Contacts of the strand formed by residues 237 - 244 (chain M) 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 SER 237 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M GLY 4.2 4.2 + - - -
236M ASP* 1.3 71.3 - - - +
238M VAL* 1.3 61.2 + - - +
290M ARG* 3.8 0.7 - - - +
291M ASP 3.1 36.0 + - - +
292M GLN 4.1 8.9 + - - -
294M SER* 4.5 8.4 + - - -
297M VAL* 3.6 14.0 - - - +
356M VAL 3.3 6.5 - - - -
357M GLY* 3.7 3.1 - - - -
358M ASP* 3.1 37.4 + - - +
362M LEU* 4.5 7.4 - - - -
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Residues in contact with VAL 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138M PRO* 3.1 37.0 - - + +
139M VAL* 4.3 11.4 - - + -
142M ALA* 4.3 4.0 - - + +
237M SER* 1.3 74.7 - - - +
239M ALA* 1.3 68.1 + - - +
240M ALA* 4.6 4.7 - - + -
288M PHE* 4.3 8.3 - - + -
289M VAL 3.6 13.2 - - - +
290M ARG* 4.0 20.6 - - + -
354M VAL 3.9 1.2 - - - +
355M ALA* 3.5 1.0 - - - -
356M VAL* 2.6 60.1 + - + +
362M LEU* 4.0 3.1 - - - +
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Residues in contact with ALA 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238M VAL* 1.3 72.4 - - - +
240M ALA* 1.3 63.2 + - - +
289M VAL* 2.8 32.5 + - - +
297M VAL* 3.5 22.8 - - + +
301M ILE* 4.2 21.5 - - + +
353M TYR* 4.2 21.3 - - + +
354M VAL 3.6 4.7 - - - -
355M ALA* 4.3 2.2 - - - +
362M LEU* 4.4 5.4 - - + -
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Residues in contact with ALA 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M ALA* 4.4 6.5 - - + -
146M LEU* 4.5 2.2 - - + -
238M VAL* 4.6 0.7 - - + -
239M ALA* 1.3 76.7 - - - +
241M ILE* 1.3 67.5 + - - +
287M LEU 3.4 14.1 - - - +
288M PHE* 3.4 28.0 - - + -
301M ILE* 5.2 1.6 - - - -
352M ASN 3.8 0.2 - - - +
353M TYR* 3.5 6.4 - - - -
354M VAL* 2.9 48.7 + - + +
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Residues in contact with ILE 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146M LEU* 3.9 5.0 - - - +
240M ALA* 1.3 80.5 - - - +
242M GLY* 1.3 59.9 + - - +
243M ILE* 4.6 13.2 - - + -
285M PHE* 3.7 4.6 - - + +
286M THR* 3.4 7.1 - - - +
287M LEU* 3.2 47.4 + - + -
301M ILE* 4.4 14.6 - - + -
304M ILE* 6.2 0.7 - - + -
305M VAL* 4.6 14.8 - - + -
308M LEU* 5.7 6.1 - - + -
348M LEU* 4.9 8.1 - - + -
351M PHE* 3.7 43.1 - - + -
352M ASN 3.0 9.4 - - - +
353M TYR* 4.1 9.9 - - + -
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Residues in contact with GLY 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146M LEU* 4.1 17.0 - - - +
150M THR* 5.1 0.4 - - - -
241M ILE* 1.3 76.0 - - - +
243M ILE* 1.3 66.2 + - - +
244M PRO* 4.5 0.7 - - - -
284M LEU* 4.4 7.4 - - - -
285M PHE 3.1 8.7 - - - -
286M THR* 4.2 2.0 - - - -
351M PHE* 3.7 1.2 - - - +
352M ASN* 2.9 40.8 + - - +
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Residues in contact with ILE 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225M LEU* 5.8 1.1 - - + -
241M ILE* 4.6 7.9 - - + -
242M GLY* 1.3 79.6 - - - +
244M PRO* 1.3 80.1 - - + +
245M VAL* 3.6 2.1 + - - +
253M TYR* 3.7 36.3 - - + +
256M LEU* 5.5 0.2 - - + -
284M LEU* 3.6 4.9 - - - +
285M PHE* 2.9 55.5 + - + +
346M PHE* 5.0 1.1 - - + -
348M LEU* 3.8 28.9 - - + -
349M GLY 6.1 0.7 - - - +
350M LYS 4.3 10.3 - - - +
351M PHE* 3.8 17.3 - - + -
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Residues in contact with PRO 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150M THR* 4.1 22.7 - - - +
151M PHE* 4.4 6.7 - - + -
223M PHE* 3.8 40.3 - - + +
225M LEU* 3.2 36.0 - - + +
242M GLY 4.3 1.6 - - - +
243M ILE* 1.3 98.0 - - + +
245M VAL* 1.3 59.5 + - - +
246M ASN* 5.2 2.1 + - - -
253M TYR* 5.3 0.9 + - - -
283M GLY 3.5 8.3 - - - +
284M LEU* 3.9 3.1 - - + -
352M ASN* 4.3 1.6 - - - +
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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