Contacts of the helix formed by residues 300 - 319 (chain B) in PDB entry 1K0Y
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 PRO 300 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B VAL 3.2 5.1 - - - +
299B ASP* 1.3 87.2 - - - +
301B GLU* 1.4 64.2 + - - +
302B ASN 3.0 0.4 - - - -
303B PHE* 3.0 34.1 + - + +
304B ARG* 3.6 8.1 + - - +
338B ALA* 5.4 0.5 - - - +
342B ALA* 3.7 25.4 - - + -
345B TYR* 3.6 29.6 - - + -
438C THR* 3.6 30.3 - - + +
802D CNO 4.0 13.2 - - + +
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ASP* 3.0 18.5 + - - +
300B PRO* 1.4 77.2 - - - +
302B ASN* 1.4 59.9 + - - +
304B ARG* 2.9 52.2 + - - +
305B LEU* 3.1 29.1 + - + +
494C ASP* 3.1 38.5 - - - +
496C VAL* 3.8 23.1 - - + +
801D CNO 5.2 6.6 + - - +
802D CNO 3.3 15.9 - - + +
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Residues in contact with ASN 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 4.7 1.6 - - - +
238B THR* 3.3 28.8 - - + +
240B ARG* 3.3 37.0 + - - +
241B PHE* 3.5 10.8 - - - -
298B VAL* 3.7 7.3 - - + +
299B ASP* 2.9 28.6 + - - +
301B GLU* 1.4 77.8 - - - +
303B PHE* 1.4 56.7 + - - +
305B LEU* 3.4 10.3 + - - +
306B LEU 2.9 23.9 + - - -
348B HEM 3.5 33.1 - - + +
494C ASP* 4.8 0.8 - - - +
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Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B HIS* 3.9 22.2 - + + -
298B VAL* 3.9 12.3 - - + -
300B PRO* 3.0 32.7 + - + +
302B ASN* 1.4 73.7 - - - +
304B ARG* 1.4 60.8 + - - +
306B LEU* 3.5 3.4 + - - +
307B GLY* 3.0 24.6 + - - -
334B VAL 5.2 0.5 - - - +
338B ALA* 3.9 28.8 - - + +
341B LEU* 3.6 44.0 - - + -
345B TYR* 3.5 22.4 - + - -
348B HEM 3.7 45.2 - + + +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PRO 3.6 4.4 + - - +
301B GLU* 2.9 45.2 + - - +
303B PHE* 1.4 75.1 - - - +
305B LEU* 1.4 67.5 + - + +
307B GLY* 3.2 3.2 + - - -
308B ASN* 3.0 35.6 + - - +
338B ALA* 4.3 19.8 - - + +
339B ASN* 5.0 9.3 - - - +
801D CNO 3.8 37.9 - - + +
802D CNO 3.3 36.1 + - - -
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 3.8 11.7 - - + -
235B TYR* 4.1 36.6 - - + -
237B TRP* 3.9 14.8 - - + +
238B THR* 4.1 17.5 - - + -
301B GLU* 3.1 23.3 + - + +
302B ASN* 3.6 9.4 - - - +
304B ARG* 1.4 78.4 - - + +
306B LEU* 1.4 62.6 + - - +
308B ASN* 3.2 8.6 + - + +
309B VAL* 3.0 25.6 + - - +
494C ASP* 3.6 23.8 - - - +
801D CNO 4.3 23.8 - - + +
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Residues in contact with LEU 306 (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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227B ALA* 4.0 37.2 - - + +
228B LEU* 4.4 8.5 - - + +
231B LEU* 3.9 17.6 - - + +
267B VAL* 3.8 29.4 - - + -
268B LEU* 5.6 5.4 - - + -
302B ASN 2.9 16.9 + - - +
303B PHE* 3.9 5.2 - - - +
305B LEU* 1.4 75.5 - - - +
307B GLY* 1.4 59.7 + - - +
309B VAL* 3.2 2.6 + - + -
310B LEU* 2.8 31.1 + - + +
348B HEM 3.8 39.5 - - + -
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Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE 3.0 15.9 + - - -
304B ARG* 3.2 4.4 + - - -
306B LEU* 1.4 77.2 - - - +
308B ASN* 1.4 62.9 + - - +
310B LEU* 3.4 5.9 + - - +
311B VAL* 3.1 26.9 + - - +
334B VAL* 3.8 30.2 - - - +
348B HEM 6.4 0.2 - - - +
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Residues in contact with ASN 308 (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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36A PHE* 5.4 0.2 - - - -
103A HIS* 3.6 26.2 + - + +
235B TYR* 5.8 4.9 - - + +
304B ARG* 3.0 26.8 + - - +
305B LEU* 3.2 10.3 + - + +
307B GLY* 1.4 74.1 - - - +
309B VAL* 1.4 65.9 + - + +
311B VAL* 3.4 1.9 + - - -
312B CYS* 3.2 27.2 + - - -
331B GLN* 3.7 21.1 + - - -
334B VAL* 5.0 1.9 - - - +
801D CNO 3.1 43.8 + - + +
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A HIS* 4.6 11.7 - - + +
227B ALA* 3.4 30.5 - - - +
230B ARG* 3.7 22.7 - - + +
231B LEU* 4.0 12.1 - - + +
234B VAL* 5.3 0.4 - - + -
235B TYR* 3.7 29.4 - - + -
305B LEU 3.0 18.4 + - - +
306B LEU* 3.6 9.2 - - - +
308B ASN* 1.4 77.1 - - + +
310B LEU* 1.4 61.3 + - - +
312B CYS* 3.3 9.2 + - - +
313B VAL* 3.0 23.2 + - + +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 4.8 4.9 - - + -
223B VAL* 3.7 30.3 - - + -
227B ALA* 4.3 17.2 - - + +
268B LEU* 4.4 18.8 - - + -
271B PHE* 3.8 38.8 - - + -
306B LEU* 2.8 23.7 + - + +
307B GLY* 3.6 7.4 - - - +
309B VAL* 1.4 72.9 - - - +
311B VAL* 1.4 56.2 + - + +
313B VAL* 3.2 4.0 + - + -
314B LEU* 2.9 48.2 + - + +
