Contacts of the helix formed by residues 243 - 260 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231O ASP* 3.5 18.8 - - + +
232O ASP* 6.0 0.9 - - - +
241O PRO* 2.9 16.1 + - + +
242O ALA* 1.3 75.5 - - - +
244O THR* 1.3 67.7 + - - +
246O GLN* 2.9 15.7 + - - +
247O MET* 2.9 21.8 + - - +
74Q ASP* 3.8 25.1 - - + +
75Q THR 3.8 10.8 - - - +
76Q ASP* 3.7 4.3 - - - -
77Q GLN* 2.5 40.2 + - - +
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Residues in contact with THR 244 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195O LEU 5.1 2.8 + - - -
196O THR* 4.7 9.5 - - - +
227O ARG* 3.5 19.8 + - - +
229O LEU* 3.6 33.3 + - - +
231O ASP* 3.0 29.9 + - - +
242O ALA 3.9 0.4 + - - -
243O THR* 1.3 70.7 - - - +
245O SER* 1.3 56.1 + - - +
247O MET* 3.5 12.9 + - - +
248O ALA* 3.1 25.6 + - - +
76Q ASP* 3.4 24.5 - - + +
79Q GLU* 6.2 0.7 - - + -
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Residues in contact with SER 245 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192O PHE* 3.5 18.0 - - - -
196O THR* 4.3 6.5 - - - -
244O THR* 1.3 71.7 + - - +
246O GLN* 1.3 59.0 + - - +
247O MET 3.3 0.2 - - - -
248O ALA* 3.8 7.4 - - - -
249O LYS* 3.1 26.2 + - - +
76Q ASP* 2.7 28.3 + - - -
77Q GLN* 3.1 18.9 + - - +
78Q LEU* 3.8 25.3 + - - -
142Q LEU* 4.3 4.0 - - - +
146Q LEU* 3.6 8.8 - - - +
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Residues in contact with GLN 246 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O ARG* 3.8 7.1 - - - +
236O TYR* 4.0 5.2 - - + -
240O THR* 3.6 15.0 - - + +
241O PRO 3.3 19.1 - - - +
243O THR* 2.9 24.2 + - - +
245O SER* 1.3 78.9 + - - +
247O MET* 1.3 65.2 + - - +
249O LYS* 3.5 5.6 + - - +
250O ASP* 3.0 54.0 + - - +
77Q GLN* 4.9 2.1 - - - +
146Q LEU* 3.3 18.3 - - + +
147Q LYS* 2.8 48.1 + - - +
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Residues in contact with MET 247 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O VAL* 4.2 12.1 - - + +
229O LEU* 3.9 20.6 - - + -
230O PHE 3.2 28.9 - - - +
233O MET* 3.8 13.5 - - + -
234O VAL* 3.9 29.2 - - - -
236O TYR* 3.3 20.0 + - + +
242O ALA* 3.9 21.8 - - + +
243O THR 2.9 13.0 + - - +
244O THR* 3.9 18.6 - - - +
246O GLN* 1.3 75.2 - - - +
248O ALA* 1.3 65.3 + - - +
250O ASP* 3.1 4.0 + - - +
251O VAL* 3.0 27.5 + - - +
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Residues in contact with ALA 248 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192O PHE* 3.8 17.9 - - + -
195O LEU* 4.0 18.4 - - + -
196O THR* 3.9 15.7 - - + -
229O LEU* 4.1 6.7 - - + +
244O THR 3.1 18.3 + - - +
245O SER 3.8 5.6 - - - +
247O MET* 1.3 76.6 - - - +
249O LYS* 1.3 61.1 + - - +
251O VAL* 3.5 7.6 - - - +
252O THR* 2.9 30.8 + - - -
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Residues in contact with LYS 249 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76O TRP* 3.6 8.6 - - + -
77O SER* 4.2 17.8 + - - -
86O ASP* 3.9 10.7 + - - -
89O SER* 3.5 19.6 + - - +
192O PHE* 3.8 12.0 - - + -
245O SER 3.1 16.0 + - - +
246O GLN* 3.7 6.5 - - - +
247O MET 3.2 0.2 - - - -
248O ALA* 1.3 78.4 - - - +
250O ASP* 1.3 59.1 + - - +
253O THR* 2.7 37.8 + - - -
143Q PHE* 3.6 36.3 - - + -
146Q LEU* 4.1 16.8 - - + -
147Q LYS* 3.0 36.7 + - - +
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Residues in contact with ASP 250 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89O SER* 2.6 33.5 + - - +
92O ARG* 3.0 35.4 + - - -
93O GLY* 3.1 25.4 - - - +
236O TYR* 3.0 29.4 + - - +
246O GLN* 3.0 22.9 + - - +
247O MET 3.1 3.8 + - - +
249O LYS* 1.3 77.0 - - - +
251O VAL* 1.3 65.0 + - - +
253O THR* 3.4 1.2 + - - -
254O PHE 3.2 13.2 + - - -
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Residues in contact with VAL 251 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O GLY* 3.4 23.7 - - - +
96O VAL* 3.8 16.2 - - + -
97O TYR* 3.7 24.2 - - + +
101O CYS* 4.1 9.4 - - - -
195O LEU* 4.0 14.4 - - + -
229O LEU* 4.9 0.4 - - + -
247O MET 3.0 20.2 + - - +
248O ALA* 3.5 10.1 - - - +
250O ASP* 1.3 74.7 - - - +
252O THR* 1.3 52.3 + - - +
254O PHE* 2.7 10.8 + - + +
255O LEU* 2.6 41.6 + - + +
523O HEC 4.6 13.0 - - + -
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Residues in contact with THR 252 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76O TRP* 3.3 28.9 - - + -
181O VAL* 4.3 1.7 - - + +
