Contacts of the strand formed by residues 238 - 241 (chain W) 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 LYS 238 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216W LEU* 3.8 34.7 - - + +
237W GLU* 1.3 85.3 + - - +
239W SER* 1.3 101.7 + - - +
240W TYR 3.9 0.5 + - - -
249W THR* 4.2 0.9 - - - -
250W ILE* 2.6 45.2 + - - +
254W ARG* 3.5 29.4 - - - +
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Residues in contact with SER 239 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216W LEU* 4.9 2.5 - - - +
238W LYS* 1.3 94.7 + - - +
240W TYR* 1.3 60.8 - - - +
241W GLU 4.4 0.3 + - - -
247W VAL* 4.3 12.2 + - - +
248W ILE 2.7 19.2 + - - -
249W THR* 3.1 21.6 + - - +
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Residues in contact with TYR 240 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208W ILE* 3.2 39.0 - - + +
211W ASP* 2.9 31.8 + - - -
212W ILE* 3.9 28.9 - - + -
215W LYS* 4.1 16.6 + - + -
216W LEU* 3.9 27.6 - - + -
238W LYS 3.9 0.8 + - - -
239W SER* 1.3 73.4 - - - +
241W GLU* 1.3 79.2 + - - +
242W LEU* 4.1 4.5 - - + -
247W VAL* 3.6 2.6 - - - -
248W ILE* 2.9 43.5 + - + +
250W ILE* 5.1 1.1 - - + -
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Residues in contact with GLU 241 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3249 THR* 3.2 32.8 - - + +
239W SER 4.4 0.8 + - - -
240W TYR* 1.3 85.9 - - - +
242W LEU* 1.3 67.4 + - - +
245W GLY* 3.2 14.8 - - - +
247W VAL* 3.5 19.6 - - + +
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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