Contacts of the helix formed by residues 287 - 303 (chain B) in PDB entry 1URC
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 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B VAL* 3.8 2.2 - - - -
285B THR 5.7 0.7 - - - +
286B TYR* 1.3 78.1 - - - +
288B LYS* 1.3 67.0 + - - +
289B LYS* 3.5 9.5 + - - +
290B GLN* 2.7 41.7 + - - +
291B VAL* 2.9 23.9 + - - +
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU 3.5 23.8 - - - +
41A THR* 3.9 26.7 - - - +
275B VAL* 3.4 21.5 - - + -
276B ALA* 3.8 32.2 - - - +
279B VAL* 3.4 21.7 - - + +
287B THR* 1.3 72.5 - - - +
289B LYS* 1.3 63.2 + - - +
291B VAL* 3.2 2.7 + - - +
292B LEU* 2.9 29.1 + - + +
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 4.7 17.9 + - - +
40A GLU* 5.1 12.7 - - - +
287B THR* 3.1 8.9 + - - +
288B LYS* 1.3 77.5 - - - +
290B GLN* 1.3 68.0 + - - +
292B LEU* 3.8 7.2 - - + +
293B ARG* 2.9 58.6 + - + +
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LYS* 4.2 18.4 - - - +
255B LEU* 4.3 10.4 - - + +
285B THR 4.1 2.3 - - - +
286B TYR* 2.9 32.1 - - + -
287B THR* 2.7 48.5 + - - +
289B LYS* 1.3 78.3 - - - +
291B VAL* 1.3 58.2 + - - +
293B ARG* 3.1 7.5 + - - +
294B MET* 2.9 28.6 + - - +
24C LYS 5.1 4.0 + - - -
25C LEU* 3.9 11.5 - - + +
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 3.6 24.0 - - + -
258B THR* 4.5 18.4 - - + -
259B ALA* 4.0 9.6 - - - +
262B LEU* 4.2 16.2 - - + -
275B VAL* 4.0 19.7 - - + -
278B PHE* 4.8 9.9 - - + -
279B VAL* 4.4 12.3 - - + +
282B THR* 6.2 0.7 - - + -
286B TYR* 4.4 10.3 - - + -
287B THR 2.9 17.4 + - - +
288B LYS* 3.7 5.4 - - - +
290B GLN* 1.3 75.1 - - - +
292B LEU* 1.3 58.9 + - - +
294B MET* 3.3 3.3 + - - +
295B GLU* 2.8 25.6 + - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR 5.2 3.8 - - - +
40A GLU* 3.6 19.1 - - - +
41A THR* 3.6 31.4 - - - +
42A GLU 4.2 1.3 - - - +
43A GLY* 3.9 25.1 - - - +
262B LEU* 4.3 7.6 - - + -
275B VAL* 3.6 31.2 - - + -
288B LYS* 2.9 24.9 + - + +
289B LYS* 3.8 5.6 - - + +
291B VAL* 1.3 75.8 - - - +
293B ARG* 1.3 64.2 + - + +
295B GLU* 3.2 13.6 + - - +
296B HIS* 3.2 21.7 + - - +
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR 5.9 2.5 - - - -
73A GLU* 3.8 29.8 + - - +
289B LYS* 2.9 50.5 + - + +
290B GLN* 3.6 4.9 - - - +
292B LEU* 1.3 76.3 - - + +
294B MET* 1.3 62.3 + - - +
296B HIS* 3.4 11.2 - - - +
297B LEU* 3.2 16.6 + - - +
2C GLU* 4.7 14.8 + - - +
3C ASN* 4.6 11.8 + - - +
24C LYS* 6.0 3.0 - - - +
25C LEU* 3.6 30.6 - - + +
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Residues in contact with MET 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 4.4 4.0 - - - -
252B LYS 5.1 0.2 - - - +
255B LEU* 3.6 34.1 - - + +
256B VAL* 4.0 24.9 - - + -
259B ALA* 3.6 17.9 - - + -
290B GLN 2.9 12.7 + - - +
291B VAL 3.7 7.0 - - - +
292B LEU 3.2 0.2 - - - -
293B ARG* 1.3 76.9 - - - +
295B GLU* 1.3 60.1 + - - +
297B LEU* 4.3 15.0 - - - -
298B VAL* 2.9 39.8 + - + +
25C LEU* 3.5 42.1 - - + +
26C THR* 4.3 3.4 - - + +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY* 3.7 8.1 - - - -
44A VAL* 3.1 32.5 + - - +
259B ALA* 3.8 12.3 - - + +
262B LEU* 4.0 15.4 - - + +
263B LEU* 3.6 25.0 - - + +
266B LYS* 2.3 40.1 + - - +
291B VAL 2.8 14.3 + - - +
292B LEU* 3.2 14.9 + - - +
294B MET* 1.3 76.6 - - - +
296B HIS* 1.3 61.6 + - - +
298B VAL* 3.2 5.4 + - - +
299B LEU* 3.0 28.5 + - + +
