Contacts of the helix formed by residues 321 - 332 (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 GLU 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311B THR* 2.9 38.6 + - + +
314B HIS* 3.9 4.9 + - - -
320B CYS* 1.3 72.5 - - - +
322B GLY* 1.3 56.2 + - - +
324B LYS* 3.2 28.0 + - - +
325B GLY* 3.0 25.6 + - - -
523D G 3.9 8.9 - - + +
524D A 3.4 43.4 + - + +
525D C 2.9 35.7 + - + -
526D C 5.1 1.9 + - - -
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Residues in contact with GLY 322 (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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320B CYS* 3.0 9.3 - - - -
321B GLU* 1.3 78.9 - - - +
323B CYS* 1.3 61.8 + - - +
325B GLY* 4.0 0.3 - - - -
326B PHE* 3.1 21.0 + - - +
329B ARG* 5.3 0.5 + - - -
354B ARG* 4.4 3.3 - - - +
361B ARG* 3.1 13.0 + - - -
523D G 3.6 38.0 + - - +
524D A 4.7 1.2 + - - -
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Residues in contact with CYS 323 (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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303B CYS* 3.7 9.6 - - - -
305B VAL* 3.9 24.7 - - + -
306B CYS* 3.9 6.7 - - - -
319B THR* 4.4 6.3 - - + -
320B CYS* 3.2 5.0 + - - +
322B GLY* 1.3 73.3 - - - +
324B LYS* 1.3 60.5 + - - +
326B PHE* 3.8 1.4 - - - +
327B PHE* 2.9 32.1 + - - +
361B ARG* 3.3 28.7 - - - +
365B CYS* 4.6 6.8 - - - -
370B MET* 4.1 3.8 - - + +
450B ZN 2.3 36.6 - - - -
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Residues in contact with LYS 324 (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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314B HIS* 3.9 37.7 - - + +
315B TYR* 3.6 27.6 - - + +
319B THR* 4.2 5.0 + - - +
320B CYS 2.9 17.4 + - - +
321B GLU* 3.2 35.3 + - - +
323B CYS* 1.3 77.2 - - - +
325B GLY* 1.3 62.2 + - - +
327B PHE 3.5 0.2 + - - -
328B ARG* 3.1 36.9 + - - +
370B MET* 4.5 2.7 - - - -
513C A 4.5 9.5 + - - +
514C G 2.7 41.5 + - - -
515C G 4.6 0.2 - - - -
525D C 3.8 2.8 - - - +
526D C 4.1 3.4 - - - +
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Residues in contact with GLY 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLU 3.0 17.6 + - - -
322B GLY 4.0 0.2 - - - -
324B LYS* 1.3 75.2 - - - +
326B PHE* 1.3 59.6 + - - +
328B ARG* 3.6 25.6 + - - +
329B ARG* 3.0 45.4 + - - +
523D G 4.9 2.9 - - - -
524D A 5.9 1.1 - - - -
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Residues in contact with PHE 326 (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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322B GLY 3.1 18.3 + - - +
323B CYS 3.8 2.5 - - - +
325B GLY* 1.3 76.6 - - - +
327B PHE* 1.3 64.2 + - - +
329B ARG* 3.4 16.0 - - + +
330B THR* 2.8 33.0 + - - -
339B TYR* 3.5 31.4 - + - -
358B GLN* 3.5 29.8 - - + -
361B ARG* 3.6 38.6 - - + +
362B PHE* 3.7 29.8 - + + -
365B CYS* 4.3 9.6 - - - -
522D T 3.5 30.1 - - - -
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Residues in contact with PHE 327 (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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315B TYR* 3.6 25.1 - + - -
323B CYS 2.9 20.3 + - - +
324B LYS 3.8 3.1 - - - +
326B PHE* 1.3 79.0 - - - +
328B ARG* 1.3 65.0 + - - +
330B THR* 3.3 3.5 + - - -
331B ILE* 3.0 33.5 + - + +
362B PHE* 3.9 25.4 - + - -
365B CYS* 3.8 20.2 - - + -
366B ILE* 4.0 12.6 - - + -
370B MET* 3.6 34.3 - - + -
371B ALA 3.8 19.3 - - - -
372B THR* 3.5 32.5 - - + -
375B VAL* 4.1 8.3 - - + -
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Residues in contact with ARG 328 (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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315B TYR* 3.3 16.2 - - - +
324B LYS* 3.1 23.4 + - - +
325B GLY* 3.6 22.4 + - - +
327B PHE* 1.3 76.8 - - - +
329B ARG* 1.3 71.2 + - - +
331B ILE* 3.5 0.7 + - - -
332B GLN* 2.9 51.8 + - + +
375B VAL* 4.0 10.9 - - + +
514C G 3.2 51.3 + - - +
515C G 3.0 39.6 + - - -
516C T 3.5 26.0 + - - +
523D G 4.6 0.4 + - - -
524D A 4.7 2.8 - - - +
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Residues in contact with ARG 329 (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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322B GLY 5.3 0.2 + - - -
325B GLY* 3.0 23.7 + - - +
326B PHE* 3.4 26.7 - - + +
328B ARG* 1.3 82.3 - - - +
330B THR* 1.3 63.0 + - - +
332B GLN* 4.1 10.8 - - - +
333B LYS* 3.1 60.1 + - - +
335B LEU* 3.8 6.7 - - + +
339B TYR* 5.3 0.4 - - - +
521D C 4.8 4.3 - - - -
522D T 2.8 72.8 + - - +
523D G 2.6 42.0 + - - -
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Residues in contact with THR 330 (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* 2.8 27.9 + - - -
327B PHE 3.6 4.7 - - - -
329B ARG* 1.3 77.1 - - - +
331B ILE* 1.3 58.3 + - - +
334B ASN* 2.9 8.7 + - - -
335B LEU* 2.9 32.8 + - - -
336B HIS* 3.4 33.5 - - + +
339B TYR* 2.8 29.6 + - + +
362B PHE* 3.5 25.8 - - + -
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Residues in contact with ILE 331 (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* 3.0 37.5 + - + +
330B THR* 1.3 74.1 - - - +
332B GLN* 1.3 65.9 + - - +
334B ASN* 3.1 12.5 + - - +
336B HIS* 3.8 16.0 + - + +
362B PHE* 3.7 25.6 - - + -
372B THR* 3.6 38.1 - - + +
375B VAL* 3.7 29.2 - - + +
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Residues in contact with GLN 332 (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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328B ARG* 2.9 44.5 + - - +
329B ARG* 4.0 10.8 - - - +
331B ILE* 1.3 75.2 - - - +
333B LYS* 1.3 64.2 + - + +
334B ASN* 5.2 0.5 - - - +
375B VAL* 3.8 15.7 - - + -
376B LEU 5.1 6.0 + - - +
381B ARG* 3.9 13.0 - - - +
514C G 3.7 24.4 + - - +
515C G 3.2 25.2 + - - -
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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