Contacts of the strand formed by residues 236 - 239 (chain S) in PDB entry 1I84
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 ASN 236 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231S LEU 3.6 2.8 - - - +
232S GLU* 2.7 53.9 + - - +
233S ALA 3.7 0.3 - - - +
235S GLY* 1.3 80.1 - - - +
237S ALA* 1.3 63.6 + - - +
244S ASN* 3.6 25.0 - - - +
245S SER 2.8 9.4 + - - +
246S SER* 2.7 45.4 + - - +
247S ARG* 5.0 0.2 - - - -
248S PHE* 4.3 5.0 - - - -
250S LYS* 5.7 0.9 + - - +
287S PHE* 3.6 1.8 - - - -
288S HIS* 3.0 28.2 + - - +
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Residues in contact with ALA 237 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236S ASN* 1.3 74.5 - - - +
238S LYS* 1.3 58.5 + - - +
239S THR* 2.9 23.2 - - - +
243S ASP 3.9 4.5 - - - -
245S SER* 2.9 17.0 + - - +
247S ARG* 4.4 6.8 - - + +
276S ARG* 4.1 13.2 - - - +
285S ARG 3.6 9.0 - - - +
286S THR 2.9 33.7 - - - +
287S PHE* 3.9 2.5 - - + +
288S HIS* 3.4 8.0 + - - -
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Residues in contact with LYS 238 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237S ALA* 1.3 72.4 - - - +
239S THR* 1.3 86.6 + - - +
240S VAL* 4.5 2.4 - - - +
242S ASN 3.6 0.9 - - - -
243S ASP* 3.0 50.7 + - + +
276S ARG* 3.9 2.9 + - - -
283S ASP* 3.4 25.6 - - - +
284S GLU* 3.4 5.1 - - - +
285S ARG* 3.0 53.5 + - + +
288S HIS* 4.0 2.6 + - - -
321S VAL* 4.7 10.5 - - + -
322S PRO 4.7 7.4 - - - +
323S ILE* 4.3 3.8 - - + -
324S PRO* 5.3 3.1 - - + -
691S LYS* 3.7 7.7 - - - +
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Residues in contact with THR 239 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237S ALA 2.9 20.2 - - - +
238S LYS* 1.3 94.0 + - - +
240S VAL* 1.3 57.1 + - - +
241S LYS* 2.6 25.1 + - - +
242S ASN 2.8 16.6 + - - +
245S SER* 3.4 23.0 - - - +
247S ARG* 4.3 15.7 - - - +
276S ARG* 4.6 2.9 - - - +
284S GLU* 3.6 20.9 - - - -
472S PHE* 3.6 16.2 - - + -
691S LYS* 4.0 0.2 + - - -
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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