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Residues in contact with HIS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.6 7.6 - - + +
44A VAL* 5.5 4.6 - - + +
71A HIS* 3.0 57.5 + + - -
72A THR* 3.0 31.5 + - - -
73A GLU* 3.8 15.6 + - - -
292B LEU 3.2 9.4 + - - +
293B ARG* 3.4 16.5 - - - +
295B GLU* 1.3 79.3 + - - +
297B LEU* 1.3 63.8 + - + +
299B LEU* 3.2 9.3 + - - +
300B LYS* 3.1 20.5 + - + +
2C GLU* 5.2 6.6 + - - -
3C ASN* 5.9 4.0 - - - -
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 4.4 6.7 - - + -
246B MET* 4.1 26.7 - - + -
293B ARG 3.2 13.9 + - - +
294B MET* 3.8 10.5 - - - +
295B GLU 3.2 0.4 - - - -
296B HIS* 1.3 79.0 - - - +
298B VAL* 1.3 66.7 + - - +
300B LYS* 3.3 28.4 + - + +
301B VAL* 3.2 26.1 + - + +
3C ASN* 4.0 18.6 - - - +
23C ASN* 4.5 5.8 - - - +
25C LEU* 4.1 22.9 - - + -
26C THR* 4.2 17.7 - - + -
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TYR* 4.7 9.0 - - + +
242B PHE* 3.9 30.5 - - + -
256B VAL* 4.9 9.6 - - + +
259B ALA* 4.5 7.9 - - + -
260B ALA* 4.9 5.4 - - + +
263B LEU* 3.6 22.2 - - + -
294B MET* 2.9 34.0 + - + +
295B GLU 3.8 3.6 - - - +
297B LEU* 1.3 74.7 - - - +
299B LEU* 1.3 64.8 + - - +
301B VAL* 3.4 0.5 + - - +
302B LEU* 3.0 48.5 + - + +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.0 21.5 - - + -
49A ILE* 3.4 35.7 - - + -
71A HIS* 4.8 1.8 - - - +
263B LEU* 3.6 21.1 - - + -
295B GLU* 3.0 23.6 + - + +
296B HIS* 3.2 7.2 + - - +
298B VAL* 1.3 77.2 - - - +
300B LYS* 1.3 57.0 + - - +
302B LEU* 4.6 2.9 - - - -
303B THR* 2.8 24.6 + - - -
304B PHE* 3.0 48.8 + - + +
306B LEU* 3.9 17.9 - - + -
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Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A HIS* 4.3 17.9 - - + -
296B HIS* 3.1 15.3 + - + +
297B LEU* 3.7 28.9 - - + +
298B VAL 3.2 0.4 - - - -
299B LEU* 1.3 76.0 - - - +
301B VAL* 1.3 59.9 + - + +
303B THR* 3.1 21.6 + - - +
304B PHE* 4.7 3.7 - - - -
3C ASN* 5.8 1.8 - - - +
4C PHE* 6.0 2.8 - - - -
68C ASP* 3.0 27.4 + - - -
70C ILE* 5.1 9.4 - - - +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG 4.7 0.7 - - - +
242B PHE* 4.2 28.0 - - + -
245B SER* 3.6 25.8 + - - +
246B MET* 3.7 36.8 - - + -
297B LEU* 3.2 20.2 + - + +
298B VAL 4.1 2.2 - - - +
300B LYS* 1.3 80.4 - - + +
302B LEU* 1.3 65.0 + - + +
303B THR* 3.2 6.7 + - - +
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Residues in contact with LEU 302 (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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238B TYR* 3.7 35.2 - - + +
241B ARG* 3.7 46.3 + - + +
242B PHE* 4.2 10.8 - - + +
298B VAL* 3.0 39.1 + - + +
299B LEU 4.1 2.0 - - - +
301B VAL* 1.3 85.2 - - + +
303B THR* 1.3 76.0 + - - +
304B PHE 4.4 2.7 - - - +
305B ASP* 3.0 17.3 + - - +
306B LEU* 3.8 19.3 - - + -
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Residues in contact with THR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 4.2 10.1 - - - +
299B LEU 2.8 9.8 + - - -
300B LYS* 3.1 12.8 + - - +
301B VAL 4.3 5.8 - - - +
302B LEU* 1.3 87.2 + - - +
304B PHE* 1.3 72.8 + - - +
305B ASP* 2.8 24.3 + - - +
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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
------------------------------------------------------------
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