Contacts of the helix formed by residues 283 - 290 (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 LEU 283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280C ASP* 3.5 41.3 - - + +
281C ILE 3.7 11.0 - - - +
282C ILE* 1.3 83.0 - - - +
284C GLY* 1.3 62.8 + - - +
285C ARG* 3.1 30.1 - - - +
286C HIS* 2.8 46.5 + - + +
287C PHE* 2.9 19.0 + - - -
307C ASP* 3.9 20.2 - - + +
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Residues in contact with GLY 284 (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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283C LEU* 1.3 74.7 - - - +
285C ARG* 1.3 56.6 + - - +
287C PHE* 4.0 2.3 - - - -
288C GLU* 2.8 42.5 + - - +
307C ASP* 4.8 0.6 + - - -
310C TRP* 3.5 47.4 - - - +
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Residues in contact with ARG 285 (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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263C ASP* 2.7 33.1 + - - +
283C LEU* 4.1 28.9 - - + +
284C GLY* 1.3 76.9 - - - +
286C HIS* 1.3 71.2 + - + +
288C GLU* 4.0 9.7 + - - +
289C GLN* 3.0 39.0 + - - +
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Residues in contact with HIS 286 (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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262C MET* 3.4 25.4 - - + +
263C ASP* 3.1 24.9 + - - -
266C CYS* 3.6 30.8 - - + +
281C ILE 3.3 22.6 + - - -
282C ILE* 3.6 1.9 - - + -
283C LEU* 2.8 43.4 + - + +
285C ARG* 1.3 87.8 + - + +
287C PHE* 1.3 65.4 + - - +
288C GLU 3.1 1.3 - - - -
289C GLN* 2.9 14.2 + - - +
290C MET* 2.9 28.6 + - + +
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Residues in contact with PHE 287 (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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282C ILE* 3.5 19.3 - - + -
283C LEU 2.9 25.5 + - - -
284C GLY 3.2 2.4 + - - +
286C HIS* 1.3 76.8 - - - +
288C GLU* 1.3 60.7 + - - +
289C GLN 3.4 0.3 + - - -
290C MET* 3.5 30.8 + - + +
296C VAL* 3.8 25.1 - - + -
306C ILE* 3.5 27.6 - - + -
307C ASP 3.6 20.9 - - - -
310C TRP* 3.8 29.6 - + + -
311C LEU* 3.7 32.8 - - + -
330C LEU* 3.3 18.2 - - + +
332C ASN* 4.8 0.3 + - - -
334C ARG* 5.1 0.7 + - - -
336C ILE* 3.9 11.5 - - + +
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Residues in contact with GLU 288 (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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284C GLY 2.8 27.2 + - - +
285C ARG* 4.0 8.8 + - - +
287C PHE* 1.3 75.9 - - - +
289C GLN* 1.3 55.2 + - + +
310C TRP* 3.8 26.8 + - + -
330C LEU* 4.4 2.2 - - + -
332C ASN* 3.3 16.0 + - - +
334C ARG* 2.6 29.9 + - - -
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Residues in contact with GLN 289 (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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263C ASP* 3.8 8.4 + - - +
266C CYS* 3.7 27.6 - - - +
267C GLN* 3.4 41.3 - - + +
285C ARG* 3.0 27.0 + - - +
286C HIS* 2.9 7.6 + - - +
288C GLU* 1.3 79.3 - - + +
290C MET* 1.3 70.7 + - - +
291C LYS* 5.0 0.5 - - - +
334C ARG* 4.1 3.3 + - - +
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Residues in contact with MET 290 (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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266C CYS 3.1 18.6 + - - +
272C PHE* 3.6 35.7 - - + -
282C ILE* 3.5 33.0 - - + -
286C HIS* 2.9 18.4 + - + +
287C PHE* 3.5 37.8 + - + +
289C GLN* 1.3 85.3 - - - +
291C LYS* 1.3 56.4 + - - +
294C ALA* 4.1 4.5 - - + -
296C VAL* 3.8 19.5 - - + -
334C ARG* 2.7 28.9 + - - -
336C ILE* 4.0 14.4 - - + -
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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