Contacts of the helix formed by residues 243 - 260 (chain D) in PDB entry 1KYO
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 243 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ASP* 3.2 15.5 - - + +
232D ASP 4.5 0.4 - - - +
241D PRO* 2.8 24.7 + - + +
242D ALA* 1.3 74.1 - - - +
244D THR* 1.3 66.7 + - - +
245D SER 2.9 1.7 + - - -
246D GLN* 2.9 26.7 + - - +
247D MET* 3.0 10.4 + - - +
74F ASP* 4.4 12.8 - - + +
75F THR 3.7 16.4 - - - +
76F ASP* 3.7 3.6 - - - -
77F GLN* 2.6 38.9 + - - +
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Residues in contact with THR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D THR* 4.5 11.5 - - - +
227D ARG* 3.6 21.9 + - - +
229D LEU* 3.5 39.4 + - - +
231D ASP* 2.9 37.7 + - - +
242D ALA 3.7 1.6 + - - -
243D THR* 1.3 70.5 - - - +
245D SER* 1.3 57.5 + - - +
247D MET* 3.7 10.9 + - - +
248D ALA* 3.3 18.0 + - - +
76F ASP* 3.9 16.6 + - + +
79F GLU* 6.0 0.4 - - + -
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Residues in contact with SER 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D PHE* 3.8 10.0 - - - -
196D THR* 4.1 22.9 - - - -
244D THR* 1.3 73.2 + - - +
246D GLN* 1.3 68.7 + - - +
247D MET 3.1 1.6 - - - -
248D ALA* 3.1 2.1 + - - +
249D LYS* 2.9 24.4 + - - +
76F ASP* 2.9 25.7 + - - -
77F GLN* 3.4 4.3 + - - -
78F LEU* 4.1 11.8 + - - -
142F LEU* 4.0 6.1 - - - +
146F LEU* 3.3 21.1 - - - +
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Residues in contact with GLN 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ARG* 3.5 6.9 - - - +
236D TYR* 3.9 7.4 - - + -
240D THR* 3.8 14.4 - - + +
241D PRO 3.1 22.0 - - - +
243D THR* 2.9 22.0 + - - +
245D SER* 1.3 79.7 + - - +
247D MET* 1.3 61.2 + - - +
249D LYS* 3.6 2.9 - - - +
250D ASP* 3.2 32.1 + - - -
77F GLN* 4.3 2.6 - - - +
146F LEU* 3.4 20.2 - - + +
147F LYS* 2.6 49.9 + - - +
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Residues in contact with MET 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D VAL* 4.1 9.2 - - + -
229D LEU* 3.7 24.7 - - + -
230D PHE 3.3 27.4 - - - +
233D MET* 3.7 10.8 - - + -
234D VAL* 3.7 33.9 - - - -
236D TYR* 3.2 26.5 - - + +
242D ALA* 3.6 20.6 - - + +
243D THR 3.0 10.8 + - - +
244D THR* 3.7 15.7 - - - +
246D GLN* 1.3 73.4 - - - +
248D ALA* 1.3 58.0 + - - +
250D ASP* 2.6 23.8 + - - +
251D VAL* 2.9 17.6 + - - +
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Residues in contact with ALA 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D PHE* 3.7 20.9 - - + -
195D LEU* 4.2 14.1 - - + -
196D THR* 3.8 13.9 - - + -
229D LEU* 3.6 10.0 - - + +
244D THR 3.3 12.6 + - - +
245D SER 3.1 8.2 + - - +
247D MET* 1.3 76.5 - - - +
249D LYS* 1.3 64.3 + - - +
251D VAL* 3.6 10.0 - - - +
252D THR* 3.1 29.1 + - - -
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Residues in contact with LYS 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TRP* 3.7 8.9 - - + -
77D SER* 4.4 17.3 + - - +
86D ASP* 3.9 11.3 + - - -
89D SER* 3.7 19.3 + - - +
192D PHE* 3.7 9.8 - - + -
245D SER 2.9 12.4 + - - +
246D GLN* 3.6 8.7 - - - +
248D ALA* 1.3 77.0 - - - +
250D ASP* 1.3 58.8 + - - +
253D THR* 2.7 34.2 + - - +
143F PHE* 3.6 41.7 - - + -
146F LEU* 4.0 17.9 - - + -
147F LYS* 3.3 38.5 + - - +
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Residues in contact with ASP 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D SER* 2.6 35.0 + - - +
92D ARG* 2.7 33.7 + - - +
93D GLY* 3.8 11.7 - - - +
96D VAL* 4.3 1.1 - - + -
236D TYR* 2.7 27.7 + - - +
246D GLN* 3.2 21.8 + - - -
247D MET 2.6 13.4 + - - +
249D LYS* 1.3 72.1 - - - +
251D VAL* 1.3 66.1 + - - +
253D THR* 2.8 15.6 + - - -
254D PHE* 2.9 11.6 + - - +
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Residues in contact with VAL 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D GLY* 3.8 15.6 - - - +
96D VAL* 3.5 34.7 - - + +
97D TYR* 3.8 11.7 - - + +
101D CYS* 3.9 15.7 - - - -
195D LEU* 4.1 13.5 - - + -
229D LEU* 4.5 3.6 - - + -
247D MET 2.9 18.4 + - - +
248D ALA* 3.6 13.7 - - - +
250D ASP* 1.3 72.3 - - - +
252D THR* 1.3 52.1 + - - +
254D PHE* 3.1 4.8 + - + +
255D LEU* 2.7 43.6 + - + +
503D HEC 4.6 10.5 - - + -
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Residues in contact with THR 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TRP* 3.2 31.0 - - + -
