0 + - - +
38B PRO 5.2 0.2 + - - -
39B ASP* 4.1 4.4 - - - +
44B GLY* 1.3 80.7 - - - +
46B VAL* 1.3 63.0 + - - +
47B ALA* 4.3 4.7 - - - +
255B ASP* 5.4 0.2 + - - -
257B HIS* 3.8 23.2 - - + +
258B VAL 3.4 11.9 - - - -
259B TYR* 3.6 18.6 - - + -
260B ARG* 3.7 11.8 - - - +
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Residues in contact with VAL 46 (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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30B ILE* 3.1 41.9 - - + +
31B ILE* 4.6 10.3 - - - +
34B GLY 3.4 23.8 - - - +
35B GLU 3.3 5.8 - - - +
36B VAL* 4.3 9.0 - - + +
45B THR* 1.3 74.2 - - - +
47B ALA* 1.3 59.4 + - - +
257B HIS* 3.2 1.4 - - - -
258B VAL* 2.9 41.9 + - + +
260B ARG* 5.4 3.6 - - - -
263B VAL* 4.9 8.7 - - + -
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Residues in contact with ALA 47 (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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194A PHE* 5.1 5.2 - - + -
30B ILE* 4.1 2.5 - - - -
34B GLY* 3.5 3.6 - - - -
35B GLU* 2.9 41.8 + - - +
37B ARG* 4.1 19.0 - - - +
45B THR* 4.3 3.6 - - - +
46B VAL* 1.3 77.0 - - - +
48B LEU* 1.3 67.4 + - - +
255B ASP* 3.7 13.2 - - - +
256B ALA 3.3 13.2 - - - +
257B HIS* 3.6 12.6 - - + -
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Residues in contact with LEU 48 (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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194A PHE* 5.0 3.8 - - - -
26B LEU* 4.6 3.8 - - + -
29B ARG* 3.6 52.3 - - + +
30B ILE* 3.9 23.3 - - + -
33B VAL* 4.0 12.6 - - + +
34B GLY* 3.8 18.2 - - - -
35B GLU* 6.0 0.2 - - + -
47B ALA* 1.3 81.9 - - - +
49B PHE* 1.3 62.5 + - - +
51B PRO* 4.6 9.0 - - + -
254B GLY 3.5 0.9 - - - +
255B ASP* 4.0 1.0 - - - -
256B ALA* 3.0 35.1 + - + +
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Residues in contact with PHE 49 (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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55A ARG* 3.9 8.0 + - - -
192A GLN* 3.5 39.5 - - + -
194A PHE* 3.3 56.9 - + + -
210A SER* 3.9 20.9 - - - -
211A CYS 4.2 1.8 - - - -
212A LEU* 3.7 30.5 - - + -
248A GLU* 5.4 1.4 - - - +
250A ILE* 4.3 4.7 - - + -
48B LEU* 1.3 75.2 - - - +
50B ALA* 1.3 79.0 + - + +
51B PRO* 3.4 2.3 - - - +
254B GLY* 3.4 31.6 - - - -
255B ASP 4.0 0.4 - - - -
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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