330B TYR* 5.9 0.4 - - + -
334B VAL* 4.5 8.7 - - + -
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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
----------------------------------------------------------
103A HIS* 4.1 2.0 - - + +
107A VAL* 3.8 16.4 - - + -
307B GLY 3.1 16.0 + - - +
308B ASN 3.7 7.4 - - - +
309B VAL 3.3 0.4 - - - -
310B LEU* 1.4 76.3 - - + +
312B CYS* 1.4 55.8 + - - +
314B LEU* 3.4 9.2 + - + +
315B ALA* 2.9 27.2 + - - +
322B PHE* 3.8 22.6 - - + -
327B GLN* 4.1 4.3 - - + -
330B TYR* 4.5 15.5 - - + -
331B GLN* 3.5 33.9 - - - +
334B VAL* 4.2 17.3 - - + -
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Residues in contact with CYS 312 (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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103A HIS* 4.3 6.5 - - - -
106A LEU* 4.3 22.4 - - - -
107A VAL* 4.1 20.6 - - - -
110A ALA* 3.7 5.1 - - + +
117A PHE* 4.5 8.7 - - + -
122A HIS* 4.0 30.3 - - + -
308B ASN* 3.2 19.3 + - - -
309B VAL* 3.3 7.8 + - - +
311B VAL* 1.4 75.3 - - - +
313B VAL* 1.4 56.3 + - - +
315B ALA* 3.3 7.7 + - - +
316B HIS* 2.9 29.3 + - - +
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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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223B VAL* 3.9 32.1 - - + +
226B GLU* 3.4 34.8 - - + +
227B ALA* 4.1 16.4 - - - -
230B ARG* 3.8 19.1 - - - +
309B VAL* 3.0 18.2 + - + +
310B LEU* 3.2 10.7 + - + +
312B CYS* 1.4 71.9 - - - +
314B LEU* 1.4 55.9 + - - +
316B HIS* 3.2 7.0 + - - +
317B HIS* 2.8 39.9 + - + +
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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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214B LEU* 4.9 2.0 - - + -
215B TRP* 4.5 4.7 - - + -
218B VAL* 4.2 15.7 - - + -
223B VAL* 4.5 20.0 - - + -
310B LEU* 2.9 34.4 + - + +
311B VAL* 3.7 6.3 - - + +
313B VAL* 1.4 74.2 - - - +
315B ALA* 1.4 57.7 + - - +
317B HIS* 4.3 2.9 - - + -
318B PHE* 2.8 56.7 + - + +
322B PHE* 3.8 22.2 - - + -
330B TYR* 3.7 39.5 - - + -
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Residues in contact with ALA 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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107A VAL* 3.7 30.1 - - + +
110A ALA* 4.1 2.2 - - + -
111A ALA* 3.5 11.4 - - + +
311B VAL 2.9 15.1 + - - +
312B CYS 3.3 5.8 + - - +
314B LEU* 1.4 76.4 - - - +
316B HIS* 1.4 56.8 + - - +
319B GLY* 2.9 30.5 + - - -
322B PHE* 3.5 30.9 - - + -
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Residues in contact with HIS 316 (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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110A ALA* 3.4 26.8 - - + +
114A PRO* 2.6 44.5 + - + +
117A PHE* 3.6 39.2 + + + +
226B GLU* 5.5 2.2 + - - -
230B ARG* 3.9 14.5 + - - +
312B CYS 2.9 17.1 + - - +
313B VAL* 3.2 8.0 + - - +
315B ALA* 1.4 77.0 - - - +
317B HIS* 1.3 63.1 + - - +
319B GLY* 4.0 4.2 + - - -
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Residues in contact with HIS 317 (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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217B LYS 4.6 7.9 + - - -
218B VAL* 5.4 0.9 - - + -
219B ASN* 5.4 3.6 + - - +
222B GLU* 3.3 26.7 + - - -
223B VAL* 4.8 14.1 - - + +
313B VAL* 2.8 26.5 + - + +
314B LEU* 3.7 4.9 - - - +
316B HIS* 1.3 78.0 + - - +
318B PHE* 1.4 94.9 + + + +
319B GLY 3.6 0.2 - - - -
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Residues in contact with PHE 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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214B LEU* 3.8 44.0 - - + -
217B LYS* 3.8 27.6 - - + -
218B VAL* 3.8 28.9 - - + -
314B LEU* 2.8 36.7 + - + +
317B HIS* 1.4 100.7 - + - +
319B GLY* 1.4 63.8 + - - +
320B LYS 3.4 0.9 + - - -
321B GLU* 3.2 49.1 + - + +
322B PHE* 4.3 9.4 - - + +
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Residues in contact with GLY 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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111A ALA* 3.5 29.7 - - - +
315B ALA 2.9 17.8 + - - -
316B HIS 4.0 3.8 + - - -
317B HIS 3.6 1.8 - - - -
318B PHE* 1.4 73.3 - - - +
320B LYS* 1.4 58.9 + - - -
322B PHE* 2.9 28.1 + - - +
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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
------------------------------------------------------------
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