Contacts of the strand formed by residues 273 - 279 (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 273 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139M VAL* 6.3 1.6 - - - -
261M THR* 6.2 1.8 - - - -
271M ILE* 3.7 4.8 - - - +
272M SER* 1.3 84.8 - - - +
274M ALA* 1.3 66.7 + - - +
275M LYS* 4.8 8.0 - - - +
287M LEU* 3.4 2.3 - - - +
288M PHE* 2.9 51.4 + - - +
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Residues in contact with ALA 274 (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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257M ALA* 3.8 18.6 - - - +
260M LEU* 4.4 6.1 - - + -
261M THR* 3.4 31.1 + - - +
271M ILE* 3.9 20.6 - - + -
273M SER* 1.3 78.6 + - - +
275M LYS* 1.3 63.1 + - - +
285M PHE* 4.8 1.1 - - + -
286M THR 3.4 8.7 - - - +
287M LEU* 4.6 8.3 - - + -
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Residues in contact with LYS 275 (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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143M GLU* 3.2 29.3 + - - -
257M ALA* 3.9 7.7 - - - +
273M SER* 4.8 9.2 - - - +
274M ALA* 1.3 75.3 - - - +
276M LEU* 1.3 61.8 + - - +
277M ASP* 3.3 29.0 + - - +
285M PHE* 3.4 9.1 - - - -
286M THR* 2.8 55.7 + - - +
288M PHE* 4.4 9.3 - - + -
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Residues in contact with LEU 276 (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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245M VAL* 3.8 30.1 - - + -
250M LEU* 3.5 34.1 - - + +
253M TYR* 4.1 8.3 - - + +
254M GLU* 3.9 30.6 + - + +
257M ALA* 4.4 2.2 - - + +
275M LYS* 1.3 78.5 - - - +
277M ASP* 1.3 65.5 + - - +
278M LYS* 3.0 35.3 + - + -
284M LEU 3.4 23.1 - - - +
285M PHE* 3.8 15.3 - - + -
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Residues in contact with ASP 277 (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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143M GLU* 5.3 1.7 - - - +
147M TYR* 2.8 35.8 + - - +
275M LYS* 3.3 35.2 + - - +
276M LEU* 1.3 73.7 - - - +
278M LYS* 1.3 60.6 + - - +
279M PHE* 4.0 11.9 - - + -
283M GLY* 3.1 8.1 - - - -
284M LEU* 2.7 42.3 + - - +
286M THR* 4.0 4.0 + - - -
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Residues in contact with LYS 278 (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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250M LEU* 4.8 12.6 - - + -
254M GLU* 2.9 47.1 + - - +
276M LEU* 3.0 34.2 + - + +
277M ASP* 1.3 75.2 - - - +
279M PHE* 1.3 74.1 + - - +
282M GLY 4.6 3.1 - - - -
325M ASN* 4.2 5.6 - - - +
328M GLN* 4.5 11.5 + - - +
329M ASN* 6.1 0.2 - - - -
335M PRO* 6.1 1.3 - - + -
336M ILE* 3.7 25.1 - - + -
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Residues in contact with PHE 279 (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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40M ARG* 4.2 7.4 - - + +
83M ASP* 6.1 0.7 - - - -
84M ARG* 4.2 20.6 - - + -
85M GLU* 4.1 25.1 - - + +
86M TYR* 6.2 0.4 - + - -
147M TYR* 3.8 28.9 - + - -
151M PHE* 4.9 0.2 - + - -
155M LEU* 3.3 32.3 - - + -
250M LEU* 4.9 5.2 - - - +
277M ASP* 4.0 17.3 - - + -
278M LYS* 1.3 81.3 - - - +
280M THR* 1.3 63.7 + - - +
281M ASP* 3.1 18.8 + - - +
282M GLY 3.5 18.3 + - - +
283M GLY* 3.8 18.4 - - - -
284M LEU 4.6 2.0 - - - -
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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