Contacts of the strand formed by residues 48 - 52 (chain O) in PDB entry 5A0Q
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 ALA 48 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O VAL 3.5 8.5 - - - +
43O ARG* 4.6 0.2 - - - +
47O CYS* 1.3 75.0 - - - +
49O VAL* 1.3 65.9 + - - +
141O ILE* 3.1 39.5 - - + +
142O GLY 4.8 2.5 - - - +
149O PRO* 3.9 20.4 - - + -
150O GLN 4.5 5.4 - - - +
151O VAL* 5.0 2.9 - - + -
218O GLY 3.5 2.5 - - - +
219O VAL* 4.7 0.2 - - - -
220O VAL* 3.9 23.3 + - + +
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Residues in contact with VAL 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O ALA* 3.1 6.5 - - - +
42O VAL* 3.0 30.4 + - + +
47O CYS* 4.9 1.6 - - - -
48O ALA* 1.3 75.3 - - - +
50O ILE* 1.4 62.5 + - - +
141O ILE* 4.5 0.3 - - - +
194O THR* 3.2 35.4 - - - +
195O VAL* 3.6 29.6 - - + +
198O ALA* 4.1 22.2 - - + -
217O VAL* 3.6 26.9 - - + -
218O GLY 3.4 5.4 - - - +
219O VAL* 4.1 8.3 - - + -
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Residues in contact with ILE 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O SER* 5.6 1.1 - - - -
40O VAL 3.5 11.9 - - - +
41O ALA* 4.0 6.1 - - + +
49O VAL* 1.4 73.3 - - - +
51O VAL* 1.3 70.5 + - - +
69O LEU* 4.2 13.2 - - + -
78O CYS 4.5 0.7 - - - -
79O VAL* 3.6 26.7 - - + +
139O ILE* 3.3 42.2 - - + +
141O ILE* 3.4 33.0 - - + -
217O VAL* 3.3 4.2 - - - +
218O GLY* 2.9 41.1 + - - +
227O PHE* 4.9 4.7 - - + -
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Residues in contact with VAL 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O SER* 3.2 6.4 - - - -
40O VAL 2.9 39.9 + - - +
49O VAL* 4.9 0.2 - - + -
50O ILE* 1.3 80.3 - - - +
52O THR* 1.4 67.1 + - - +
69O LEU* 5.1 0.2 - - - -
198O ALA* 3.6 22.9 - - + +
199O ILE* 4.8 6.7 - - + -
202O LEU* 3.4 38.4 - - + -
215O ILE* 3.9 17.3 - - + -
216O GLU 3.2 14.8 - - - +
217O VAL* 4.0 15.5 - - + -
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Residues in contact with THR 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O LEU* 4.3 20.6 - - + -
38O THR 4.5 5.4 - - - +
39O SER* 3.5 25.1 - - - +
51O VAL* 1.4 76.6 + - - +
68O HIS* 4.1 23.0 - - + +
69O LEU* 3.8 6.4 - - - +
79O VAL* 3.5 27.7 - - + +
80O MET 5.3 0.2 - - - +
202O LEU* 4.3 15.3 - - - -
214O GLU 3.1 24.2 - - - +
215O ILE* 3.5 2.6 - - - -
216O GLU* 3.1 37.3 + - - +
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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