Contacts of the strand formed by residues 274 - 280 (chain B) in PDB entry 1XR2
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 LYS 274 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B LYS 2.8 11.2 + - - +
249B ARG* 3.5 17.2 - - + +
250B LEU 3.2 23.2 + - - -
269B PHE* 3.9 3.8 - - - -
273B LYS* 1.3 73.8 - - - +
275B LEU* 1.3 61.7 + - - +
276B VAL 4.0 0.3 + - - -
303B SER* 4.6 17.3 - - - -
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Residues in contact with LEU 275 (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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250B LEU 3.6 4.9 - - - +
252B PHE* 3.5 32.1 - - + -
254B PHE* 4.5 8.1 - - + -
264B LEU* 3.9 21.5 - - + -
269B PHE* 3.4 31.3 - - + -
274B LYS* 1.3 75.3 - - - +
276B VAL* 1.3 72.9 + - - +
277B ALA* 4.5 0.7 - - + +
300B LEU* 4.2 23.3 - - + +
302B ALA* 4.0 23.3 - - + +
303B SER* 3.3 11.4 + - - +
304B ALA* 3.3 21.0 + - - +
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Residues in contact with VAL 276 (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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4B TYR* 3.9 26.7 - - + -
228B THR* 4.4 16.2 - - + -
230B PHE* 5.0 1.8 - - + -
249B ARG* 5.0 3.4 - - + -
250B LEU 3.1 24.5 + - - +
251B HIS* 3.3 32.4 - - + +
252B PHE 3.4 5.5 + - - -
274B LYS 4.9 1.1 - - - +
275B LEU* 1.3 76.8 - - - +
277B ALA* 1.3 61.4 + - - +
278B GLY 3.5 0.3 + - - -
304B ALA* 3.4 14.8 - - + -
305B ILE 4.1 6.5 - - - +
306B SER* 3.7 22.0 - - - +
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Residues in contact with ALA 277 (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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254B PHE* 4.1 20.0 - - + -
275B LEU* 4.0 2.1 - - + -
276B VAL* 1.3 69.7 - - - +
278B GLY* 1.3 61.0 + - - +
279B VAL* 3.0 29.3 + - + +
297B VAL* 5.0 3.1 - - + -
300B LEU* 4.5 6.3 - - + -
302B ALA* 4.2 15.5 - - + -
304B ALA 2.9 15.4 + - - +
305B ILE* 3.4 6.3 - - + -
306B SER* 3.0 21.6 + - - -
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B HIS* 3.7 7.1 + - - -
252B PHE 2.9 21.1 + - - -
254B PHE* 3.0 29.5 + - - +
255B VAL* 4.0 0.9 - - - +
276B VAL 3.5 3.0 + - - -
277B ALA* 1.3 69.4 - - - +
279B VAL* 1.3 59.2 + - - -
280B ILE 3.8 1.1 - - - -
306B SER* 3.4 9.4 - - - -
307B ASN 3.5 15.7 - - - -
308B SER* 3.8 11.7 - - - -
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B PHE* 4.6 3.1 - - + -
255B VAL* 3.6 16.0 - - - +
277B ALA* 3.6 28.7 - - + +
278B GLY* 1.3 79.1 - - - +
280B ILE* 1.3 69.1 + - + +
281B ASN 3.9 0.3 + - - -
288B VAL* 5.7 0.7 - - - +
293B VAL* 3.5 33.2 - - + +
296B LEU* 3.9 27.4 - - + -
297B VAL* 4.2 12.1 - - + -
305B ILE* 4.5 4.5 - - + -
306B SER 2.9 6.2 + - - +
342B LEU* 5.3 0.2 - - + -
345B LEU* 4.0 16.8 - - + -
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Residues in contact with ILE 280 (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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279B VAL* 1.3 87.1 - - + +
281B ASN* 1.3 63.5 + - - +
288B VAL* 4.1 18.6 - - + -
290B LEU* 4.1 13.2 - - + -
293B VAL* 4.5 7.6 - - + -
306B SER 3.4 1.8 + - - -
307B ASN* 3.1 17.0 - - + +
308B SER* 2.8 26.3 + - - -
338B LYS* 3.8 41.7 - - + +
341B GLU* 3.7 22.2 - - + +
342B LEU* 3.7 27.4 - - + +
345B LEU* 4.8 3.6 - - + -
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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
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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