Contacts of the helix formed by residues 322 - 335 (chain D) in PDB entry 1NBF
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 THR 322 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320D SER 4.5 2.5 - - - +
321D ASP* 1.3 77.1 - - - +
323D ILE* 1.3 60.6 + - - +
324D GLU* 3.6 20.8 + - - +
325D ASN* 2.9 51.6 + - - +
326D VAL* 3.0 14.2 + - - +
353D GLY* 4.3 9.0 - - - +
354D ARG 3.4 12.6 - - - +
355D THR* 4.1 12.6 - - + +
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Residues in contact with ILE 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D THR* 1.3 72.3 - - - +
324D GLU* 1.3 57.1 + - - +
326D VAL* 3.3 5.8 + - + +
327D LYS* 2.9 41.4 + - - +
343D LEU* 4.2 9.2 - - + -
350D LEU* 3.6 46.2 - - + +
351D GLU 3.1 26.7 - - - +
352D ASP* 3.7 15.9 - - - +
354D ARG 3.1 12.3 + - - +
355D THR 4.5 2.0 - - - +
356D LEU* 4.3 16.2 - - + -
359D TYR* 3.8 19.1 - - + -
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Residues in contact with GLU 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D THR* 3.0 15.8 + - - +
323D ILE* 1.3 78.9 - - - +
325D ASN* 1.3 63.6 + - - +
327D LYS* 3.5 8.1 + - - +
328D ALA* 3.0 21.8 + - - +
338D PRO* 5.5 1.6 - - - +
352D ASP* 3.9 22.2 - - + +
353D GLY* 3.8 28.9 + - - +
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Residues in contact with ASN 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D SER 4.9 0.2 - - - +
321D ASP* 3.5 25.1 - - + +
322D THR* 2.9 42.1 + - - +
324D GLU* 1.3 76.4 - - - +
326D VAL* 1.3 61.1 + - - +
328D ALA* 2.9 27.2 - - - +
329D LYS* 2.9 18.7 + - - +
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Residues in contact with VAL 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D ILE* 4.9 1.8 - - + -
315D LEU* 3.9 19.3 - - + -
317D VAL* 4.4 9.9 - - + -
321D ASP* 4.6 3.1 - - + -
322D THR 3.0 13.1 + - - +
323D ILE* 3.6 9.0 - - - +
325D ASN* 1.3 76.2 - - - +
327D LYS* 1.3 64.0 + - - +
329D LYS* 3.0 20.6 + - - +
330D ILE* 3.0 14.2 + - + +
343D LEU* 3.7 21.5 - - + -
356D LEU* 3.9 37.0 - - + -
367D LEU* 4.2 14.6 - - + -
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Residues in contact with LYS 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D ILE* 2.9 28.9 + - - +
324D GLU* 3.7 7.4 - - - +
326D VAL* 1.3 75.6 - - - +
328D ALA* 1.3 57.0 + - - +
330D ILE* 3.3 2.6 + - - -
331D GLN* 3.1 14.9 + - - +
338D PRO* 3.9 32.5 + - + +
341D GLN* 2.9 63.6 + - + +
342D ARG* 5.4 0.2 - - - +
343D LEU* 3.9 17.0 - - + +
350D LEU 4.7 7.2 + - - -
352D ASP* 2.9 38.0 + - - +
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Residues in contact with ALA 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D GLU 3.0 13.4 + - - +
325D ASN* 2.9 18.1 + - - +
327D LYS* 1.3 74.4 - - - +
329D LYS* 1.3 63.3 + - + +
331D GLN* 3.2 17.2 + - - +
332D ASP* 3.3 18.2 + - - +
338D PRO* 4.5 10.7 - - + +
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Residues in contact with LYS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D LEU* 3.9 25.0 - - + +
316D GLU 3.4 27.9 + - - +
317D VAL* 3.7 19.5 - - + +
321D ASP* 4.1 19.7 + - - -
325D ASN* 2.9 20.8 + - - +
326D VAL* 3.0 9.8 + - - +
328D ALA* 1.3 76.5 - - + +
330D ILE* 1.3 60.8 + - - +
332D ASP* 3.5 24.9 - - - +
333D LYS* 3.5 7.4 + - - +
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Residues in contact with ILE 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D VAL* 4.1 22.0 - - + -
313D ILE* 5.2 4.7 - - + -
315D LEU* 3.7 19.7 - - + -
326D VAL* 3.0 17.7 + - + +
327D LYS 3.4 8.3 - - - +
329D LYS* 1.3 75.8 - - - +
331D GLN* 1.3 59.7 + - - +
333D LYS* 3.3 2.6 + - - +
334D GLU* 2.8 43.9 + - + +
336D ILE* 5.3 2.0 - - + -
341D GLN* 3.5 26.2 - - - +
343D LEU* 3.7 31.4 - - + -
369D LEU* 4.0 18.4 - - + -
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Residues in contact with GLN 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D LYS 3.1 12.0 + - - +
328D ALA* 3.4 12.4 - - - +
330D ILE* 1.3 77.6 - - - +
332D ASP* 1.3 63.0 + - - +
335D GLY* 2.7 35.2 + - - +
336D ILE 3.4 22.7 - - - +
337D PRO* 3.9 11.3 - - - +
338D PRO* 3.5 28.6 - - + +
341D GLN* 3.9 0.2 - - - +
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Residues in contact with ASP 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D ALA 3.5 14.3 - - - +
329D LYS* 3.5 17.9 - - - +
330D ILE 3.2 0.8 - - - -
331D GLN* 1.3 82.7 - - - +
333D LYS* 1.3 62.1 + - + +
335D GLY* 4.7 0.3 + - - -
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Residues in contact with LYS 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ASP* 3.4 25.7 + - - +
377A ASN* 2.8 24.7 + - - +
313D ILE* 4.3 22.4 - - + -
314D THR* 2.6 39.5 + - - +
315D LEU* 4.4 5.8 - - + -
329D LYS 3.5 8.4 + - - +
330D ILE* 3.3 5.1 + - - +
332D ASP* 1.3 84.8 - - + +
334D GLU* 1.3 68.9 + - - +
335D GLY 3.5 0.2 - - - -
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Residues in contact with GLU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A TYR* 4.8 4.0 - - - -
413A PRO* 5.9 1.9 - - - +
307D THR* 3.5 41.3 + - + +
308D LEU* 5.1 0.7 + - - +
309D THR* 4.7 9.0 + - - +
313D ILE* 4.1 22.0 - - + +
330D ILE* 2.8 23.1 + - + +
333D LYS* 1.3 84.0 - - - +
335D GLY* 1.3 62.8 + - - +
336D ILE* 3.5 26.2 + - + +
369D LEU* 5.0 0.9 - - + -
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Residues in contact with GLY 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A TYR* 3.3 23.0 + - - -
331D GLN* 2.7 32.2 + - - +
332D ASP 4.5 0.6 - - - -
333D LYS 3.5 0.8 - - - -
334D GLU* 1.3 73.3 - - - +
336D ILE* 1.3 61.6 + - - +
337D PRO* 3.7 1.4 - - - +
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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