Contacts of the strand formed by residues 335 - 342 (chain C) in PDB entry 2NT0
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 MET 335 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LYS* 5.4 0.7 - - + -
228C TRP* 3.7 31.6 - - + -
279C LEU* 4.2 5.8 - - + -
306C HIS* 3.7 36.6 + - + +
307C GLY* 3.8 10.3 - - - -
308C ILE* 2.8 29.5 + - - +
333C ASN 4.1 1.8 + - - -
334C THR* 1.3 75.2 - - - +
336C LEU* 1.3 59.8 + - - +
337C PHE* 3.6 24.5 - - + -
376C VAL* 3.8 35.9 - - + -
500C SO4 5.7 1.3 - - - +
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Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU* 4.2 4.5 - - + -
308C ILE* 3.5 22.2 - - + -
310C VAL* 4.3 3.1 - - + -
324C LEU* 3.8 41.7 - - + +
327C THR* 4.0 21.8 - - + -
328C HIS* 4.3 19.5 - - + +
334C THR 3.6 6.2 + - - +
335C MET* 1.3 74.6 - - - +
337C PHE* 1.3 55.8 + - - +
373C TYR 4.0 16.4 - - - +
374C HIS* 4.4 9.2 + - + +
375C VAL* 3.3 16.3 - - + -
376C VAL* 2.8 36.6 + - - +
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Residues in contact with PHE 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LYS* 4.4 3.8 - - + -
118C ILE* 3.6 30.3 - - + -
175C LEU* 3.7 21.3 - - + -
228C TRP* 3.9 25.1 - + - -
279C LEU* 4.2 13.9 - - + -
308C ILE 2.9 8.9 + - - +
309C ALA* 3.1 6.6 - - + -
310C VAL* 2.7 33.5 + - - +
335C MET* 3.6 17.0 - - + -
336C LEU* 1.3 75.7 - - - +
338C ALA* 1.3 60.7 + - - +
339C SER* 3.4 8.4 + - - -
375C VAL* 3.7 3.1 - - - -
376C VAL* 3.9 9.0 - - + -
377C GLY* 3.7 26.7 - - - -
379C THR* 3.2 27.6 - - - -
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Residues in contact with ALA 338 (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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310C VAL* 3.3 15.3 - - + +
311C HIS 6.4 0.2 - - - -
312C TRP 6.3 0.2 - - - +
337C PHE* 1.3 72.5 - - - +
339C SER* 1.3 58.6 + - - +
340C GLU 3.6 4.3 - - - +
341C ALA* 6.4 1.1 - - + -
370C ASN* 3.6 23.1 - - - +
375C VAL* 3.4 2.6 - - + +
377C GLY 3.0 18.8 + - - +
378C TRP* 3.4 21.0 - - + +
379C THR* 2.9 31.5 + - - +
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Residues in contact with SER 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ARG* 3.2 22.7 + - - -
175C LEU* 4.1 12.8 - - - -
231C THR* 5.1 0.2 - - - -
282C ASP* 2.6 28.0 + - - -
309C ALA* 3.4 19.8 - - - +
310C VAL 2.8 11.6 + - - -
311C HIS* 3.1 11.4 - - - -
337C PHE* 3.4 14.0 + - - -
338C ALA* 1.3 71.4 - - - +
340C GLU* 1.3 58.1 + - - +
379C THR* 3.5 18.2 - - - +
380C ASP 4.5 0.9 - - - +
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Residues in contact with GLU 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ARG* 3.0 23.9 + - - +
179C TRP* 4.0 4.0 - - - -
234C ASN* 3.5 0.9 - - - +
310C VAL 3.7 2.0 + - - +
311C HIS* 3.2 29.8 + - + +
312C TRP 3.1 22.2 + - - -
313C TYR* 3.7 12.0 + - - -
338C ALA* 3.6 2.4 - - - +
339C SER* 1.3 85.0 + - - +
341C ALA* 1.3 64.2 + - - +
342C CYS* 4.6 3.8 - - - -
379C THR 3.2 7.9 + - - -
380C ASP 4.6 1.1 - - - -
381C TRP* 4.0 30.6 - - + -
1592C GOL 2.9 41.3 + - - -
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Residues in contact with ALA 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C TRP* 3.3 11.9 - - + +
314C LEU* 4.6 9.2 - - + -
338C ALA* 6.4 1.1 - - + -
340C GLU* 1.3 75.8 - - - +
342C CYS* 1.3 70.0 + - - +
363C TYR* 4.3 0.7 - - - -
378C TRP* 3.4 43.3 - - + +
379C THR 3.1 8.0 + - - +
380C ASP* 3.4 5.5 - - - +
381C TRP* 3.3 21.0 + - - +
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Residues in contact with CYS 342 (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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312C TRP 3.2 5.2 + - - -
313C TYR* 3.7 33.2 - - - -
314C LEU* 3.0 27.8 + - - +
315C ASP* 3.8 1.8 - - - +
340C GLU* 4.6 4.9 - - - -
341C ALA* 1.3 80.0 - - - +
343C VAL* 1.3 63.0 + - - +
363C TYR* 3.9 9.9 - - - +
381C TRP* 4.2 23.1 - - + -
397C PHE* 5.2 0.9 - - - -
398C VAL* 3.7 30.3 - - + -
399C ASP 5.1 3.1 - - - +
1592C GOL 5.5 0.7 - - - -
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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
------------------------------------------------------------
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