Contacts of the helix formed by residues 312 - 327 (chain B) in PDB entry 1UN0
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 SER 312 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLN* 4.8 7.6 - - - +
271B THR* 5.0 7.5 - - - +
310B HIS* 3.0 21.8 + - - -
311B GLU* 1.3 81.7 - - - +
313B THR* 1.3 57.3 + - - +
314B LEU* 3.2 30.8 + - - +
315B VAL* 3.1 22.5 + - - +
316B GLN* 3.1 16.6 + - - +
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Residues in contact with THR 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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128A GLN* 3.5 29.1 + - + +
311B GLU 3.8 3.0 + - - +
312B SER* 1.3 69.7 + - - +
314B LEU* 1.3 60.7 + - - +
315B VAL 3.0 5.2 - - - -
316B GLN* 3.7 24.5 - - - +
317B THR* 3.0 33.2 + - - -
352B SER* 5.5 2.0 - - - +
353B PRO* 6.2 2.5 - - + -
354B LYS* 4.0 30.9 - - + -
357B ILE* 4.8 7.6 - - + -
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Residues in contact with LEU 314 (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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124A ASP* 3.6 31.6 - - + +
125A VAL* 3.6 42.4 - - + +
128A GLN* 4.3 17.9 - - + +
271B THR* 5.6 1.1 - - + -
275B VAL* 3.5 29.9 - - + +
279B TRP* 4.6 0.7 + - - -
312B SER* 3.1 15.0 - - - +
313B THR* 1.3 80.1 - - - +
315B VAL* 1.3 57.7 + - - +
317B THR* 5.3 0.7 - - - -
318B PRO* 3.4 20.3 - - - +
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B THR* 4.8 3.1 - - + -
274B LEU* 4.1 17.7 - - + -
275B VAL* 4.0 18.6 - - + +
278B CYS* 4.3 8.7 - - - -
307B LEU* 4.1 24.0 - - + +
310B HIS* 3.9 46.9 - - + +
312B SER* 3.1 12.1 + - - +
313B THR 3.0 0.4 - - - -
314B LEU* 1.3 78.9 - - - +
316B GLN* 1.3 69.3 + - - +
317B THR 3.2 1.7 + - - -
318B PRO* 3.3 6.2 - - - +
319B ALA* 3.1 21.7 + - - +
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Residues in contact with GLN 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU 4.3 4.7 - - - +
308B LEU* 3.5 25.2 - - - +
309B SER* 4.8 0.6 - - - +
310B HIS 2.5 27.8 + - - +
311B GLU 3.8 12.5 + - - -
312B SER 3.1 11.5 + - - +
313B THR* 3.4 20.1 + - - +
315B VAL* 1.3 76.4 - - - +
317B THR* 1.3 59.2 + - - +
319B ALA* 3.6 3.8 - - - +
320B LEU* 2.7 35.8 + - - +
348B LEU* 5.9 2.3 - - - +
349B LEU* 3.6 20.2 - - + +
352B SER* 4.9 5.0 + - - -
357B ILE* 4.2 15.2 - - + +
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TRP* 4.1 7.2 - - + -
313B THR* 3.0 17.1 + - - -
314B LEU* 5.3 0.4 - - - -
315B VAL 3.2 0.2 + - - -
316B GLN* 1.3 76.0 - - - +
318B PRO* 1.3 66.4 - - + +
320B LEU* 3.6 1.9 + - - +
321B ARG 3.1 5.4 + - - -
357B ILE* 3.2 23.6 - - - +
45D LYS* 1.2 89.6 + - + +
50D PHE* 3.6 29.7 - - + -
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Residues in contact with PRO 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL 4.3 0.7 - - - +
278B CYS* 3.8 15.6 - - + +
279B TRP* 3.7 53.2 - - + +
282B SER* 3.6 7.3 - - - +
314B LEU* 3.4 23.1 - - - +
315B VAL 3.3 7.0 - - - +
317B THR* 1.3 96.8 - - + +
319B ALA* 1.3 60.0 + - - +
321B ARG* 3.2 5.8 + - + +
322B ALA* 3.0 28.1 + - - +
45D LYS* 3.4 3.6 - - - +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B CYS* 4.3 15.6 - - - +
304B LEU* 4.3 17.5 - - + +
307B LEU* 4.3 17.0 - - + +
308B LEU* 3.8 13.9 - - + -
315B VAL 3.1 21.1 + - - +
316B GLN* 3.6 3.4 - - - +
318B PRO* 1.3 75.1 - - - +
320B LEU* 1.3 66.8 + - - +
322B ALA* 3.2 4.5 + - - +
323B VAL* 3.1 26.2 + - - +
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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
----------------------------------------------------------
308B LEU* 3.5 15.6 - - + +
316B GLN 2.7 22.6 + - - +
317B THR 3.8 4.3 - - - +
