Contacts of the helix formed by residues 319 - 332 (chain B) in PDB entry 1N1E
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 MET 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B VAL* 4.0 22.4 - - + -
240B GLU* 3.3 52.7 - - + +
244B LEU* 4.2 9.0 - - + -
308B LEU* 4.0 18.2 - - + -
312B ALA* 3.7 22.9 - - + -
317B VAL* 3.5 19.3 + - + +
318B LYS* 1.3 79.2 - - - +
320B PRO* 1.3 63.0 - - - +
322B CYS* 3.3 21.0 + - + -
323B HIS* 2.8 30.0 + - - +
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Residues in contact with PRO 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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240B GLU* 3.4 16.4 - - + +
318B LYS* 3.5 13.7 - - + +
319B MET* 1.3 89.0 - - - +
321B LEU* 1.3 59.6 + - + +
323B HIS* 3.5 6.2 + - + +
324B GLN* 3.2 29.3 + - - +
342B LEU* 4.4 15.3 - - + -
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Residues in contact with LEU 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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213B LEU* 3.9 12.6 - - + -
233B LEU* 3.8 34.1 - - + +
236B ARG* 3.9 13.0 - - + -
237B GLY* 3.5 34.1 - - - +
240B GLU* 2.8 21.6 + - - +
320B PRO* 1.3 71.4 - - + +
322B CYS* 1.3 64.8 + - - +
324B GLN* 3.2 6.1 + - + +
325B ILE* 3.0 31.3 + - + +
342B LEU* 3.7 33.4 - - + -
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Residues in contact with CYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 3.8 29.4 - - - -
212B VAL* 4.1 12.0 - - + +
213B LEU* 3.8 15.3 - - - -
240B GLU* 3.0 22.1 + - - +
308B LEU* 3.9 22.4 - - + -
319B MET* 3.3 16.1 + - + +
321B LEU* 1.3 75.8 - - - +
323B HIS* 1.3 56.7 + - - +
325B ILE* 3.8 8.0 - - - +
326B TYR* 2.9 30.2 + - - +
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Residues in contact with HIS 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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309B MET* 4.5 20.2 - - + +
319B MET* 2.8 19.6 + - - +
320B PRO* 3.7 7.9 - - + +
321B LEU 3.1 0.2 - - - -
322B CYS* 1.3 77.3 - - - +
324B GLN* 1.3 79.0 + - - +
326B TYR* 3.3 17.3 + + - +
327B GLU* 3.0 56.2 + - + +
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Residues in contact with GLN 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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320B PRO 3.2 12.4 + - - +
321B LEU* 3.2 7.6 + - - +
323B HIS* 1.3 96.0 - - - +
325B ILE* 1.3 58.0 + - + +
327B GLU* 3.3 5.4 + - - +
328B ILE* 3.0 33.3 + - + +
333B LYS* 2.8 33.7 + - - +
338B ALA* 3.5 34.2 - - + +
341B ASP* 4.0 12.2 - - - +
342B LEU* 4.2 19.7 - - + +
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Residues in contact with ILE 325 (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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212B VAL* 3.4 39.7 - - + +
213B LEU* 3.9 16.4 - - + +
215B ILE* 4.0 22.0 - - + -
216B GLY* 3.6 24.5 - - - -
219B VAL* 6.1 0.7 - - + -
233B LEU* 5.5 0.7 - - + -
305B ALA* 5.3 0.4 - - + -
321B LEU* 3.0 32.6 + - + +
322B CYS* 3.8 7.4 - - - +
324B GLN* 1.3 73.8 - - + +
326B TYR* 1.3 57.1 + - - +
328B ILE* 3.2 14.1 + - + +
329B VAL* 2.8 40.2 + - + +
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Residues in contact with TYR 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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305B ALA* 3.6 37.4 - - + +
306B ASP* 3.4 32.1 + - - -
309B MET* 3.8 44.2 - - + +
322B CYS 2.9 18.2 + - - +
323B HIS* 3.4 12.1 - - - +
325B ILE* 1.3 77.7 - - - +
327B GLU* 1.3 77.6 + - - +
329B VAL 4.5 0.2 - - - +
330B TYR* 2.8 47.9 + + + +
331B LYS* 4.1 23.4 + - + +
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Residues in contact with GLU 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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309B MET* 5.6 0.2 - - - +
323B HIS* 3.0 51.2 + - - +
324B GLN* 3.5 13.2 - - - +
325B ILE 3.3 0.2 - - - -
326B TYR* 1.3 85.8 - - - +
328B ILE* 1.3 58.8 + - - +
331B LYS* 2.9 52.1 + - - +
333B LYS* 3.1 45.4 + - + +
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Residues in contact with ILE 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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215B ILE* 5.9 0.4 - - + -
219B VAL* 4.2 24.0 - - + -
282B LEU* 4.0 36.5 - - + +
288B ILE* 5.7 1.0 - - - +
324B GLN* 3.0 18.4 + - + +
325B ILE* 3.4 16.4 - - + +
327B GLU* 1.3 79.0 - - - +
329B VAL* 1.3 63.3 + - + +
332B LYS* 3.5 15.1 + - - -
333B LYS* 3.6 20.3 - - + +
335B PRO* 4.0 20.2 - - + +
338B ALA* 3.6 28.3 - - + -
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Residues in contact with VAL 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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215B ILE* 4.1 24.9 - - + -
282B LEU* 4.2 13.0 - - + -
288B ILE* 3.7 29.4 - - + +
302B VAL* 3.8 33.9 - - + +
305B ALA* 4.5 5.4 - - + -
325B ILE* 2.8 38.3 + - + +
326B TYR 4.1 1.8 - - - +
328B ILE* 1.3 77.5 - - + +
330B TYR* 1.3 77.8 + - + +
332B LYS* 4.7 0.9 + - - -
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Residues in contact with TYR 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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129B ARG* 3.6 26.1 + - - -
302B VAL* 3.0 24.6 - - + +
303B ALA* 3.6 16.1 + - - -
305B ALA* 4.0 4.9 - - + -
306B ASP* 3.5 47.1 - - + +
326B TYR* 2.8 28.2 + + + +
329B VAL* 1.3 86.0 - - + +
331B LYS* 1.3 67.7 + - + +
332B LYS 3.6 1.1 - - - -
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Residues in contact with LYS 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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326B TYR* 4.1 24.5 + - + +
327B GLU* 2.9 47.1 + - - +
330B TYR* 1.3 83.0 - - + +
332B LYS* 1.3 71.5 + - - +
333B LYS* 3.0 4.6 + - + +
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Residues in contact with LYS 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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287B PRO* 3.6 21.4 - - - +
288B ILE* 4.1 6.9 - - - +
289B GLU* 2.5 38.4 + - - +
327B GLU 3.1 2.4 + - - -
328B ILE 3.5 13.4 + - - -
329B VAL 4.7 0.6 + - - -
330B TYR 3.6 2.4 - - - -
331B LYS* 1.3 79.4 - - - +
333B LYS* 1.3 65.7 + - - +
334B ASN* 3.3 3.3 + - - -
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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