Contacts of the helix formed by residues 217 - 232 (chain A) in PDB entry 1K63
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ARG* 4.2 1.8 - - - +
209A ARG 3.5 24.2 - - - +
210A GLN* 3.6 21.8 - - - +
211A ILE 3.5 13.2 - - - +
212A PRO* 4.7 0.7 - - + -
216A THR* 1.3 92.9 - - + +
218A ALA* 1.3 65.7 + - - +
219A ASP* 3.1 13.6 + - - +
220A VAL* 3.2 14.1 + - + -
221A VAL* 3.2 17.8 + - - +
1004A CL 3.7 3.8 - - + -
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A GLY 3.5 15.1 + - - +
217A PRO* 1.3 71.4 - - - +
219A ASP* 1.3 62.4 + - - +
221A VAL* 3.4 4.9 + - - +
222A ALA* 3.0 23.9 + - - +
1004A CL 3.1 20.9 - - + +
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 5.7 0.2 - - - +
83A ALA* 5.2 11.1 + - - +
210A GLN* 4.9 3.6 - - - +
217A PRO* 3.5 19.4 - - - +
218A ALA* 1.3 74.7 - - - +
220A VAL* 1.3 75.6 + - - +
222A ALA* 3.2 7.7 + - - +
223A ILE* 3.1 32.2 + - + +
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 3.9 20.0 - - + -
109A TRP* 4.0 21.1 - - + -
112A ALA* 6.2 0.4 - - + -
210A GLN* 3.3 51.1 - - + +
212A PRO* 4.1 10.5 - - + -
217A PRO* 3.2 9.7 + - + +
219A ASP* 1.3 85.3 + - - +
221A VAL* 1.3 66.2 + - - +
223A ILE* 3.1 12.5 + - + +
224A ALA* 2.9 24.2 + - + +
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Residues in contact with VAL 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PRO* 3.6 19.7 - - + +
212A PRO* 3.6 29.1 - - + +
215A GLY* 3.5 40.2 - - - +
216A THR 3.8 2.0 - - - +
217A PRO 3.2 10.2 + - - +
218A ALA* 3.6 9.9 - - - +
219A ASP 3.3 0.2 - - - -
220A VAL* 1.3 76.8 - - - +
222A ALA* 1.3 64.8 + - - +
224A ALA 3.2 0.3 + - - -
225A ARG* 2.9 27.1 + - + +
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ALA 3.0 14.3 + - - +
219A ASP* 3.5 10.3 - - - +
220A VAL 3.2 0.2 - - - -
221A VAL* 1.3 79.1 - - - +
223A ILE* 1.3 62.8 + - + +
225A ARG* 3.4 10.1 + - - +
226A ASP* 3.1 31.1 + - - +
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 3.6 37.2 - - + +
83A ALA* 5.8 2.5 - - + -
86A ARG* 3.9 20.4 - - - +
116A ASP* 3.4 29.2 - - - +
119A ARG* 5.3 0.5 + - - -
219A ASP* 3.1 22.8 + - + +
220A VAL* 3.1 13.9 + - + +
222A ALA* 1.3 77.3 - - + +
224A ALA* 1.3 61.9 + - - +
226A ASP* 3.2 11.9 + - - +
227A TYR* 3.2 28.9 + - + -
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ILE* 5.2 0.2 - - + -
136A MET 4.3 2.0 - - - -
137A PRO* 3.9 24.6 - - + +
212A PRO* 4.2 13.2 - - + -
220A VAL* 2.9 16.8 + - + +
223A ILE* 1.3 73.1 - - - +
225A ARG* 1.3 62.8 + - - +
227A TYR* 3.5 32.6 - - + +
228A ALA* 2.9 32.6 + - - +
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PRO* 3.7 16.0 - - + +
221A VAL* 2.9 21.3 + - + +
222A ALA* 3.5 10.5 + - - +
224A ALA* 1.3 77.8 - - - +
226A ASP* 1.3 78.6 + - - +
228A ALA* 3.8 3.0 - - - +
229A GLY* 3.1 21.1 + - - -
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Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ARG* 3.7 31.6 + - - +
222A ALA* 3.1 20.3 + - - +
223A ILE* 3.3 12.5 - - - +
225A ARG* 1.3 94.3 + - - +
227A TYR* 1.3 63.3 + - - +
229A GLY* 3.5 1.4 + - - -
230A TRP* 3.2 21.8 + - - +
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Residues in contact with TYR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 5.5 0.4 - + - -
112A ALA* 3.3 39.6 - - + +
115A PHE* 3.7 40.8 - + + +
116A ASP* 3.8 21.1 - - + -
119A ARG* 3.9 12.5 - - + +
134A ILE* 2.7 33.0 + - - +
135A ALA 4.0 8.7 - - - -
223A ILE* 3.2 26.7 + - + +
224A ALA* 3.5 31.4 - - + +
226A ASP* 1.3 75.9 - - - +
228A ALA* 1.3 73.0 + - - +
230A TRP* 3.8 3.1 - - + +
231A LEU* 2.9 29.7 + - + +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ALA 3.4 24.0 - - - +
136A MET* 4.0 9.9 - - + -
137A PRO* 4.8 0.7 - - + -
224A ALA 2.9 20.9 + - - +
225A ARG* 3.8 5.6 - - - +
227A TYR* 1.3 79.4 - - - +
229A GLY* 1.3 62.9 + - - +
231A LEU* 3.4 4.7 + - - +
232A SER* 3.1 25.3 + - - -
256A PHE* 3.6 21.0 - - + -
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Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG 3.1 13.6 + - - -
226A ASP 4.0 1.6 - - - -
227A TYR 3.3 0.2 - - - -
228A ALA* 1.3 79.8 - - - +
230A TRP* 1.3 59.7 + - - +
232A SER* 2.8 20.9 + - - -
233A GLU* 3.8 15.5 + - - +
256A PHE* 5.4 0.7 - - - -
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Residues in contact with TRP 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE 3.8 5.8 - - - -
118A ALA* 3.6 36.6 - - + -
119A ARG* 3.5 38.1 - - + -
122A ARG* 3.4 43.5 - - + +
128A ILE* 4.4 2.7 - - + -
226A ASP 3.2 16.9 + - - +
227A TYR 3.8 3.8 - - - +
228A ALA 3.2 0.6 - - - -
229A GLY* 1.3 74.6 - - - +
231A LEU* 1.3 102.8 + - + +
233A GLU* 2.9 15.9 + - + +
234A SER* 3.0 36.7 + - - -
236A ILE* 3.9 18.8 - - + -
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.5 37.0 - - + -
128A ILE* 4.0 20.2 - - + -
227A TYR* 2.9 28.2 + - + +
228A ALA* 3.9 2.7 - - - +
230A TRP* 1.3 99.9 - - + +
232A SER* 1.3 63.4 + - - +
233A GLU 3.0 1.6 + - - -
234A SER* 3.3 10.9 + - - -
238A LYS* 3.5 30.7 - - + -
260A TRP* 3.4 42.2 - - + -
261A PRO* 3.8 3.8 - - - +
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ALA 3.1 13.7 + - - -
229A GLY* 2.8 24.4 + - - -
231A LEU* 1.3 76.6 - - - +
233A GLU* 1.3 63.2 + - - +
256A PHE* 4.0 14.9 - - - -
259A THR* 4.7 5.8 - - - +
260A TRP* 3.7 23.3 - - - -
261A PRO* 3.1 18.0 - - - +
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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
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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