Contacts of the strand formed by residues 265 - 270 (chain B) in PDB entry 3SRF
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 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237B ASP 3.6 3.8 + - - -
238B MET* 3.3 12.7 - - + +
239B VAL* 2.8 32.2 + - - +
262B LYS 5.9 0.2 + - - -
263B ASN* 4.0 9.5 + - - +
264B ILE* 1.3 77.5 - - - +
266B ILE* 1.3 56.1 + - - +
267B ILE* 3.9 2.7 - - + -
287B ASP* 3.5 31.6 + - + +
438B HIS* 5.6 9.8 - - - -
461B GLN* 3.4 38.6 - - + +
464B LEU* 4.4 18.4 - - + -
465B TYR* 5.4 11.5 + - + +
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Residues in contact with ILE 266 (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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239B VAL* 3.6 7.0 - - + +
241B ALA* 4.4 13.9 - - + -
250B VAL* 4.1 22.4 - - + +
253B VAL* 4.1 11.9 - - + -
254B ARG* 3.5 65.7 - - + +
257B LEU* 3.8 22.4 - - + -
265B LYS* 1.3 74.7 - - - +
267B ILE* 1.3 71.2 + - - +
268B SER* 4.3 3.8 - - - +
286B SER* 3.7 1.9 - - - -
287B ASP* 3.1 30.7 + - - +
288B GLY 3.4 4.5 + - - +
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B MET* 4.6 8.1 - - + -
239B VAL 2.6 13.7 + - - +
240B PHE* 3.3 29.4 - - + -
241B ALA* 2.7 34.3 + - - +
265B LYS* 4.7 5.2 - - + -
266B ILE* 1.3 75.2 - - - +
268B SER* 1.3 58.0 + - - +
287B ASP 4.6 3.6 - - - +
288B GLY* 3.3 20.2 - - - +
289B ILE 3.6 27.1 - - - +
290B MET* 3.7 10.1 - - + +
322B PRO* 5.3 2.9 - - + +
324B ILE* 3.9 16.8 - - + -
464B LEU* 3.9 30.5 - - + -
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Residues in contact with SER 268 (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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241B ALA* 4.1 3.1 - - - -
244B ILE* 4.2 13.9 - - - +
250B VAL* 3.5 16.1 - - - +
266B ILE* 3.8 3.5 + - - +
267B ILE* 1.3 73.5 - - - +
269B LYS* 1.3 62.5 + - - +
270B ILE* 3.7 0.8 + - - -
282B ILE* 3.8 10.5 - - - -
286B SER* 2.6 29.0 + - - -
288B GLY 2.8 9.5 + - - -
289B ILE* 3.3 22.2 - - - +
290B MET 2.8 22.8 + - - +
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Residues in contact with LYS 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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112B ASP* 2.7 38.4 + - - +
240B PHE* 3.7 13.2 - - + -
241B ALA 2.9 29.8 + - - +
242B SER* 2.7 17.9 + - - +
244B ILE* 3.5 26.2 + - - +
267B ILE 4.7 0.2 - - - +
268B SER* 1.3 72.5 - - - +
270B ILE* 1.3 62.5 + - - +
271B GLU* 3.7 22.6 + - + +
290B MET* 3.4 32.3 - - + +
292B ALA* 4.3 2.5 - - + -
532B K 3.4 6.7 - - - -
533B MG 4.2 1.2 - - - -
534B PYR 3.3 26.1 + - - -
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Residues in contact with ILE 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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244B ILE 4.4 3.6 - - - +
268B SER* 4.2 1.3 - - - +
269B LYS* 1.3 76.8 - - - +
271B GLU* 1.3 60.5 + - - +
272B ASN 4.4 1.3 - - - +
275B GLY* 3.7 38.1 - - - +
276B VAL* 3.8 14.8 - - + -
279B PHE* 3.9 9.6 - - + -
282B ILE* 4.0 31.6 - - + -
289B ILE* 4.1 15.7 - - + -
290B MET 2.9 10.5 + - - +
291B VAL* 4.4 0.3 - - - -
292B ALA 3.5 17.8 + - - -
296B LEU* 3.7 12.3 - - + +
312B MET* 3.7 35.2 - - + -
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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