Contacts of the strand formed by residues 263 - 269 (chain D) in PDB entry 4G5S
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 SER 263 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D THR 3.3 5.9 + - - -
220D ALA* 3.2 17.3 - - - +
221D ILE 2.9 27.7 + - - +
261D GLU 4.1 2.6 + - - -
262D THR* 1.3 72.5 - - - +
264D ILE* 1.3 60.9 + - - +
265D ILE* 3.9 4.4 + - - -
313D ARG* 5.6 0.4 - - - +
318D GLU 5.8 0.2 - - - -
320D TYR* 4.4 13.0 - - - -
342D VAL* 5.4 3.1 - - - -
343D ILE* 5.5 4.7 - - - -
346D ASN* 2.4 36.9 + - - +
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Residues in contact with ILE 264 (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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221D ILE* 3.8 39.0 - - + +
223D PHE* 5.6 0.4 - - + -
250D PHE* 3.8 33.9 - - + -
253D ILE* 4.9 9.2 - - + -
254D CYS* 4.2 15.7 - - - -
259D PHE* 4.9 5.8 - - + -
262D THR* 3.4 13.9 + - + +
263D SER* 1.3 74.7 - - - +
265D ILE* 1.3 65.8 + - - +
313D ARG* 3.8 25.5 - - - +
318D GLU 4.7 1.4 + - - +
319D ILE* 3.6 11.1 - - + +
320D TYR* 2.9 32.1 + - - -
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Residues in contact with ILE 265 (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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36D LEU* 5.2 0.7 - - + -
220D ALA* 4.3 19.7 - - + -
221D ILE 2.8 15.0 + - - +
222D ILE* 3.4 16.7 - - + -
223D PHE* 2.8 29.3 + - - +
263D SER* 4.5 5.6 - - - +
264D ILE* 1.3 80.9 - - - +
266D LEU* 1.3 62.2 + - - +
267D PHE* 3.4 30.5 + - + -
320D TYR* 3.4 25.1 - - + +
322D HIS* 4.3 1.6 - - + -
339D VAL* 3.4 39.7 - - + +
342D VAL* 5.9 2.9 - - + -
343D ILE* 4.9 5.4 - - + -
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Residues in contact with LEU 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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223D PHE* 3.7 19.3 - - + +
225D VAL* 3.9 15.5 - - + -
250D PHE* 4.1 14.8 - - + -
264D ILE 4.2 0.4 + - - -
265D ILE* 1.3 71.6 - - - +
267D PHE* 1.3 67.5 + - - +
268D LEU* 3.6 28.5 - - + -
304D GLN 4.9 3.1 - - - +
307D PHE* 3.7 29.4 - - + -
308D GLU* 5.0 2.0 - - + -
319D ILE* 4.1 14.1 - - + -
320D TYR 2.9 10.0 + - - +
321D THR* 3.8 26.2 - - + +
322D HIS 2.9 28.9 + - - +
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Residues in contact with PHE 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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49D ILE* 4.2 29.2 - - + -
222D ILE* 3.7 31.6 - - + -
223D PHE 2.8 15.1 + - - +
224D CYS* 3.6 11.1 - - + -
225D VAL* 2.9 26.9 + - - +
265D ILE* 3.4 24.5 - - + -
266D LEU* 1.3 77.7 - - - +
268D LEU* 1.3 63.2 + - - +
269D ASN* 3.0 5.0 + - + +
322D HIS* 3.7 5.4 - - + -
324D THR* 3.5 29.8 - - + +
332D VAL* 5.6 5.4 - - + -
335D VAL* 3.6 27.8 - - + -
336D PHE* 5.3 8.1 - + + -
339D VAL* 4.1 8.7 - - + -
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Residues in contact with LEU 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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225D VAL* 3.7 18.4 - - + -
227D LEU* 3.3 33.2 - - + +
266D LEU* 3.6 29.4 - - + -
267D PHE* 1.3 70.0 - - - +
269D ASN* 1.3 62.5 + - - +
271D LYS* 4.3 0.9 - - - +
300D ALA 4.5 0.2 - - - +
303D ILE* 4.7 0.7 - - + -
304D GLN* 4.0 24.9 - - + +
307D PHE* 4.8 8.3 - - + -
321D THR* 4.0 11.2 - - + -
322D HIS 2.9 14.8 + - - +
323D PHE* 3.7 36.6 - - + -
324D THR* 3.2 18.9 + - - +
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Residues in contact with ASN 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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44D SER 3.2 31.0 + - - +
45D GLY* 3.8 9.5 - - - -
49D ILE* 5.9 1.8 - - - -
224D CYS* 5.3 0.7 - - + -
225D VAL 2.7 14.2 + - - +
227D LEU* 3.2 19.8 + - - +
267D PHE* 3.0 9.4 + - + +
268D LEU* 1.3 72.1 - - - +
270D LYS* 1.3 96.3 + - + +
271D LYS 3.2 3.3 + - - -
324D THR* 3.2 19.8 + - - +
326D ALA* 2.9 38.2 + - - +
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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