188O CYS* 3.5 31.8 - - + +
191O ILE* 3.2 27.2 - - + +
192O PHE* 3.9 7.8 + - - -
195O LEU* 4.2 3.8 - - - +
248O ALA 2.9 17.5 + - - -
251O VAL* 1.3 78.2 - - - +
253O THR* 1.3 56.1 + - - +
255O LEU* 3.7 7.5 - - - +
256O ASN* 2.8 28.2 + - - +
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Residues in contact with THR 253 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76O TRP* 3.5 14.0 - - - -
77O SER* 6.0 0.9 - - - +
78O HIS* 3.7 26.5 - - + -
85O PHE* 4.4 6.5 - - + -
86O ASP* 4.4 6.7 - - + +
89O SER* 3.6 25.1 + - - +
90O ILE* 4.3 18.1 - - + +
249O LYS* 2.7 26.9 + - - +
250O ASP 3.8 2.9 - - - -
251O VAL 3.1 1.0 - - - -
252O THR* 1.3 75.7 - - - +
254O PHE* 1.3 57.5 + - - +
256O ASN* 3.4 6.5 + - - +
257O TRP* 3.1 24.6 + - - +
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Residues in contact with PHE 254 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90O ILE* 3.7 35.6 - - + +
93O GLY 3.9 13.0 - - - -
94O TYR* 3.6 36.8 - + + -
97O TYR* 3.8 20.2 - + + -
107O LEU* 3.6 20.6 - - + -
110O VAL* 5.9 0.4 - - + -
115O LEU* 4.1 8.5 - - + -
155O ILE* 5.4 0.7 - - + -
250O ASP 3.2 12.5 + - - +
251O VAL* 2.7 14.3 + - + +
253O THR* 1.3 69.2 - - - +
255O LEU* 1.3 72.1 + - + +
257O TRP* 3.1 18.0 + + - +
258O CYS* 2.8 52.8 + - - -
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Residues in contact with LEU 255 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97O TYR* 5.1 1.8 - - + -
107O LEU* 4.6 3.4 - - + -
177O LEU* 3.8 44.5 - - + +
178O SER 4.7 0.5 - - - +
180O ILE* 4.1 20.0 - - + -
181O VAL* 3.8 13.3 + - + +
191O ILE* 4.7 12.1 - - + -
251O VAL* 2.6 28.1 + - + +
252O THR* 3.7 6.3 - - - +
254O PHE* 1.3 92.5 - - + +
256O ASN* 1.3 63.4 + - - +
258O CYS* 3.5 8.8 + - - +
259O ALA* 3.0 23.7 + - - +
523O HEC 4.0 16.6 - - + -
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Residues in contact with ASN 256 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O HIS* 3.3 13.0 + - - +
85O PHE* 3.2 20.4 - - + -
181O VAL* 3.7 17.8 - - - +
188O CYS* 2.8 30.0 - - - -
252O THR 2.8 17.9 + - - +
253O THR* 3.5 7.9 - - - +
254O PHE 3.2 0.2 - - - -
255O LEU* 1.3 74.1 - - - +
257O TRP* 1.3 54.5 + - - +
259O ALA* 3.2 1.9 + - - -
260O GLU* 2.7 60.7 + - - +
263O HIS* 5.0 0.7 - - - -
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Residues in contact with TRP 257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85O PHE* 3.4 30.0 - + + -
87O HIS* 5.9 2.0 - + - -
90O ILE* 4.3 14.8 - - + -
110O VAL* 4.0 14.6 - - + -
114O THR* 3.0 50.3 - - - -
115O LEU* 3.8 23.3 - - + -
118O VAL* 3.2 30.2 - - + +
253O THR 3.1 14.2 + - - +
254O PHE* 3.1 22.4 + + - +
256O ASN* 1.3 75.2 - - - +
258O CYS* 1.3 88.2 + - - +
260O GLU 2.9 1.0 + - - -
261O PRO* 2.8 59.1 + - + +
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Residues in contact with CYS 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N ARG* 2.9 30.7 + - - -
107O LEU* 4.0 15.0 - - - -
110O VAL* 4.1 15.1 - - + +
177O LEU 5.0 0.2 - - - +
178O SER* 3.6 13.2 - - - +
254O PHE* 2.8 61.6 + - - -
255O LEU* 3.5 14.6 - - + +
257O TRP* 1.3 85.0 - - - +
259O ALA* 1.3 60.8 + - - +
261O PRO* 3.4 1.7 - - - +
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Residues in contact with ALA 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70N ARG* 4.0 2.1 + - - -
178O SER 3.2 15.9 + - - +
179O LEU* 3.8 26.8 - - + +
181O VAL* 4.3 15.0 - - + -
182O LYS* 3.7 26.3 + - + -
255O LEU 3.0 17.0 + - - +
256O ASN 3.7 3.1 - - - +
258O CYS* 1.3 80.0 - - - +
260O GLU* 1.3 59.7 + - + +
261O PRO* 3.2 8.2 - - - +
262O GLU* 4.7 0.7 - - - +
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Residues in contact with GLU 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N TYR* 4.6 0.9 + - - -
248N PRO* 4.9 1.2 - - - +
249N ASN* 4.1 15.1 + - - -
85O PHE* 3.9 1.9 - - - -
181O VAL* 4.7 3.3 - - - +
182O LYS* 3.8 27.8 - - + +
256O ASN* 2.7 41.8 + - - +
257O TRP 3.1 4.0 - - - -
259O ALA* 1.3 78.0 - - + +
261O PRO* 1.3 58.2 - - - +
262O GLU* 3.1 19.9 - - - +
263O HIS* 2.9 33.4 + - + +
266O ARG* 3.1 25.2 + - - +
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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
------------------------------------------------------------
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