Contacts of the strand formed by residues 254 - 257 (chain K) in PDB entry 1I43
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 LEU 254 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K MET* 4.7 7.4 - - + -
149K LEU* 3.4 32.5 - - + -
203K LEU* 4.9 3.4 - - + -
232K LEU* 5.1 1.6 - - + -
233K VAL 3.0 6.3 + - - +
234K CYS* 3.2 24.2 - - + -
235K ILE* 2.9 24.6 + - - -
248K LEU* 4.2 2.9 - - - -
252K ALA* 4.0 4.7 - - - +
253K ASP* 1.3 87.0 - - + +
255K VAL* 1.3 60.8 + - - +
256K LEU 4.2 0.4 - - - -
274K ILE* 4.5 18.4 - - + -
275K SER 3.5 11.4 - - - +
276K GLY* 4.2 7.4 - - - -
280K LEU* 4.0 32.1 - - + -
281K VAL* 4.5 7.9 - - - +
284K ILE* 4.5 3.4 - - + -
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Residues in contact with VAL 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K GLU* 3.7 23.1 - - - +
235K ILE 3.2 10.5 - - - +
237K GLY* 4.4 7.9 - - - +
247K ALA* 4.2 22.9 - - + -
248K LEU* 3.6 22.4 - - + -
254K LEU* 1.3 75.4 - - - +
256K LEU* 1.3 62.5 + - - +
257K HIS* 3.5 25.0 - - + +
274K ILE* 4.6 0.2 - - - -
275K SER* 2.9 45.5 + - - +
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Residues in contact with LEU 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K GLY* 4.5 2.7 - - - +
141K ALA* 4.3 8.1 - - + -
142K SER* 4.1 33.7 - - - +
145K MET* 4.5 4.7 - - + -
205K PHE* 3.7 27.1 - - + -
234K CYS* 3.8 13.7 - - - -
235K ILE 3.0 7.2 + - - +
236K ASP* 3.0 37.7 - - - +
237K GLY 3.2 14.2 + - - -
254K LEU 4.2 0.6 - - - -
255K VAL* 1.3 74.9 - - - +
257K HIS* 1.3 77.2 + - - +
258K SER* 6.0 0.2 - - - -
273K CYS 2.9 16.2 - - - +
274K ILE* 3.9 12.3 - - + -
500K PLP 6.0 2.2 - - + -
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Residues in contact with HIS 257 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K ILE* 5.8 0.9 - - + -
127K GLU* 2.4 29.0 + - + -
138K GLY* 4.1 5.0 - - - -
237K GLY* 3.0 34.6 + - - -
238K THR* 3.7 12.1 + - - -
241K THR* 3.9 2.7 - - - -
242K PRO* 3.3 31.6 - - + +
255K VAL* 3.5 15.3 - - + +
256K LEU* 1.3 93.4 - - - +
258K SER* 1.3 63.5 + - - +
259K ALA 3.9 1.1 - - - -
263K LEU* 4.0 18.5 - - + +
273K CYS* 3.0 39.7 + - + +
275K SER* 5.1 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