Contacts of the strand formed by residues 254 - 257 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C MET* 4.8 2.9 - - + -
149C LEU* 3.5 30.3 - - + -
203C LEU* 4.9 2.0 - - + -
232C LEU* 4.8 4.0 - - + -
233C VAL 3.2 4.1 + - - +
234C CYS* 3.4 26.9 - - + -
235C ILE 3.0 23.0 + - - -
248C LEU* 4.3 2.7 - - - -
252C ALA* 3.9 6.0 - - - +
253C ASP* 1.3 86.5 - - + +
255C VAL* 1.3 61.9 + - - +
256C LEU 4.3 0.2 - - - -
274C ILE* 4.3 19.1 - - + -
275C SER 3.5 12.8 - - - +
276C GLY* 4.3 6.5 - - - -
280C LEU* 3.8 34.3 - - + -
281C VAL* 4.4 3.8 - - - +
284C ILE* 4.4 8.1 - - + -
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C GLU* 3.6 16.8 - - - +
235C ILE 3.2 11.4 - - - +
237C GLY* 4.4 6.1 - - - +
247C ALA* 4.2 23.8 - - + -
248C LEU* 3.7 22.2 - - + -
254C LEU* 1.3 76.0 - - - +
256C LEU* 1.3 62.9 + - - +
257C HIS* 3.5 26.3 - - + +
274C ILE* 3.6 0.8 - - - -
275C SER* 2.9 44.9 + - - +
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C GLY* 4.6 2.7 - - - +
141C ALA* 4.3 7.9 - - + -
142C SER* 4.2 30.5 - - - +
145C MET* 4.3 4.7 - - - -
205C PHE* 3.5 31.6 - - + -
234C CYS* 3.8 16.5 - - - -
235C ILE 3.0 6.9 + - - -
236C ASP* 3.0 36.5 - - - +
237C GLY 3.1 14.7 + - - -
254C LEU 4.3 0.2 - - - -
255C VAL* 1.3 73.5 - - - +
257C HIS* 1.3 77.2 + - - +
258C SER* 6.2 0.2 - - - -
273C CYS 2.9 14.8 - - - +
274C ILE* 4.0 11.4 - - + -
500C PLP 6.0 2.7 - - + -
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Residues in contact with HIS 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ILE* 6.0 1.1 - - + -
127C GLU* 2.6 28.6 + - + -
138C GLY* 4.1 4.9 - - - -
237C GLY* 2.8 35.0 + - - -
238C THR* 3.8 12.3 + - - -
241C THR* 3.8 2.9 - - - -
242C PRO* 3.5 30.7 - - + +
255C VAL* 3.5 15.2 - - + +
256C LEU* 1.3 91.1 - - - +
258C SER* 1.3 63.3 + - - +
259C ALA 3.8 1.1 - - - -
263C LEU* 4.0 17.8 - - + +
273C CYS* 2.9 42.5 + - + +
275C SER* 5.4 1.1 - - - -
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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