Contacts of the strand formed by residues 254 - 257 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145L MET* 4.5 9.6 - - + -
149L LEU* 3.4 33.7 - - + -
203L LEU* 4.9 1.8 - - + -
232L LEU* 4.8 4.3 - - + -
233L VAL 3.1 6.6 + - - +
234L CYS* 3.2 21.4 - - + -
235L ILE 2.9 24.1 + - - -
248L LEU* 4.3 3.4 - - - -
252L ALA* 4.0 5.2 - - - +
253L ASP* 1.3 84.6 - - + +
255L VAL* 1.3 61.5 + - - +
256L LEU 4.3 0.2 - - - -
274L ILE* 4.5 17.5 - - + -
275L SER 3.5 11.2 - - - +
276L GLY* 4.2 8.1 - - - +
280L LEU* 3.9 32.1 - - + -
281L VAL* 4.5 7.2 - - - +
284L ILE* 4.6 2.9 - - + -
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Residues in contact with VAL 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127L GLU* 3.9 22.2 - - - +
235L ILE 3.2 11.4 - - - +
237L GLY* 4.4 7.6 - - - +
247L ALA* 4.0 26.0 - - + -
248L LEU* 3.8 20.4 - - + -
254L LEU* 1.3 76.0 - - - +
256L LEU* 1.3 62.8 + - - +
257L HIS* 3.7 23.2 - - + +
274L ILE* 3.7 0.4 - - - -
275L SER* 2.9 41.8 + - - +
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Residues in contact with LEU 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L GLY* 4.5 3.1 - - - +
141L ALA* 4.5 7.4 - - + -
142L SER* 4.1 33.0 - - - +
145L MET* 4.5 5.2 - - + -
205L PHE* 3.7 27.8 - - + -
234L CYS* 3.7 14.8 - - - -
235L ILE 3.0 7.4 + - - +
236L ASP* 2.9 39.3 - - + +
237L GLY 3.2 13.5 + - - -
254L LEU 4.3 0.4 - - - -
255L VAL* 1.3 74.8 - - - +
257L HIS* 1.3 77.7 + - - +
273L CYS 2.9 17.3 - - - +
274L ILE* 4.0 10.8 - - + -
500L PLP 6.1 2.5 - - + -
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Residues in contact with HIS 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L ILE* 6.0 1.3 - - + -
127L GLU* 2.5 27.3 + - + -
138L GLY* 4.2 2.8 - - - -
237L GLY* 3.1 32.6 + - - -
238L THR* 3.8 13.4 + - - +
241L THR* 3.7 3.6 - - - -
242L PRO* 3.4 31.7 - - + +
255L VAL* 3.7 15.0 - - + +
256L LEU* 1.3 90.2 - - - +
258L SER* 1.3 62.7 + - - +
259L ALA 3.9 1.1 - - - -
263L LEU* 4.1 17.4 - - + +
272L GLY* 4.1 1.9 - - - -
273L CYS* 3.0 40.8 + - + +
275L SER* 5.3 2.2 - - - -
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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