Contacts of the helix formed by residues 322 - 335 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320C SER 4.4 3.4 - - - +
321C ASP* 1.3 75.0 - - - +
323C ILE* 1.3 66.6 + - - +
324C GLU* 3.6 8.2 + - - +
325C ASN* 2.8 42.0 + - - +
326C VAL* 3.0 26.2 + - - +
353C GLY* 4.2 15.7 - - - +
354C ARG 3.3 14.4 - - - +
355C THR* 4.1 12.1 - - + -
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Residues in contact with ILE 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C THR* 1.3 75.3 - - - +
324C GLU* 1.3 56.9 + - - +
326C VAL* 3.1 5.8 + - + +
327C LYS* 2.8 44.7 + - + +
343C LEU* 4.7 7.4 - - + -
350C LEU* 3.6 49.1 - - + +
351C GLU 3.0 27.1 - - - +
352C ASP* 3.8 15.7 - - - +
353C GLY 4.7 0.8 - - - +
354C ARG 3.2 9.7 + - - +
355C THR 4.8 1.6 - - - -
356C LEU* 4.3 19.1 - - + -
359C TYR* 4.1 13.9 - - + -
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Residues in contact with GLU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C THR* 3.1 9.4 + - - +
323C ILE* 1.3 79.1 - - - +
325C ASN* 1.3 65.5 + - - +
327C LYS* 3.3 7.8 + - + +
328C ALA* 3.1 22.0 + - - +
338C PRO* 5.3 2.4 - - - +
352C ASP* 3.6 35.5 + - + +
353C GLY* 4.7 4.5 + - - +
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Residues in contact with ASN 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C SER 4.8 0.5 - - - +
321C ASP* 3.7 21.9 - - + +
322C THR* 2.8 45.5 + - - +
324C GLU* 1.3 80.2 - - - +
326C VAL* 1.3 64.6 - - - +
328C ALA* 3.1 9.9 + - - +
329C LYS* 3.0 30.0 + - - +
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Residues in contact with VAL 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ILE* 4.7 2.9 - - + -
315C LEU* 3.7 22.0 - - + -
317C VAL* 4.5 5.2 - - + -
321C ASP* 4.4 7.2 - - + -
322C THR 3.0 15.8 + - - +
323C ILE* 3.5 9.4 - - + +
325C ASN* 1.3 76.4 - - - +
327C LYS* 1.3 57.7 + - - +
329C LYS* 3.0 11.6 + - - +
330C ILE* 2.9 27.9 + - + +
343C LEU* 4.1 20.0 - - + -
356C LEU* 3.9 33.7 - - + -
367C LEU* 4.2 13.2 - - + -
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Residues in contact with LYS 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C ILE* 2.8 27.2 + - - +
324C GLU* 3.6 6.7 - - + +
326C VAL* 1.3 76.3 - - - +
328C ALA* 1.3 56.5 + - - +
330C ILE* 3.3 1.8 + - - -
331C GLN* 2.9 24.6 + - - +
338C PRO* 3.6 33.3 + - + +
339C ASP* 5.8 0.2 - - - +
341C GLN* 3.0 58.6 + - + +
342C ARG* 5.2 0.4 - - - +
343C LEU* 4.3 17.9 - - + +
350C LEU 5.0 6.0 + - - -
352C ASP* 3.0 38.4 + - - +
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Residues in contact with ALA 328 (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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324C GLU 3.1 13.0 + - - +
325C ASN* 3.1 11.9 + - - +
327C LYS* 1.3 72.9 - - - +
329C LYS* 1.3 66.2 + - + +
331C GLN* 3.2 7.8 + - - +
332C ASP* 3.1 30.2 + - - +
338C PRO* 4.2 12.0 - - + +
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Residues in contact with LYS 329 (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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315C LEU* 4.0 22.6 - - + +
316C GLU 3.4 27.1 + - - +
317C VAL* 3.7 21.5 - - + +
321C ASP* 4.0 23.4 + - - -
325C ASN* 3.0 23.5 + - - +
326C VAL* 3.0 10.1 + - - +
328C ALA* 1.3 75.7 - - + +
330C ILE* 1.3 62.9 + - - +
332C ASP* 3.3 23.4 + - - +
333C LYS* 3.4 7.6 + - - +
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Residues in contact with ILE 330 (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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305C VAL* 4.0 22.2 - - + -
313C ILE* 5.3 2.7 - - + -
315C LEU* 3.8 19.1 - - + -
326C VAL* 2.9 17.6 + - + +
327C LYS 3.4 1.8 - - - +
329C LYS* 1.3 73.5 - - - +
331C GLN* 1.3 55.9 + - - +
333C LYS* 3.3 3.1 + - - +
334C GLU* 2.7 56.7 + - + +
336C ILE* 5.1 1.6 - - + -
341C GLN* 3.2 34.3 - - - +
343C LEU* 3.7 36.1 - - + -
369C LEU* 4.3 14.1 - - + -
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Residues in contact with GLN 331 (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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327C LYS 2.9 12.4 + - - +
328C ALA* 3.2 12.4 + - - +
330C ILE* 1.3 76.0 - - - +
332C ASP* 1.3 63.5 + - - +
335C GLY* 2.7 32.4 + - - +
336C ILE 3.2 23.1 - - - +
337C PRO* 3.4 26.7 - - - +
338C PRO* 3.4 18.3 - - + +
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Residues in contact with ASP 332 (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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328C ALA* 3.1 18.7 + - - +
329C LYS* 3.4 14.7 - - - +
330C ILE 3.1 0.4 - - - -
331C GLN* 1.3 84.6 - - - +
333C LYS* 1.3 59.8 + - + +
335C GLY* 4.8 0.5 + - - -
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Residues in contact with LYS 333 (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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376B ASP* 3.2 23.2 + - + +
377B ASN* 2.9 24.9 + - - +
313C ILE* 3.7 35.9 - - + -
314C THR* 2.9 25.4 + - - -
315C LEU* 4.6 7.2 - - + -
329C LYS 3.4 7.2 + - - +
330C ILE 3.3 3.7 + - - +
332C ASP* 1.3 79.3 - - + +
334C GLU* 1.3 69.5 + - + +
335C GLY 3.8 0.2 - - - -
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Residues in contact with GLU 334 (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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413B PRO* 3.6 16.6 - - - +
307C THR* 3.4 31.1 + - + +
309C THR* 5.3 2.8 + - - +
311C LYS* 5.1 4.5 + - - +
313C ILE* 3.6 34.9 - - + +
330C ILE* 2.7 32.3 + - + +
333C LYS* 1.3 86.0 - - - +
335C GLY* 1.3 60.7 + - - +
336C ILE* 3.4 18.3 + - + +
369C LEU* 5.1 1.8 - - + -
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Residues in contact with GLY 335 (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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411B TYR* 3.1 20.1 + - - -
413B PRO* 4.1 15.2 - - - +
331C GLN* 2.7 29.9 + - - -
332C ASP 4.6 0.8 + - - -
333C LYS 3.8 0.4 - - - -
334C GLU* 1.3 73.7 - - - +
336C ILE* 1.3 60.3 + - - +
337C PRO* 3.6 3.1 - - - +
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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