Contacts of the strand formed by residues 238 - 242 (chain C) in PDB entry 3NJ4
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 238 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A LEU 5.5 3.6 + - - -
403A ASN* 5.9 2.4 + - - +
238B ARG* 5.4 13.7 - - - +
239B VAL 5.9 0.4 - - - -
256B GLY* 3.6 25.3 - - - +
257B TYR* 4.5 0.6 - - - +
258B GLU* 3.2 56.8 + - - +
213C GLY 5.4 1.3 - - - +
214C LYS 3.1 10.3 + - - +
215C VAL* 3.3 30.7 - - + +
216C ALA 2.8 30.2 + - - +
236C GLY 4.1 1.4 + - - -
237C ALA* 1.3 69.0 - - - +
239C VAL* 1.3 62.1 + - - +
240C ILE* 4.3 17.0 - - + +
258C GLU* 4.3 9.2 + - + -
268C GLU* 4.2 17.2 + - - +
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Residues in contact with VAL 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ARG* 5.8 0.7 - - - -
216C ALA* 3.2 10.3 - - + +
218C VAL* 3.8 20.2 - - + -
229C ALA* 3.6 24.5 - - + +
232C LEU* 3.8 11.9 - - + -
233C ARG* 3.8 10.3 - - + +
237C ALA 3.4 15.2 + - - +
238C ARG* 1.3 78.1 - - - +
240C ILE* 1.3 66.4 + - - +
241C ILE* 3.4 22.4 - - + -
256C GLY 5.3 0.3 - - - +
257C TYR* 3.7 29.2 - - + -
258C GLU* 3.9 9.9 + - - +
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C VAL* 3.9 25.8 - - + -
216C ALA 2.7 12.4 + - - +
217C VAL* 3.3 11.5 - - + +
218C VAL 2.8 26.0 + - - -
238C ARG* 4.3 15.9 - - + +
239C VAL* 1.3 77.7 - - - +
241C ILE* 1.3 72.2 + - - +
258C GLU* 3.3 37.5 - - + +
260C THR* 3.8 22.0 - - - +
265C ALA* 4.4 13.0 - - + -
268C GLU* 4.2 22.2 - - + +
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Residues in contact with ILE 241 (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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218C VAL* 3.4 16.6 - - + +
220C GLY 4.5 0.4 - - - +
221C TYR* 3.7 38.6 - - + -
229C ALA* 4.4 3.8 - - + -
239C VAL* 3.4 24.0 - - + -
240C ILE* 1.3 78.6 - - - +
242C THR* 1.3 80.5 + - - +
243C GLU* 4.2 4.0 - - + -
252C ALA* 4.2 13.9 - - + -
257C TYR* 3.6 30.1 - - + -
258C GLU 2.8 12.8 + - - +
259C VAL* 3.0 13.8 - - + +
260C THR 3.0 24.1 + - - -
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Residues in contact with THR 242 (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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217C VAL* 4.2 22.7 - - + -
218C VAL 3.2 3.4 + - - +
219C ALA* 3.0 23.4 - - - +
220C GLY 2.9 22.4 + - - -
240C ILE* 5.5 0.7 - - + -
241C ILE* 1.3 80.2 - - - +
243C GLU* 1.3 69.9 + - - +
259C VAL* 4.5 0.2 - - - -
260C THR 3.2 21.8 - - - +
261C THR 4.0 2.5 - - - +
262C MET* 4.0 24.8 - - + +
265C ALA* 4.8 2.0 - - + -
503C NAD 3.4 10.1 - - - -
407D THR* 4.2 6.7 - - - -
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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