Contacts of the strand formed by residues 232 - 236 (chain C) in PDB entry 3N6J
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 ARG 232 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C LYS 3.1 8.4 + - - +
204C ASP* 3.4 26.2 + - - +
205C PHE 3.2 22.4 + - - +
225C LYS* 5.0 2.0 - - - +
230C ASP 3.7 5.3 + - - +
231C ALA* 1.3 67.9 - - - +
233C ILE* 1.3 60.4 + - - +
234C THR* 4.6 3.6 - - + +
258C THR* 3.4 40.0 - - + +
259C TYR* 5.0 4.9 - - - -
310C ILE* 5.6 2.6 - - - +
336C THR* 6.0 0.6 - - - +
364C THR* 3.0 29.9 + - - +
365C ALA* 5.8 1.6 - - - +
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Residues in contact with ILE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C PHE* 3.5 20.6 - - + +
221C VAL* 3.9 26.7 - - + +
224C LEU* 3.6 54.3 - - + +
225C LYS* 3.9 8.2 - - + +
228C PHE* 3.7 9.6 - - + +
231C ALA* 3.2 35.1 + - + +
232C ARG* 1.3 70.2 - - - +
234C THR* 1.3 75.1 + - - +
256C VAL 3.8 10.4 + - - +
257C LEU* 3.7 3.4 - - - -
258C THR* 2.9 31.3 + - - -
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Residues in contact with THR 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU* 5.0 1.4 - - - +
205C PHE 3.1 5.4 + - - -
206C LYS* 3.3 31.8 - - - +
207C LEU* 3.1 22.2 + - - +
221C VAL* 4.4 0.3 - - - +
232C ARG* 4.6 4.9 - - + +
233C ILE* 1.3 88.1 - - - +
235C LEU* 1.3 62.4 + - - +
257C LEU* 3.6 10.3 - - - -
258C THR* 3.9 6.7 - - + -
259C TYR* 3.4 57.0 + - + +
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LYS* 4.9 1.6 - - - -
207C LEU* 3.3 42.6 - - + +
209C GLY* 3.9 16.2 - - - +
217C GLU* 4.2 10.1 - - + +
218C ILE* 3.9 26.2 - - + -
221C VAL* 3.8 15.9 - - + -
234C THR* 1.3 78.4 - - - +
236C ASP* 1.3 61.2 + - - +
237C PRO* 3.6 12.5 - - + +
241C TRP* 3.9 16.2 - - + -
257C LEU* 3.5 20.7 - - + +
259C TYR 3.7 0.8 + - - -
260C ALA* 3.8 4.5 - - + +
261C GLU* 2.9 25.8 + - - -
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Residues in contact with ASP 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C TYR* 3.5 10.5 + - - +
206C LYS* 4.4 5.6 - - + +
207C LEU 3.0 11.7 + - - +
208C LYS* 3.1 32.4 + - - +
209C GLY 2.7 25.0 + - - -
235C LEU* 1.3 73.8 - - - +
237C PRO* 1.3 55.0 - - - +
238C ASN* 3.4 15.1 + - - +
261C GLU* 3.0 55.0 - - + +
262C ASP* 3.8 6.8 - - - +
290C ASN* 4.7 1.4 - - - +
340C HIS* 5.2 2.4 - - - -
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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