Contacts of the strand formed by residues 404 - 410 (chain D) in PDB entry 3SZ9
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 VAL 404 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294D LEU* 3.6 12.2 - - - +
306D SER* 5.2 0.3 - - - -
353D ILE* 3.9 17.0 - - + -
357D ILE* 3.8 31.2 - - + -
384D THR* 3.3 9.9 - - + -
386D PHE* 3.6 29.2 - - + -
395D ILE* 5.9 0.2 - - + -
400D ILE* 4.1 25.0 - - + +
402D GLY 2.9 10.7 + - - +
403D PRO* 1.3 78.4 - - + +
405D MET* 1.3 59.0 + - - +
406D GLN* 2.9 35.3 + - - +
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Residues in contact with MET 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ALA* 3.5 30.5 - - + +
291D HIS* 3.9 8.7 - - + +
294D LEU* 3.7 23.5 - - + +
295D PHE* 3.8 22.2 - - + -
305D GLY 5.7 0.2 - - - +
308D THR* 4.1 17.9 - - - +
318D PHE* 5.8 0.7 - - - -
322D SER* 4.7 13.0 - - - +
384D THR 2.8 16.4 + - - +
385D VAL* 4.3 15.7 - - + -
386D PHE* 2.8 35.2 + - - +
404D VAL* 1.3 70.9 - - - +
406D GLN* 1.3 63.9 + - - +
407D ILE* 4.2 26.5 - - + -
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Residues in contact with GLN 406 (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 LYS* 4.5 1.4 - - - +
306D SER* 3.0 33.9 + - - +
307D ARG* 4.4 4.0 - - + -
308D THR* 2.7 36.4 + - - +
386D PHE* 3.7 3.1 - - - -
389D VAL* 4.0 24.0 - - + -
395D ILE* 3.3 38.2 + - + +
396D ALA* 4.7 0.7 - - - +
400D ILE* 3.7 10.8 - - - +
404D VAL* 2.9 41.2 + - - +
405D MET* 1.3 75.3 - - - +
407D ILE* 1.3 60.7 + - - +
408D LEU* 3.9 3.7 - - + +
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Residues in contact with ILE 407 (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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308D THR* 3.4 5.2 - - - +
310D VAL* 3.7 27.8 - - + -
315D TYR* 3.8 9.3 + - + +
318D PHE* 4.4 6.7 - - + -
319D VAL* 3.6 42.6 - - + -
322D SER* 4.3 8.3 - - - -
368D LEU* 5.3 0.2 - - + -
385D VAL* 3.8 24.7 - - + -
386D PHE 3.0 16.0 + - - +
387D GLY* 3.8 1.3 - - - -
388D ASP 3.3 9.9 + - - -
389D VAL* 3.0 23.0 + - - +
405D MET* 4.2 17.9 - - + -
406D GLN* 1.3 77.8 - - - +
408D LEU* 1.3 62.5 + - - +
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Residues in contact with LEU 408 (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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307D ARG* 3.8 34.8 - - + -
308D THR 2.9 19.2 + - - +
309D PHE* 3.5 24.0 - - + -
310D VAL* 2.9 29.8 + - - +
315D TYR* 4.0 3.8 - - - -
388D ASP 5.3 0.2 - - - -
389D VAL* 3.5 38.4 - - + +
390D GLN 4.4 0.2 - - - -
391D ASP* 3.5 27.8 - - - +
396D ALA* 4.7 6.5 - - + -
406D GLN* 3.9 9.0 - - + +
407D ILE* 1.3 74.8 - - - +
409D LYS* 1.3 60.3 + - - +
419D ARG* 3.7 6.1 - - - +
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Residues in contact with LYS 409 (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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310D VAL 3.6 2.7 - - - +
312D GLU* 3.8 33.7 - - + +
315D TYR* 3.7 42.5 - - + -
316D ASP* 5.9 0.4 + - - -
388D ASP* 4.6 13.5 + - - +
389D VAL 4.8 2.4 + - - +
408D LEU* 1.3 73.4 - - - +
410D PHE* 1.3 64.3 + - - +
415D GLU* 4.4 0.2 - - - +
419D ARG* 2.9 21.9 + - - +
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Residues in contact with PHE 410 (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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276D ILE* 4.1 2.7 - - + -
277D ILE 3.8 2.9 - - - -
278D MET* 3.8 25.6 - - + -
309D PHE* 3.6 25.1 - - + -
310D VAL 3.1 31.9 + - - -
311D GLN* 3.2 41.8 - - + -
312D GLU* 2.9 30.2 + - - +
409D LYS* 1.3 76.1 - - - +
411D LYS* 1.3 63.1 + - - +
412D THR 3.3 27.6 - - - -
415D GLU* 3.8 11.0 - - + +
416D VAL* 3.6 22.9 - - + -
419D ARG* 3.6 13.5 - - - +
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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