Contacts of the helix formed by residues 358 - 368 (chain B) in PDB entry 2NLL
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 GLN 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326B PHE* 3.5 20.0 - - + -
335B LEU* 6.2 0.4 - - - +
339B TYR* 3.7 42.0 + - + -
354B ARG 5.5 0.7 - - - -
355B ASN* 4.8 10.3 - - - +
357B CYS* 1.3 73.0 - - - +
359B GLU* 1.3 61.7 + - - +
361B ARG* 3.4 2.1 + - - +
362B PHE* 3.0 20.8 + - - +
521D C 3.9 10.5 + - - -
522D T 3.0 31.3 + - - +
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Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B TYR* 3.6 36.7 - - + +
340B SER* 3.4 3.6 - - - +
341B CYS* 2.7 49.5 + - + +
357B CYS* 3.3 1.6 - - - -
358B GLN* 1.3 78.2 - - - +
360B CYS* 1.3 59.1 + - - +
362B PHE* 3.3 3.4 + - + +
363B LYS* 2.8 36.6 + - + +
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Residues in contact with CYS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B CYS* 3.8 2.0 - - - -
345B GLY* 3.7 23.1 - - - -
347B CYS* 3.4 34.5 - - + +
349B ILE* 3.8 11.2 - - + +
357B CYS* 3.5 5.1 + - - -
358B GLN 3.4 0.4 - - - -
359B GLU* 1.3 76.0 - - - +
361B ARG* 1.3 59.9 + - - +
363B LYS* 4.1 5.9 - - - +
364B LYS* 2.9 31.0 + - - +
451B ZN 2.3 35.7 - - - -
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Residues in contact with ARG 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B VAL* 4.4 5.1 - - + +
322B GLY 3.1 26.7 - - - -
323B CYS* 3.2 21.8 - - - +
326B PHE* 3.6 41.5 - - + +
349B ILE* 3.6 22.6 - - + +
354B ARG* 3.4 38.2 - - - +
355B ASN* 3.0 21.2 - - - +
357B CYS 3.1 17.3 + - - +
358B GLN* 3.8 5.2 - - - +
359B GLU 3.2 0.2 - - - -
360B CYS* 1.3 78.4 - - - +
362B PHE* 1.3 57.5 + - - +
364B LYS* 3.3 3.4 + - - +
365B CYS* 3.0 30.7 + - - -
522D T 4.7 1.2 - - - -
523D G 3.0 29.1 + - - -
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Residues in contact with PHE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B PHE* 3.7 11.1 - + + -
327B PHE* 3.9 22.4 - + - -
330B THR* 3.5 31.0 - - + -
331B ILE* 3.7 27.6 - - + -
336B HIS* 3.8 33.2 - + + -
339B TYR* 3.9 11.9 - + + -
358B GLN 3.0 17.3 + - - +
359B GLU* 3.8 4.3 - - + +
361B ARG* 1.3 74.2 - - - +
363B LYS* 1.3 69.7 + - + +
365B CYS* 3.1 4.7 + - + +
366B ILE* 3.0 48.3 + - + +
372B THR* 4.9 0.4 - - + -
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Residues in contact with LYS 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B GLU* 2.8 28.8 + - + +
360B CYS* 4.1 4.9 - - - +
362B PHE* 1.3 77.5 - - + +
364B LYS* 1.3 56.9 + - - +
366B ILE* 3.5 21.9 + - - +
367B TYR* 2.9 54.5 + - - +
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Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B VAL 4.0 7.1 + - - -
305B VAL* 2.8 46.7 + - + +
349B ILE* 4.4 20.0 + - + -
360B CYS 2.9 19.5 + - - +
361B ARG* 3.5 6.3 - - - +
362B PHE 3.1 0.2 - - - -
363B LYS* 1.3 74.7 - - - +
365B CYS* 1.3 65.5 + - - +
367B TYR* 3.3 11.2 + - + +
368B VAL* 3.1 37.8 + - + +
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Residues in contact with CYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B VAL* 4.1 18.8 - - - -
323B CYS* 4.6 7.9 - - - -
326B PHE* 4.3 18.6 - - - -
327B PHE* 3.8 20.9 - - + -
361B ARG* 3.0 23.6 + - - -
362B PHE* 3.1 8.0 + - - +
364B LYS* 1.3 75.2 - - - +
366B ILE* 1.3 63.3 + - - +
368B VAL* 3.4 7.6 - - - +
370B MET* 3.1 51.5 + - - +
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Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B PHE* 4.0 8.1 - - + -
362B PHE* 3.0 41.9 + - + +
363B LYS* 3.7 26.2 - - - +
365B CYS* 1.3 75.7 - - - +
367B TYR* 1.3 65.7 + - - +
369B GLY* 2.8 17.2 + - - -
370B MET 4.0 7.7 + - - +
372B THR* 3.8 28.9 - - + -
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Residues in contact with TYR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LYS* 2.9 34.1 + - + +
364B LYS* 3.3 13.4 + - + +
366B ILE* 1.3 76.1 - - - +
368B VAL* 1.3 71.5 + - + +
369B GLY* 3.2 2.1 + - - -
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Residues in contact with VAL 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B VAL* 3.8 40.6 - - + +
305B VAL* 3.7 19.7 - - + -
317B CYS* 3.5 18.9 - - - -
364B LYS* 3.1 26.6 + - + +
365B CYS 3.4 15.7 - - - +
367B TYR* 1.3 82.1 - - + +
369B GLY* 1.3 56.1 + - - +
370B MET* 4.2 1.8 - - + -
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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