Contacts of the strand formed by residues 240 - 245 (chain B) in PDB entry 1KTW
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 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B TYR 3.0 8.0 + - - +
219B GLY* 3.4 3.6 - - - -
220B LEU 3.3 18.3 + - - -
221B ILE 4.4 3.8 + - - +
236B SER* 4.3 3.4 - - - -
238B GLY 3.6 1.2 + - - -
239B GLY* 1.3 79.1 - - - +
241B ALA* 1.3 66.1 + - - +
242B LEU 3.7 8.3 - - - +
243B ARG* 3.6 61.2 - - + +
273B LEU* 3.8 22.0 - - + -
274B ALA* 3.3 17.0 - - + +
275B ALA 4.1 2.2 - - - +
277B MET* 3.7 33.9 - - + +
303B ARG* 4.6 6.1 - - - +
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Residues in contact with ALA 241 (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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220B LEU* 3.4 7.7 - - + +
221B ILE* 2.9 31.9 + - - +
234B LEU* 4.7 8.3 - - + +
235B HIS* 4.8 0.7 - - - -
236B SER* 3.8 21.4 + - - +
240B ILE* 1.3 72.8 - - - +
242B LEU* 1.3 60.6 + - - +
267B ILE* 3.9 11.4 - - + -
268B ARG 3.4 25.1 - - - +
269B CYS* 5.4 0.8 - - - +
274B ALA 3.5 5.6 + - - +
275B ALA* 3.4 12.1 - - - +
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Residues in contact with LEU 242 (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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221B ILE* 4.0 22.4 - - + -
223B THR* 4.6 1.8 - - + -
231B PHE* 3.9 36.1 - - + -
234B LEU* 5.2 1.3 - - + -
240B ILE* 3.7 2.7 - - - -
241B ALA* 1.3 74.1 - - - +
243B ARG* 1.3 57.7 + - - +
244B MET* 3.5 37.0 + - + +
262B ILE* 5.7 0.7 - - + -
264B ALA* 3.8 28.7 - - + -
267B ILE* 4.0 18.4 - - + -
275B ALA 3.0 13.4 + - - +
276B VAL* 3.8 6.9 - - + -
277B MET 3.2 23.7 + - - +
290B VAL* 5.3 1.1 - - + -
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Residues in contact with ARG 243 (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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216B PHE 3.3 11.3 + - - -
217B GLY* 3.2 28.6 + - - -
218B TYR* 2.9 32.1 + - - +
221B ILE 3.0 18.3 + - - +
222B GLN* 3.3 32.0 - - - +
223B THR* 3.2 22.0 + - - -
240B ILE* 3.6 39.9 - - + +
241B ALA 3.8 0.2 - - - -
242B LEU* 1.3 70.7 - - - +
244B MET* 1.3 58.4 + - - +
245B GLU* 3.1 40.5 + - + -
273B LEU* 4.2 4.0 - - - +
277B MET* 4.1 12.6 - - - +
303B ARG* 5.9 1.4 - - - +
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Residues in contact with MET 244 (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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223B THR* 3.4 22.0 - - + +
242B LEU* 3.5 34.5 + - + +
243B ARG* 1.3 70.7 - - - +
245B GLU* 1.3 58.9 + - - +
246B THR* 3.8 3.8 + - - -
259B ILE* 3.8 23.6 - - + -
262B ILE* 4.8 6.5 - - - -
276B VAL* 3.8 20.2 - - + -
277B MET 2.9 25.8 + - - +
278B PHE* 3.5 37.9 - - + -
279B GLY 3.1 21.4 + - - +
288B VAL* 4.1 15.9 - - + -
290B VAL* 4.9 1.3 - - + -
375B PHE* 3.7 15.9 - - + -
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Residues in contact with GLU 245 (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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222B GLN* 3.1 21.5 - - - +
223B THR 3.6 9.0 + - - +
224B TYR* 4.0 1.7 - - - -
243B ARG* 3.1 48.0 + - + -
244B MET* 1.3 73.3 - - - +
246B THR* 1.3 57.3 + - - +
247B ASP* 3.1 19.3 + - - +
277B MET* 3.8 21.4 - - + +
279B GLY* 3.2 6.2 - - - +
281B HIS* 2.9 36.3 + - + +
303B ARG* 5.5 1.0 + - - -
305B ASP* 5.1 1.7 - - - +
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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