Contacts of the strand formed by residues 265 - 270 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D ASP 3.2 8.7 + - - +
238D MET* 3.3 9.3 - - + +
239D VAL* 2.8 28.4 + - - +
263D ASN 4.5 4.7 - - - +
264D ILE* 1.3 73.6 - - - +
266D ILE* 1.3 61.3 + - - +
267D ILE* 4.7 1.8 - - + -
287D ASP* 3.6 32.8 + - + +
438D HIS* 4.6 18.8 + - - -
461D GLN* 3.4 42.6 - - + +
464D LEU* 4.5 15.0 - - + -
465D TYR* 5.0 10.0 + - - +
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Residues in contact with ILE 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D VAL* 3.9 5.8 - - + +
241D ALA* 4.7 9.0 - - + -
244D ILE* 6.4 0.2 - - + -
250D VAL* 3.8 26.7 - - + +
253D VAL* 3.8 20.2 - - + -
254D ARG* 3.5 66.6 - - + +
257D LEU* 4.0 15.7 - - + -
265D LYS* 1.3 73.6 - - - +
267D ILE* 1.3 70.8 + - - +
268D SER* 3.9 4.4 + - - +
286D SER* 4.0 0.7 - - - -
287D ASP* 3.1 32.4 + - - +
288D GLY 3.3 5.4 + - - +
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Residues in contact with ILE 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D MET* 4.6 6.3 - - + -
239D VAL 2.7 15.1 + - - +
240D PHE* 3.4 26.4 - - + -
241D ALA 3.0 25.3 + - - -
265D LYS* 4.7 2.0 - - + -
266D ILE* 1.3 76.1 - - - +
268D SER* 1.3 62.1 + - - +
269D LYS 3.6 0.3 + - - -
287D ASP* 4.4 5.4 - - + -
288D GLY* 3.5 24.9 - - - +
289D ILE 3.7 26.5 - - - +
290D MET* 3.7 14.8 - - + +
322D PRO* 4.9 4.3 - - + -
324D ILE* 3.9 11.4 - - + -
464D LEU* 3.8 33.0 - - + -
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Residues in contact with SER 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ALA* 4.1 4.4 - - - +
244D ILE* 3.7 14.3 - - - +
250D VAL* 3.6 19.2 - - - +
266D ILE* 3.9 4.1 + - - +
267D ILE* 1.3 70.5 - - - +
269D LYS* 1.3 63.2 + - - +
270D ILE* 3.5 2.7 + - - +
282D ILE* 3.7 16.8 - - - -
286D SER* 2.9 26.1 + - - -
288D GLY 3.1 8.3 + - - -
289D ILE* 3.5 11.1 - - - +
290D MET 2.8 24.5 + - - +
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Residues in contact with LYS 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ASP* 2.7 39.8 + - - +
240D PHE* 3.8 14.1 - - + -
241D ALA 2.9 21.0 + - - +
242D SER* 2.7 24.4 + - - +
243D PHE 3.7 2.3 + - - -
244D ILE* 3.5 24.4 + - - +
268D SER* 1.3 70.5 - - - +
270D ILE* 1.3 63.9 + - - +
271D GLU* 3.4 17.6 + - + +
290D MET* 3.5 39.9 - - + -
292D ALA* 4.4 0.2 - - + -
532D K 3.6 4.2 - - - -
533D MG 4.0 0.6 - - - -
534D PYR 2.8 30.8 + - - +
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Residues in contact with ILE 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D ILE 4.4 5.2 - - - +
268D SER* 4.1 3.1 - - - +
269D LYS* 1.3 72.2 - - - +
271D GLU* 1.3 61.7 + - - +
272D ASN 4.3 1.3 - - - +
275D GLY* 3.4 39.3 - - - +
276D VAL* 3.6 20.4 - - + +
279D PHE* 4.2 8.3 - - + -
282D ILE* 3.9 31.9 - - + -
289D ILE* 3.9 19.1 - - + -
290D MET 3.1 6.2 + - - +
291D VAL* 4.7 0.2 - - - -
292D ALA* 3.5 19.2 + - - +
296D LEU* 3.8 11.0 - - - +
312D MET* 3.7 28.0 - - + -
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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