Contacts of the strand formed by residues 247 - 250 (chain 5) in PDB entry 1O19
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 VAL 247 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1985 TYR* 5.2 1.2 + - - -
2395 SER* 4.3 12.9 + - - +
2405 TYR 3.6 6.5 - - - +
2415 GLU* 3.5 26.9 - - + +
2455 GLY 2.6 19.1 + - - +
2465 GLN* 1.3 75.5 + - - +
2485 ILE* 1.3 62.9 + - - +
2495 THR* 4.0 1.4 + - - -
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Residues in contact with ILE 248 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1935 LEU* 5.5 0.2 - - + -
1985 TYR* 3.3 52.0 - - + -
1995 SER 6.0 0.2 - - - +
2005 PHE* 3.7 27.6 - - + -
2125 ILE* 4.3 6.5 - - + -
2385 LYS 4.2 0.3 - - - +
2395 SER* 2.7 18.1 + - - -
2405 TYR* 2.9 43.7 + - + +
2425 LEU* 3.4 27.1 - - + -
2465 GLN* 3.0 9.3 + - - +
2475 VAL* 1.3 72.6 - - - +
2495 THR* 1.3 52.6 + - - +
2505 ILE* 3.7 18.6 - - + +
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Residues in contact with THR 249 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965 ARG* 2.9 36.6 + - - +
1985 TYR* 2.9 24.8 + - - +
2375 GLU* 2.7 24.0 + - - +
2385 LYS 3.9 3.4 + - - -
2395 SER* 3.1 21.5 + - - -
2475 VAL 4.0 1.9 + - - -
2485 ILE* 1.3 70.6 - - - +
2505 ILE* 1.3 69.1 + - - +
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Residues in contact with ILE 250 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1895 LEU* 5.5 2.2 - - + -
1935 LEU* 3.3 38.8 - - + -
1965 ARG* 3.5 1.6 - - - +
2125 ILE* 4.5 17.3 - - + -
2165 LEU* 4.6 11.7 - - + -
2175 CYS* 6.2 0.2 - - - -
2385 LYS* 2.6 47.4 + - - +
2485 ILE* 3.7 29.2 - - + +
2495 THR* 1.3 80.5 + - - +
2515 GLY* 1.3 57.6 + - - +
2535 GLU* 3.5 9.2 - - + +
2545 ARG* 3.6 39.6 - - + +
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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