Contacts of the strand formed by residues 267 - 270 (chain E) in PDB entry 1XFB
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 GLY 267 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E VAL* 4.2 4.0 - - - -
228E LEU* 3.2 25.1 - - - +
229E LEU 3.2 13.7 + - - -
265E VAL* 3.4 6.9 - - - +
266E PRO* 1.3 86.2 - - - +
268E VAL* 1.3 64.8 + - - -
296E TRP* 4.1 2.0 - - - -
297E ALA* 3.5 18.6 - - - -
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Residues in contact with VAL 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 5.5 0.4 - - - +
229E LEU* 3.2 13.7 - - + +
231E PRO* 3.3 37.7 - - + -
257E LEU* 3.8 26.0 - - + -
261E VAL* 4.9 5.6 - - + -
265E VAL* 5.2 0.4 - - + -
267E GLY* 1.3 75.2 - - - +
269E THR* 1.3 60.7 + - - +
270E PHE* 3.6 9.6 + - + -
296E TRP* 4.1 17.9 - - + -
297E ALA 2.8 12.5 + - - +
298E LEU* 3.6 19.6 - - + -
299E THR 3.2 25.3 + - - +
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Residues in contact with THR 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 3.8 26.9 - - + -
30E ILE* 3.9 19.4 - - + +
186E ILE* 4.5 3.5 - - - +
228E LEU* 4.2 12.6 - - + -
229E LEU 2.7 12.7 + - - +
230E LYS* 3.2 28.8 - - - +
231E PRO* 4.5 0.2 - - - -
268E VAL* 1.3 75.6 - - - +
270E PHE* 1.3 65.4 - - - +
299E THR* 3.8 11.4 - - - +
300E PHE 3.9 5.8 - - - -
301E SER* 3.2 23.8 + - - -
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Residues in contact with PHE 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E PRO* 3.6 21.1 - - + -
232E ASN 4.5 0.7 - - - -
233E MET* 3.6 38.4 - - + -
253E THR* 3.3 29.8 - - + -
257E LEU* 3.5 29.2 - - + -
268E VAL* 3.7 8.0 - - + +
269E THR* 1.3 72.7 - - - +
271E LEU* 1.3 59.2 + - - +
284E LEU* 4.2 6.7 - - + -
287E ILE* 3.8 23.3 - - + -
298E LEU* 4.0 24.0 - - + -
299E THR 3.1 26.4 + - - +
301E SER 2.7 31.2 + - - +
302E TYR* 3.5 6.8 - - + +
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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