Contacts of the strand formed by residues 325 - 334 (chain D) in PDB entry 3IFS
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 LEU 325 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301C PHE* 3.6 27.1 - - + -
266D LYS* 3.6 9.1 + - - +
268D ILE* 3.4 34.5 - - + +
270D MSE 4.3 16.6 - - - -
317D TYR* 4.1 14.6 - - + -
318D VAL* 4.1 21.5 - - + +
322D ARG 4.0 8.3 - - - +
323D ARG* 3.5 24.0 - - - +
324D ASP* 1.3 80.8 - - + +
326D PHE* 1.3 64.7 + - - +
327D GLU* 5.9 0.2 - - + -
378D GLY 4.5 1.2 - - - +
379D VAL* 3.9 14.5 - - + +
380D PRO* 3.4 19.1 - - - +
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Residues in contact with PHE 326 (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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258D ARG* 4.2 13.0 - - + -
261D LEU* 3.6 27.1 - - + -
266D LYS* 3.7 31.6 - - + -
268D ILE 3.0 12.5 + - - +
269D GLU* 3.4 52.5 - - + -
270D MSE 2.9 26.0 + - - +
300D ILE* 4.0 20.2 - - + -
325D LEU* 1.3 75.0 - - - +
327D GLU* 1.3 66.8 + - - +
328D THR* 3.8 5.8 - - - -
379D VAL* 4.0 2.2 - - - -
380D PRO* 3.5 22.2 - - + +
382D LEU* 3.9 18.4 - - + -
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Residues in contact with GLU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D MSE 3.3 18.1 - - + +
272D ILE* 3.7 19.4 - - + +
307D PHE* 3.6 22.1 - - - -
318D VAL* 3.7 12.9 - - + +
325D LEU* 5.9 0.2 - - + -
326D PHE* 1.3 77.4 - - - +
328D THR* 1.3 59.3 + - - +
329D VAL* 4.1 2.5 - - + -
374D HIS* 2.8 34.7 + - - -
379D VAL* 3.5 9.2 - - + +
380D PRO 2.9 10.4 + - - +
381D ASN* 3.3 29.4 + - - +
382D LEU* 2.8 32.4 + - - +
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Residues in contact with THR 328 (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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7D PHE* 5.2 0.2 - - + -
254D TYR* 3.7 19.0 - - + +
269D GLU* 2.5 28.5 + - - +
270D MSE 3.0 7.8 + - - -
271D LEU* 3.4 19.8 - - + +
272D ILE 2.8 24.7 + - - -
326D PHE* 3.8 0.9 + - - -
327D GLU* 1.3 73.3 + - - +
329D VAL* 1.3 61.8 + - - +
382D LEU* 3.4 26.0 - - + +
384D VAL* 3.8 27.4 - - + -
401D PHE* 5.2 0.4 - - + -
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Residues in contact with VAL 329 (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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272D ILE* 3.5 23.3 - - + +
274D TYR* 4.0 16.6 - - + -
327D GLU* 4.6 1.8 - - + -
328D THR* 1.3 75.4 - - - +
330D LEU* 1.3 70.3 + - - +
331D LYS* 3.4 2.3 + - + +
367D TYR* 3.7 36.8 - - + -
371D LEU* 5.1 3.6 - - + -
381D ASN* 3.9 21.8 - - - +
382D LEU 2.8 17.4 + - - +
383D ILE* 3.5 4.7 - - + +
384D VAL 2.8 32.2 + - - +
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Residues in contact with LEU 330 (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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271D LEU* 4.1 22.9 - - + -
272D ILE 2.8 18.4 + - - +
273D ASN* 3.9 17.8 - - + +
274D TYR* 4.2 6.6 + - - +
278D LEU* 4.2 26.3 - - + +
281D PHE* 3.9 28.0 - - + -
282D ALA* 6.4 0.2 - - + -
329D VAL* 1.3 74.9 - - - +
331D LYS* 1.3 59.2 + - - +
332D VAL* 4.0 2.5 + - - +
384D VAL* 3.4 32.1 - - + -
386D ILE* 4.0 18.6 - - + -
397D LEU* 4.8 0.2 - - + -
401D PHE* 4.0 20.4 - - + -
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Residues in contact with LYS 331 (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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274D TYR* 5.4 8.7 - - + -
329D VAL* 3.4 1.3 + - - +
330D LEU* 1.3 72.9 - - - +
332D VAL* 1.3 86.1 + - - +
333D GLY* 3.7 5.1 + - - -
360D ASP* 5.6 2.4 + - - -
363D ASN 5.8 0.4 - - - -
364D THR* 3.9 27.7 + - - +
367D TYR* 3.3 62.1 - - + +
383D ILE* 4.3 4.9 - - + -
384D VAL 2.9 10.1 + - - +
385D ASN* 3.6 20.8 - - - +
386D ILE* 2.9 27.6 + - - +
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Residues in contact with VAL 332 (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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275D GLU* 4.6 17.5 - - + +
278D LEU* 4.2 19.7 - - + -
330D LEU 4.0 1.7 + - - +
331D LYS* 1.3 94.4 + - - +
333D GLY* 1.3 66.7 + - - +
334D LYS* 3.4 26.0 - - - +
335D SER* 5.3 1.3 - - - -
360D ASP* 5.4 3.5 - - - +
386D ILE* 3.2 16.4 - - + +
388D GLU* 4.1 12.1 - - - -
389D LEU* 4.0 31.0 - - + -
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Residues in contact with GLY 333 (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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331D LYS* 3.7 6.7 + - - +
332D VAL* 1.3 73.4 - - - +
334D LYS* 1.3 58.9 + - - +
335D SER 4.3 0.4 + - - -
360D ASP* 4.6 7.4 - - - +
386D ILE 2.7 15.4 + - - -
387D PRO* 3.4 9.4 - - - -
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Residues in contact with LYS 334 (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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332D VAL* 3.4 19.1 - - - +
333D GLY* 1.3 75.9 - - - +
335D SER* 1.3 87.3 + - - +
336D THR* 3.7 7.5 + - - +
338D GLU* 3.1 28.4 + - - +
360D ASP* 5.3 0.4 - - - -
387D PRO 2.9 16.8 + - - +
388D GLU* 4.2 24.7 - - + +
389D LEU* 4.7 2.4 + - - +
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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