Contacts of the strand formed by residues 254 - 257 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H MET* 4.7 1.6 - - + -
149H LEU* 3.3 34.3 - - + -
203H LEU* 5.0 2.2 - - + -
232H LEU* 5.0 2.7 - - + -
233H VAL 3.1 3.1 + - - +
234H CYS* 3.2 28.2 - - + -
235H ILE 2.9 24.8 + - - -
248H LEU* 4.3 2.5 - - - -
252H ALA* 4.1 4.5 - - - +
253H ASP* 1.3 88.5 - - + +
255H VAL* 1.3 61.1 + - - +
274H ILE* 4.5 9.9 - - + -
275H SER 3.5 10.8 - - - +
276H GLY* 4.1 8.1 - - - -
280H LEU* 3.8 33.4 - - + -
281H VAL* 4.4 7.2 - - - +
284H ILE* 4.5 12.3 - - + -
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Residues in contact with VAL 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H GLU* 3.7 18.2 - - - +
235H ILE 3.3 9.2 - - - +
237H GLY* 4.4 6.7 - - - +
247H ALA* 4.2 20.6 - - + -
248H LEU* 3.6 23.8 - - + -
254H LEU* 1.3 74.7 - - - +
256H LEU* 1.3 63.7 + - - +
257H HIS* 3.6 24.4 - - + +
274H ILE* 4.6 0.7 - - - -
275H SER* 2.9 48.1 + - - +
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Residues in contact with LEU 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H GLY* 4.5 2.9 - - - +
141H ALA* 4.4 8.5 - - + -
142H SER* 4.1 29.6 - - - +
145H MET* 4.3 4.0 - - - -
205H PHE* 3.6 31.2 - - + -
234H CYS* 4.0 15.0 - - - -
235H ILE 3.0 7.9 + - - +
236H ASP* 3.0 33.5 - - - +
237H GLY 3.2 15.1 + - - -
254H LEU 4.2 0.4 - - - -
255H VAL* 1.3 75.6 - - - +
257H HIS* 1.3 76.4 + - - +
258H SER* 6.0 0.4 - - - -
273H CYS 2.8 16.2 - - - +
274H ILE* 4.0 13.2 - - + -
500H PLP 6.1 2.5 - - + -
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Residues in contact with HIS 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H ILE* 5.9 1.6 - - + -
127H GLU* 2.5 28.2 + - + -
138H GLY* 4.2 4.0 - - - -
237H GLY* 2.9 34.7 + - - -
238H THR* 3.7 13.4 + - - +
240H ALA* 5.6 0.2 - - + -
241H THR* 3.8 2.9 - - - -
242H PRO* 3.4 31.7 - - + +
255H VAL* 3.6 14.5 - - + +
256H LEU* 1.3 91.9 - - - +
258H SER* 1.3 64.3 + - - +
259H ALA 3.8 1.1 - - - -
263H LEU* 4.1 18.3 - - + +
272H GLY 4.1 0.3 - - - -
273H CYS* 2.9 39.4 + - + -
275H SER* 5.3 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
------------------------------------------------------------
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