Contacts of the helix formed by residues 224 - 231 (chain A) in PDB entry 1KEK
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 ILE 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A GLN* 3.8 34.9 + - + +
221A ASN 4.8 0.2 - - - +
223A ASP* 1.3 102.7 + - - +
225A TYR* 1.3 67.9 + - - +
226A PHE 3.5 2.0 - - - -
227A GLN* 3.4 11.8 + - - +
228A GLY* 3.1 17.2 + - - -
646B ILE* 3.8 29.8 - - + -
651B GLY 4.0 6.3 - - - +
659B PHE* 3.7 37.3 - - + -
665B PHE* 4.2 5.2 - - + -
848B ALA* 4.0 20.2 - - + +
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Residues in contact with TYR 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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220A GLN* 3.5 21.5 - - + +
221A ASN 3.1 18.1 + - - +
222A PRO* 4.2 1.8 + - + -
223A ASP 4.0 0.2 - - - -
224A ILE* 1.3 76.0 - - - +
226A PHE* 1.3 65.7 + - - +
228A GLY* 3.0 3.3 + - - -
229A ARG* 2.9 39.8 + - + +
115B ALA* 3.8 7.8 - - + +
116B ILE 3.0 18.6 + - - -
118B ALA 5.0 0.6 + - - -
119B HIS* 3.5 19.9 - + - -
120B ALA* 3.6 23.3 - - + -
121B LEU 4.5 0.2 - - - -
122B SER* 3.6 22.0 - - - -
126B ASP* 4.0 8.5 - - - -
128B GLN* 2.7 31.1 + - - -
365B LEU* 4.1 7.2 - - + +
366B GLY* 3.8 22.2 - - - +
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Residues in contact with PHE 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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222A PRO 5.0 0.2 + - - -
224A ILE 3.5 0.6 - - - -
225A TYR* 1.3 76.3 - - - +
227A GLN* 1.3 63.6 + - - +
229A ARG* 3.0 13.0 + - - +
230A GLU* 3.1 38.6 + - + +
362B ARG* 3.8 28.7 - - + -
363B TYR* 3.8 1.3 - - - -
364B GLY 3.8 14.8 - - - -
365B LEU* 3.6 39.1 + - + +
368B LYS* 3.6 39.3 - - + +
391B THR* 4.0 14.4 - - + -
392B VAL 3.7 19.3 - - - -
394B ILE* 3.8 14.6 - - + -
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Residues in contact with GLN 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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223A ASP 2.8 21.0 + - - +
224A ILE* 3.5 13.0 + - - +
226A PHE* 1.3 70.4 - - - +
228A GLY* 1.4 62.8 + - - +
230A GLU 3.1 10.4 + - - +
231A ALA* 3.1 12.3 + - - +
368B LYS* 2.9 32.1 + - - +
394B ILE* 3.7 20.6 - - + +
651B GLY 3.3 8.1 - - - +
652B ASP 4.0 5.0 - - - +
654B LEU 3.1 26.9 - - - +
655B PRO 4.3 5.6 - - - -
656B VAL* 3.7 22.3 - - - +
659B PHE* 3.5 23.2 - - + -
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Residues in contact with GLY 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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220A GLN* 4.5 1.8 - - - -
224A ILE 3.1 6.7 + - - -
225A TYR 3.0 8.0 + - - -
227A GLN* 1.4 81.4 - - - +
229A ARG* 1.3 60.5 + - - +
230A GLU 3.4 0.2 + - - -
231A ALA* 3.5 13.6 + - - +
232A ALA* 4.6 0.5 + - - +
119B HIS* 3.5 31.5 - - - +
659B PHE* 4.5 18.1 - - - -
660B GLU 5.0 1.7 - - - +
661B ALA 4.6 4.3 - - - +
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Residues in contact with ARG 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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98A TYR* 4.6 13.7 - - - -
101A SER* 5.7 2.0 + - - -
102A GLY* 5.1 6.1 - - - -
136A THR 5.9 0.4 + - - -
225A TYR* 2.9 30.6 + - + +
226A PHE* 3.4 9.0 - - - +
228A GLY* 1.3 79.1 - - - +
230A GLU* 1.4 59.9 + - + +
231A ALA 3.4 0.2 - - - -
232A ALA* 4.2 8.5 + - - +
233A ASN* 4.6 0.2 + - - -
118B ALA* 3.4 25.1 - - - +
119B HIS* 3.3 17.1 + - + +
128B GLN* 3.2 29.9 - - - +
331B LYS* 3.3 44.5 + - + +
333B PRO* 4.0 22.7 - - - +
365B LEU* 4.0 24.2 - - + -
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Residues in contact with GLU 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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226A PHE* 3.1 29.2 + - + +
227A GLN 3.1 4.4 + - - +
229A ARG* 1.4 75.7 - - - +
231A ALA* 1.3 61.3 - - - +
232A ALA 3.2 2.7 - - - -
233A ASN* 2.9 48.9 + - - +
234A PRO* 4.6 0.7 - - - +
331B LYS* 3.2 19.0 - - + +
362B ARG* 2.8 38.3 + - - -
391B THR* 3.8 12.0 - - - +
394B ILE* 3.9 15.0 - - + -
396B ASP* 5.0 2.4 - - - +
398B VAL* 5.6 0.5 - - - +
399B THR* 5.0 0.5 + - - -
401B THR* 4.5 4.2 + - - +
656B VAL* 4.0 12.4 - - + +
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Residues in contact with ALA 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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227A GLN 3.1 10.0 + - - +
228A GLY 3.8 11.2 - - - +
229A ARG 3.4 1.8 - - - -
230A GLU* 1.3 77.0 - - - +
232A ALA* 1.3 60.2 + - - +
234A PRO* 3.4 14.1 - - - +
235A TYR* 4.6 0.7 - - - -
398B VAL* 5.0 2.1 - - - +
656B VAL* 3.7 19.7 - - + +
659B PHE* 4.2 13.2 - - + +
660B GLU 4.1 5.6 - - - +
661B ALA* 3.4 30.3 - - - +
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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
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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