181D VAL* 4.4 1.8 - - + +
188D CYS* 3.7 30.3 - - + +
191D ILE* 3.8 16.2 - - + +
192D PHE* 3.6 20.1 + - - -
195D LEU* 4.1 4.0 - - - +
248D ALA 3.1 18.3 + - - -
249D LYS 3.9 0.2 - - - -
251D VAL* 1.3 76.6 - - - +
253D THR* 1.3 56.9 + - - +
255D LEU* 3.0 9.4 + - - +
256D ASN* 2.8 27.7 + - - +
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Residues in contact with THR 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TRP* 3.6 13.2 - - - -
77D SER* 5.3 2.0 + - - +
78D HIS* 4.1 24.7 - - + -
85D PHE* 4.4 5.7 - - + -
86D ASP* 4.4 7.4 - - + +
89D SER* 3.7 23.6 + - - -
90D ILE* 4.1 18.8 - - + -
249D LYS* 2.7 21.9 + - - +
250D ASP 2.8 7.9 + - - -
252D THR* 1.3 77.1 - - - +
254D PHE* 1.3 64.2 + - - +
256D ASN* 3.0 16.8 + - - +
257D TRP* 3.0 13.9 + - - +
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Residues in contact with PHE 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE* 3.9 27.5 - - + +
93D GLY* 3.6 33.7 - - - -
94D TYR* 3.7 31.6 - + + -
97D TYR* 3.6 28.3 - + + -
107D LEU* 3.6 18.6 - - + -
115D LEU* 5.2 4.5 - - + -
119D SER* 6.0 0.9 - - - -
155D ILE* 5.6 0.9 - - + -
250D ASP 2.9 4.9 + - - -
251D VAL* 3.3 8.3 - - + +
253D THR* 1.3 76.0 - - - +
255D LEU* 1.3 71.7 + - + +
257D TRP* 3.0 22.1 + + - +
258D CYS* 2.9 46.7 + - - -
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Residues in contact with LEU 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D TYR* 5.1 4.0 - - + -
107D LEU* 4.4 7.6 - - + -
177D LEU* 3.9 31.4 - - + +
178D SER 4.6 0.9 - - - +
180D ILE* 3.8 21.8 - - + -
181D VAL* 3.6 17.9 + - + +
191D ILE* 4.5 11.7 - - + -
251D VAL* 2.7 27.0 + - + +
252D THR* 3.5 4.7 - - - +
254D PHE* 1.3 95.4 - - + +
256D ASN* 1.3 62.0 + - - +
258D CYS* 3.6 6.3 - - - +
259D ALA* 3.2 19.2 + - - +
503D HEC 4.2 25.8 - - + -
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Residues in contact with ASN 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D HIS* 3.1 29.7 + - - +
85D PHE* 3.3 17.1 - - + -
181D VAL* 3.7 18.2 - - + +
188D CYS* 3.1 18.9 - - - -
252D THR 2.8 11.7 + - - +
253D THR* 3.0 12.3 + - - +
255D LEU* 1.3 75.6 - - - +
257D TRP* 1.3 54.6 + - - +
259D ALA* 3.1 3.1 + - - -
260D GLU* 2.7 58.2 + - - +
263D HIS* 5.5 0.5 - - - -
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Residues in contact with TRP 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 3.5 28.1 - + + -
87D HIS* 6.0 0.9 - - - -
90D ILE* 4.0 21.1 - - + -
110D VAL* 4.0 7.4 - - + -
114D THR* 2.9 37.7 - - - -
115D LEU* 3.3 33.9 - - + -
118D VAL* 3.4 33.3 - - + +
119D SER* 5.8 0.9 - - - -
253D THR 3.0 9.5 + - - +
254D PHE* 3.0 19.6 + + - +
256D ASN* 1.3 77.4 - - - +
258D CYS* 1.3 99.7 + - - +
260D GLU 4.3 0.2 - - - +
261D PRO* 2.9 54.9 + - + +
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Residues in contact with CYS 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ARG* 2.8 29.8 + - - -
107D LEU* 3.9 7.9 - - - -
110D VAL* 3.8 20.5 - - + +
177D LEU 4.8 1.8 - - - +
178D SER* 3.5 13.7 - - - +
254D PHE* 2.9 52.6 + - - -
255D LEU* 3.6 13.7 - - - +
257D TRP* 1.3 93.2 - - - +
259D ALA* 1.3 58.3 + - - +
261D PRO* 3.8 0.9 - - - +
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Residues in contact with ALA 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ARG* 4.0 9.8 + - - +
178D SER 3.1 17.5 - - - +
179D LEU* 3.8 21.3 - - + +
181D VAL* 4.6 7.4 - - + -
182D LYS* 3.4 30.6 + - + -
255D LEU 3.2 12.2 + - - +
256D ASN 3.1 3.8 + - - +
258D CYS* 1.3 79.6 - - - +
260D GLU* 1.3 62.4 + - + +
261D PRO* 3.4 7.5 - - - +
262D GLU* 4.5 0.7 - - - +
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Residues in contact with GLU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C TYR* 4.7 3.1 + - - -
248C PRO* 4.9 2.1 - - - +
249C ASN* 4.7 4.5 + - - -
85D PHE* 3.8 5.0 - - + -
181D VAL* 5.3 1.4 - - - +
182D LYS* 3.9 30.5 - - + +
256D ASN* 2.7 38.0 + - - +
257D TRP 3.2 3.6 - - - -
259D ALA* 1.3 78.7 - - + +
261D PRO* 1.3 63.9 - - - +
262D GLU* 3.2 16.8 - - - +
263D HIS* 3.0 30.4 + - + +
266D ARG* 2.8 28.6 + - - -
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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