Contacts of the strand formed by residues 268 - 272 (chain B) in PDB entry 5T4S
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 ILE 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B VAL* 4.1 14.8 - - + -
209B SER 3.2 9.4 - - - +
210B VAL* 4.6 1.6 - - + -
242B LEU* 4.1 13.9 - - + -
246B LEU* 3.8 24.5 - - + -
266B PRO 3.6 1.3 + - - +
267B ASP* 1.3 75.3 - - - +
269B SER* 1.3 61.3 + - - +
270B PHE* 3.8 27.6 - - + -
277B TYR 3.7 1.9 - - - +
278B THR* 3.5 0.6 - - - -
279B LEU* 2.8 44.1 + - + +
284B TYR* 3.6 34.5 - - + +
300B ILE* 3.7 25.8 - - + -
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Residues in contact with SER 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLY 3.7 0.9 - - - +
208B VAL* 3.3 8.0 - - - +
209B SER* 2.7 51.1 + - - -
211B GLY 4.9 4.7 + - - -
267B ASP* 4.1 2.3 - - - +
268B ILE* 1.3 73.2 - - - +
270B PHE* 1.3 62.3 + - - +
271B HIS 4.0 0.4 - - - -
276B GLU* 3.3 21.5 - - - +
277B TYR 3.3 3.8 - - - -
278B THR* 2.7 30.1 + - - +
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Residues in contact with PHE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B MET* 3.7 26.7 - - + -
207B GLY 3.6 3.1 - - - -
208B VAL* 3.8 14.6 - - + -
232B ILE* 3.7 47.6 - - + -
268B ILE* 3.8 29.8 - - + -
269B SER* 1.3 73.4 - - - +
271B HIS* 1.3 60.3 + - - +
272B LEU* 3.3 11.5 + - + -
276B GLU* 3.8 1.1 - - - -
277B TYR* 2.7 50.2 + - - +
279B LEU* 4.3 8.3 - - + -
300B ILE* 5.7 3.1 - - + -
313B TRP* 4.1 19.1 - + - -
315B LEU* 4.2 7.0 - - + -
319B PHE* 3.8 21.1 - + + -
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Residues in contact with HIS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B MET* 3.6 7.2 - - - +
206B LYS* 2.8 60.5 + - + +
207B GLY* 2.9 27.1 + - - +
270B PHE* 1.3 68.0 - - - +
272B LEU* 1.3 58.3 + - - +
274B GLY* 2.9 32.4 + - - -
275B LYS 3.1 21.5 - - - -
276B GLU* 3.5 28.6 + - - +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B HIS* 4.4 0.5 + - - -
193B ILE* 3.8 12.9 - - + +
203B ILE* 3.7 18.8 - - + -
204B GLN 3.9 10.1 - - - +
205B MET* 3.7 26.2 - - + -
223B ALA* 4.5 4.3 - - + -
270B PHE* 3.3 10.7 + - + +
271B HIS* 1.3 80.8 - - - +
273B GLY* 1.3 66.5 + - - +
274B GLY 3.3 1.1 - - - -
275B LYS* 2.9 20.6 + - - +
277B TYR* 3.5 26.0 - - + -
315B LEU* 3.9 12.1 - - + -
319B PHE* 3.8 30.1 - - + -
336B PHE* 4.0 13.7 - - + -
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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