Contacts of the helix formed by residues 309 - 323 (chain B) in PDB entry 1NUA
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 LYS 309 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306B GLY 6.1 1.1 - - - +
307B ILE 4.2 1.5 + - - +
308B LEU* 1.3 82.0 - - - +
310B GLY* 1.3 69.3 + - - +
311B VAL* 4.5 18.6 - - + +
312B ALA* 3.0 21.9 + - + +
313B VAL* 3.3 4.6 + - - +
369B SER 4.6 2.0 + - - -
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Residues in contact with GLY 310 (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 ARG* 3.1 31.3 - - - +
309B LYS* 1.3 73.2 - - - +
311B VAL* 1.3 55.8 + - - +
313B VAL* 2.8 30.3 + - - +
314B SER* 3.0 15.7 + - - -
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LYS* 4.5 17.3 - - + -
310B GLY* 1.3 72.7 - - - +
312B ALA* 1.3 64.8 + - + +
314B SER* 3.6 9.5 + - - -
315B ARG* 3.0 33.9 + - + +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 3.4 24.2 - - + -
309B LYS* 3.0 14.6 + - + +
310B GLY 3.0 0.8 - - - -
311B VAL* 1.3 83.6 - - + +
313B VAL* 1.3 60.2 + - - +
315B ARG* 3.0 11.6 + - - +
316B ILE* 2.7 28.4 + - + +
370B ALA* 5.1 1.3 - - - -
371B ILE* 3.9 27.4 - - + +
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Residues in contact with VAL 313 (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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296B VAL 4.8 0.9 - - - +
299B ALA* 3.6 20.0 - - + +
300B GLU* 4.3 22.4 - - + -
303B ARG* 4.0 18.4 - - + -
308B LEU* 3.3 27.4 - - + -
309B LYS 3.7 9.2 - - - +
310B GLY* 2.8 16.5 + - - +
312B ALA* 1.3 72.0 - - - +
314B SER* 1.3 61.3 + - - +
316B ILE* 3.2 11.1 + - + +
317B VAL* 3.1 32.0 + - + +
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Residues in contact with SER 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B GLY 3.0 13.5 + - - -
311B VAL* 3.7 12.8 - - - -
312B ALA 3.2 0.2 - - - -
313B VAL* 1.3 77.1 - - - +
315B ARG* 1.3 53.5 + - - +
317B VAL* 3.3 8.3 + - - +
318B LYS* 2.7 53.4 + - - +
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Residues in contact with ARG 315 (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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204B GLU* 2.6 32.9 + - - +
207B PHE* 3.7 11.1 - - + -
208B THR* 4.0 13.1 + - - +
211B GLU* 2.6 41.4 + - - +
311B VAL* 3.0 20.6 - - + +
312B ALA* 3.0 8.2 + - - +
314B SER* 1.3 76.0 - - - +
316B ILE* 1.3 57.6 + - - +
318B LYS* 3.9 6.2 - - - +
319B CYS* 2.7 37.8 + - - +
371B ILE* 3.3 30.4 - - + +
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ILE* 5.4 1.7 - - + +
200B ALA* 5.1 2.5 - - + -
207B PHE* 4.1 15.9 - - + -
269B TRP* 3.9 33.0 - - + -
295B MET* 4.6 1.6 - - - +
296B VAL* 4.5 16.6 - - - +
299B ALA* 4.6 8.1 - - + -
308B LEU* 5.2 3.6 - - + -
312B ALA* 2.7 38.3 + - + +
313B VAL* 3.3 10.3 - - - +
315B ARG* 1.3 75.2 - - - +
317B VAL* 1.3 59.1 + - - +
319B CYS* 3.9 0.7 - - - +
320B LEU* 2.9 55.1 + - + +
368B LEU* 5.5 3.8 - - + -
371B ILE* 3.7 23.3 - - + -
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Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B VAL* 3.9 28.3 - - + -
313B VAL* 3.1 22.4 + - + +
314B SER* 3.4 10.1 - - - +
316B ILE* 1.3 77.0 - - + +
318B LYS* 1.3 72.1 + - + +
320B LEU* 3.5 1.1 + - - -
321B ALA* 3.0 24.0 + - + +
327B THR* 3.6 27.9 - - + +
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Residues in contact with LYS 318 (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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211B GLU* 5.7 1.6 - - - +
314B SER* 2.7 36.9 + - - +
315B ARG* 3.9 6.5 - - - +
317B VAL* 1.3 78.6 - - + +
319B CYS* 1.3 59.1 + - - +
321B ALA* 3.3 6.1 + - + +
322B ALA* 2.8 30.9 + - - +
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Residues in contact with CYS 319 (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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196B ILE* 4.0 13.5 - - + -
207B PHE* 3.6 21.1 - - + -
210B LEU* 4.3 10.8 - - - -
211B GLU* 3.9 26.1 + - + +
315B ARG 2.7 22.4 + - - +
316B ILE 3.9 1.1 - - - +
318B LYS* 1.3 72.2 - - - +
320B LEU* 1.3 66.7 + - - +
322B ALA* 3.2 14.4 + - - +
323B TYR* 3.3 36.0 - - - -
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Residues in contact with LEU 320 (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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196B ILE* 3.9 29.2 - - + -
292B ALA* 3.5 15.3 - - + +
295B MET* 3.5 28.9 - - + -
296B VAL* 3.5 32.3 - - + -
316B ILE* 2.9 36.2 + - + +
317B VAL 3.8 3.8 - - - +
319B CYS* 1.3 75.6 - - - +
321B ALA* 1.3 61.3 + - - +
323B TYR* 3.2 8.8 + - - +
325B LEU* 3.0 44.7 + - + +
327B THR* 4.2 7.4 - - + -
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Residues in contact with ALA 321 (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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218B LEU* 5.0 0.7 - - - +
317B VAL* 3.0 20.4 + - + +
318B LYS* 3.7 5.6 - - + +
320B LEU* 1.3 74.0 - - - +
322B ALA* 1.3 56.5 + - - +
323B TYR 2.9 5.2 - - - -
324B GLY* 2.9 19.9 + - - -
325B LEU 3.6 15.2 + - - +
327B THR* 4.2 7.6 - - + +
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Residues in contact with ALA 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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211B GLU* 5.4 0.7 - - - +
214B ALA* 3.7 29.4 - - + +
215B GLU* 4.9 1.2 + - - -
218B LEU* 3.2 23.2 - - - +
318B LYS 2.8 18.5 + - - +
319B CYS* 3.2 10.5 + - - +
321B ALA* 1.3 74.9 - - - +
323B TYR* 1.3 57.6 + - - +
324B GLY 3.4 0.9 - - - -
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Residues in contact with TYR 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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189B ILE* 3.3 22.5 - - - +
192B MET* 3.5 40.3 - - + +
196B ILE* 3.7 17.0 - - + -
210B LEU* 2.6 50.6 + - + +
214B ALA* 3.6 26.6 + - + -
217B ILE* 3.6 35.7 - - + +
218B LEU* 3.9 16.1 - - + +
319B CYS* 3.3 26.0 + - - -
320B LEU 3.2 8.2 + - - +
321B ALA 2.9 1.6 - - - -
322B ALA* 1.3 81.2 - - - +
324B GLY* 1.3 60.1 - - - +
325B LEU* 3.2 5.0 + - + +
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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