319B ALA* 1.3 72.0 - - - +
321B ARG* 1.3 65.0 + - - +
323B VAL* 3.2 3.5 + - + +
324B GLY* 2.9 20.4 + - - -
346B LEU* 3.9 18.6 - - + -
349B LEU* 3.8 23.3 - - + -
357B ILE* 3.7 34.3 - - + +
360B GLU* 3.4 34.5 - - + +
361B ALA* 3.8 2.2 - - - +
363B TRP* 5.2 0.6 - - + -
364B THR* 3.9 13.8 + - + +
45D LYS* 5.3 0.9 - - - +
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B SER* 4.2 9.6 - - - +
286B ASP* 5.1 1.8 + - - -
317B THR 3.1 2.8 + - - -
318B PRO* 3.4 9.2 - - + +
319B ALA 3.1 0.4 - - - -
320B LEU* 1.3 81.4 - - - +
322B ALA* 1.3 56.8 + - - +
324B GLY* 3.2 1.7 + - - -
325B ASN* 2.9 46.1 + - - +
360B GLU* 2.7 40.7 + - - -
363B TRP* 3.9 10.5 - - - -
40D LYS* 3.0 27.4 - - - +
42D ALA 2.6 31.5 + - - -
43D MET* 2.8 17.4 + - - +
45D LYS* 3.2 44.5 - - + +
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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
----------------------------------------------------------
278B CYS 5.0 0.2 - - - +
281B ILE* 4.1 6.1 - - + -
282B SER* 3.9 21.2 - - - +
285B SER* 3.7 15.7 + - - +
304B LEU* 3.8 24.2 - - + -
318B PRO 3.0 12.7 + - - +
319B ALA* 3.5 9.4 - - - +
321B ARG* 1.3 74.0 - - - +
323B VAL* 1.3 65.7 + - - +
325B ASN* 3.0 12.1 + - - +
326B ILE* 3.0 19.6 + - - +
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PRO* 5.6 1.1 - - + +
304B LEU* 3.9 25.8 - - + -
305B VAL* 4.8 6.5 - - + +
308B LEU* 4.3 18.4 - - + -
319B ALA 3.1 14.3 + - - +
320B LEU* 3.2 10.5 + - + +
322B ALA* 1.3 76.3 - - - +
324B GLY* 1.3 62.5 + - - +
326B ILE* 3.2 12.7 + - + +
327B VAL* 3.1 22.6 + - + +
337B VAL* 3.9 11.8 - - + +
342B VAL* 3.5 28.9 - - + -
364B THR* 4.1 13.7 - - + -
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Residues in contact with GLY 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 LEU 2.9 12.1 + - - -
321B ARG 3.6 3.4 - - - -
323B VAL* 1.3 77.8 - - - +
325B ASN* 1.3 59.7 + - - +
327B VAL* 3.3 13.3 - - - +
328B THR* 3.3 22.2 + - - +
363B TRP* 3.6 18.8 - - - -
364B THR* 3.6 21.5 + - - -
367B ASN* 4.8 0.3 + - - -
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Residues in contact with ASN 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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282B SER 2.9 29.1 + - - -
285B SER* 3.3 26.8 + - - +
286B ASP* 3.4 21.4 + - - +
292B ILE* 3.5 7.8 - - - +
321B ARG* 2.9 31.1 + - - +
322B ALA 3.0 2.9 + - - +
324B GLY* 1.3 76.3 - - - +
326B ILE* 1.3 58.7 + - - +
328B THR* 2.5 29.5 + - - +
363B TRP* 3.6 15.4 - - - -
39D ARG* 3.8 11.9 + - - +
40D LYS* 5.3 1.2 - - - +
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Residues in contact with ILE 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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285B SER* 4.4 11.7 - - - -
292B ILE* 3.9 29.3 - - + +
295B VAL* 4.2 17.0 - - + -
296B ILE* 4.2 8.1 - - + -
301B PRO* 4.4 10.1 - - + -
304B LEU* 4.1 24.5 - - + -
322B ALA 3.0 18.4 + - - +
323B VAL* 3.5 11.0 - - + +
325B ASN* 1.3 74.9 - - - +
327B VAL* 1.3 57.3 + - - +
329B GLY* 3.0 21.0 + - - -
333B GLN* 3.9 16.6 - - - +
334B THR* 4.5 0.2 + - - -
337B VAL* 3.4 30.7 - - + -
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL 3.1 12.6 + - - +
324B GLY* 3.3 20.0 - - - +
326B ILE* 1.3 73.2 - - - +
328B THR* 1.3 56.9 + - - +
329B GLY 3.0 4.9 - - - -
334B THR* 3.6 26.7 - - + +
337B VAL* 4.2 17.7 - - + -
364B THR* 3.9 18.2 - - + +
367B ASN* 3.6 18.6 - - + +
368B ILE* 3.8 24.5 - - + -
36D MET* 2.8 34.2 - - - +
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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
------------------------------------------------------------
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