Contacts of the helix formed by residues 244 - 253 (chain B) in PDB entry 3KXK
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 244 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ILE* 3.8 21.5 - - + +
90B LEU* 3.6 43.1 - - + -
91B LEU* 3.5 35.2 - - + -
94B PHE* 3.9 11.6 - - + -
110B ALA* 4.2 5.4 - - + +
240B ILE* 3.9 7.2 - - + -
241B PRO* 3.0 23.3 + - + +
243B GLN* 1.3 81.5 - - + +
245B VAL* 1.3 64.6 + - - +
246B ASP 3.4 2.2 - - - -
247B ALA* 3.6 7.8 + - + +
248B PHE* 3.1 22.7 + - - +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE* 4.4 17.0 - - + +
241B PRO 3.6 5.8 - - - +
242B PRO* 3.3 33.8 + - + +
243B GLN 3.5 0.2 - - - -
244B ILE* 1.3 77.4 - - - +
246B ASP* 1.3 72.9 + - - +
248B PHE* 3.3 2.9 + - - +
249B PHE* 3.1 53.1 + - + -
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Residues in contact with ASP 246 (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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106B GLN* 4.4 17.1 + - - +
242B PRO 5.0 0.2 + - - -
243B GLN 5.0 2.4 + - - +
244B ILE 3.4 0.4 - - - -
245B VAL* 1.3 85.7 - - - +
247B ALA* 1.3 63.0 + - - +
248B PHE 3.2 0.2 + - - -
249B PHE* 3.3 4.9 + - - +
250B VAL* 3.0 32.6 + - + +
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Residues in contact with ALA 247 (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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91B LEU* 4.4 8.5 - - + -
94B PHE* 4.2 10.1 - - + -
106B GLN* 3.8 32.8 + - - +
107B ILE* 3.9 18.4 - - + +
110B ALA* 4.4 7.2 - - + -
243B GLN 5.6 0.2 + - - -
244B ILE* 3.6 8.4 + - - +
245B VAL 3.4 0.2 - - - -
246B ASP* 1.3 78.3 - - - +
248B PHE* 1.3 57.3 + - - +
250B VAL* 3.7 1.9 + - - +
251B THR* 2.7 33.5 + - - -
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Residues in contact with PHE 248 (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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94B PHE* 3.5 33.8 - + + -
234B VAL* 4.2 10.9 - - + +
235B PRO 3.6 24.0 - - - -
236B PHE* 4.4 4.3 - + - -
237B ILE* 4.2 13.2 - - + -
240B ILE* 3.7 32.1 - - + -
244B ILE 3.1 19.4 + - - +
245B VAL* 3.5 4.7 - - - +
246B ASP 3.1 0.2 - - - -
247B ALA* 1.3 77.1 - - - +
249B PHE* 1.3 85.3 + + - +
251B THR* 3.0 6.6 + - - -
252B LEU* 2.8 56.3 + - + +
284B ILE* 5.1 5.2 - - + -
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Residues in contact with PHE 249 (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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240B ILE* 5.6 4.7 - - + -
245B VAL* 3.1 46.2 + - + +
246B ASP* 4.1 3.6 - - - +
248B PHE* 1.3 102.5 - + - +
250B VAL* 1.3 53.4 + - + +
252B LEU* 3.9 2.6 - - - +
253B SER* 2.7 44.6 + - - +
284B ILE* 5.0 4.7 - - + -
287B GLU* 3.1 48.9 - - + -
288B ILE* 3.8 24.0 - - + -
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Residues in contact with VAL 250 (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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120A LYS* 6.5 0.4 - - - -
100B SER* 4.8 1.6 + - - +
102B GLU* 4.0 23.8 - - + +
103B ALA* 3.7 30.8 - - + +
106B GLN* 3.9 25.8 - - + +
246B ASP* 3.0 20.5 + - + +
247B ALA 4.0 3.4 - - - +
249B PHE* 1.3 77.7 - - + +
251B THR* 1.3 62.0 + - - +
253B SER* 3.8 11.0 + - - -
254B GLU* 3.8 12.3 - - - +
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Residues in contact with THR 251 (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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94B PHE* 3.8 25.2 - - - +
97B HIS* 4.4 3.5 - - + +
98B ALA* 4.2 16.2 - - - +
103B ALA* 4.0 10.0 - - - +
107B ILE* 3.5 20.1 - - - +
233B THR* 5.8 1.6 - - - -
234B VAL* 3.7 25.9 + - + +
247B ALA 2.7 18.1 + - - -
248B PHE* 3.0 11.1 + - - -
250B VAL* 1.3 76.2 - - - +
252B LEU* 1.3 63.2 + - - +
254B GLU* 3.2 23.0 - - - +
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Residues in contact with LEU 252 (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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185B VAL* 4.9 2.7 - - + -
233B THR* 4.5 11.9 - - - +
234B VAL* 3.6 32.0 - - + +
236B PHE* 3.9 16.2 - - + -
248B PHE* 2.8 37.6 + - + +
249B PHE* 3.9 5.6 - - - +
251B THR* 1.3 71.6 - - - +
253B SER* 1.3 57.1 + - - +
254B GLU 2.9 10.9 + - - -
255B ALA* 2.9 27.8 + - + +
284B ILE* 3.6 30.5 - - + -
285B LEU* 5.9 0.2 - - + -
288B ILE* 3.8 25.4 - - + +
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Residues in contact with SER 253 (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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249B PHE* 2.7 30.4 + - - +
250B VAL* 4.0 9.1 - - - -
251B THR 3.3 0.4 - - - -
252B LEU* 1.3 67.6 - - - +
254B GLU* 1.3 56.7 + - - +
255B ALA 2.9 10.8 + - - -
256B LYS* 3.0 35.6 + - - +
257B TYR* 4.0 8.0 - - - -
288B ILE* 4.1 20.8 + - - +
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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