Contacts of the strand formed by residues 49 - 52 (chain A) in PDB entry 2OLO
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 GLU 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A SER 4.8 0.2 - - - +
47A GLY* 3.6 2.9 - - - -
48A ALA* 1.3 89.4 + - - +
50A ARG* 1.3 89.8 + - - +
149A THR* 3.7 10.8 - - - +
150A ILE 3.3 6.3 - - - +
152A VAL* 3.5 2.4 - - - +
260A PHE* 3.5 34.1 - - + +
261A GLY 5.2 0.5 - - - +
263A ASN* 3.0 34.2 + - - +
265A TRP* 4.1 0.7 - - + -
271A VAL* 5.0 0.5 - - - -
272A ARG* 3.0 52.7 + - - +
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLY 2.9 24.4 + - - -
45A THR* 3.8 1.9 - - - +
46A SER* 3.0 43.1 + - - +
49A GLU* 1.3 104.1 + - - +
51A HIS* 1.3 59.7 + - - +
149A THR* 3.3 5.9 + - - -
150A ILE* 2.7 37.7 + - + +
152A VAL* 3.5 15.3 - - + -
260A PHE* 4.0 15.1 - - - -
321A CYS* 3.5 8.9 - - - -
357A PHE* 3.7 30.8 - - + -
358A LYS 5.5 0.2 - - - +
1001A FAD 2.8 58.0 + - + +
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Residues in contact with HIS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ARG* 1.3 74.3 - - - +
52A TRP* 1.3 66.7 + - - +
53A ARG* 3.5 19.7 + - + +
88A GLY 3.9 5.8 - - - -
89A SER* 2.9 34.0 + - - -
91A TRP* 6.0 0.2 - - - -
148A GLY 2.9 30.8 + - - -
149A THR* 4.6 2.1 - - - +
150A ILE* 3.7 1.4 - - - +
242A PHE* 3.3 61.4 - + + +
260A PHE* 3.9 4.4 + - + -
358A LYS* 4.1 3.8 - - - +
1001A FAD 2.7 45.5 + - - +
2001A 6PC 4.2 13.4 - - - +
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Residues in contact with TRP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A HIS* 1.3 75.8 - - - +
53A ARG* 1.3 70.4 + - - +
56A TYR* 3.7 0.8 + - - -
65A THR* 3.1 52.5 + - + +
68A THR* 4.3 5.6 - - - -
69A LEU* 3.8 34.5 - - + -
72A TRP* 3.3 38.1 - + - -
84A ILE* 4.0 27.8 - - + -
146A ASP 4.6 1.4 - - - +
147A GLY* 3.8 1.0 - - - -
148A GLY* 2.9 36.0 + - - +
150A ILE* 3.5 15.9 - - + -
358A LYS* 3.5 33.2 - - + +
359A PHE* 4.2 2.3 - + - -
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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