Contacts of the strand formed by residues 267 - 271 (chain B) in PDB entry 4UTX
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 VAL 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B LEU* 5.6 0.2 - - - -
241B CYS* 3.2 23.3 - - + +
243B VAL* 4.4 10.8 - - + -
248B SER* 3.6 24.5 - - - +
257B ALA* 4.2 11.0 - - + +
260B VAL* 4.5 1.8 - - + -
261B ALA* 4.0 17.9 - - + -
265B VAL 3.9 8.5 - - - +
266B PRO* 1.3 81.3 - - - +
268B ALA* 1.3 64.9 + - - +
269B GLU* 4.6 1.8 - - + -
281B PHE* 4.1 15.3 - - + -
282B LYS* 3.5 18.8 + - + +
283B TYR* 3.3 26.1 + - - +
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 3.9 27.1 - - + -
240B LEU* 5.4 1.6 - - + -
241B CYS 3.1 5.7 + - - -
242B LEU* 3.5 10.1 - - + -
243B VAL 3.0 22.6 + - - +
267B VAL* 1.3 75.4 - - - +
269B GLU* 1.3 64.6 + - - +
270B PHE* 3.6 20.7 - - + -
283B TYR* 3.6 15.3 - - + -
285B PHE* 4.7 1.6 - - + -
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Residues in contact with GLU 269 (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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243B VAL* 3.3 12.1 - - + +
247B SER* 3.7 11.1 + - - -
248B SER* 3.0 46.8 + - - +
249B ILE* 5.5 0.9 - - - +
267B VAL* 4.6 4.0 - - + -
268B ALA* 1.3 72.4 - - - +
270B PHE* 1.3 68.7 + - - +
271B ASN* 3.4 20.7 + - - +
281B PHE* 3.8 22.4 + - - +
283B TYR 3.1 14.1 + - - +
284B HIS* 3.6 21.7 + - - +
285B PHE* 2.9 26.7 + - - +
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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
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39B PHE* 4.4 9.0 - + - -
242B LEU* 4.0 12.3 - - + -
243B VAL 2.8 12.8 + - - +
244B VAL* 3.4 16.1 - - + -
245B GLY 2.8 26.3 + - - -
268B ALA* 3.6 28.7 - - + -
269B GLU* 1.3 76.9 - - - +
271B ASN* 1.3 60.3 + - - +
285B PHE* 3.6 39.5 - + + -
287B GLY 4.7 0.9 - - - -
289B CYS* 3.5 8.3 - - - -
292B THR* 3.3 28.0 - - - +
293B LEU* 3.7 27.8 - - + -
296B ALA* 3.8 23.6 - - + -
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Residues in contact with ASN 271 (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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245B GLY* 4.2 4.5 - - - +
246B THR 2.8 38.5 + - - +
247B SER* 3.9 6.1 - - - +
269B GLU* 3.4 25.7 + - - +
270B PHE* 1.3 75.0 - - - +
272B MET* 1.3 63.2 + - - +
273B GLU* 3.5 26.0 + - - +
284B HIS* 3.1 22.9 - - - -
285B PHE 3.6 2.4 + - - -
286B GLU* 3.3 7.8 - - - -
287B GLY 2.9 26.4 + - - +
289B CYS* 4.7 3.1 - - - -
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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