Contacts of the strand formed by residues 384 - 393 (chain M) in PDB entry 5DST
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 GLU 384 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378M PHE 3.2 11.2 - - - +
379M LYS* 3.5 37.4 - - + +
380M GLY 5.0 1.3 - - - +
383M CYS* 1.3 81.5 - - - +
385M THR* 1.3 73.5 + - - +
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Residues in contact with THR 385 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344M ASP* 5.8 7.2 - - + +
346M LEU* 4.0 23.3 - - + +
376M LEU* 3.8 6.2 - - - +
377M ASP* 3.5 1.7 - - - -
378M PHE* 2.9 33.9 + - - +
383M CYS* 5.1 5.1 - - + -
384M GLU* 1.3 83.1 - - - +
386M SER* 1.3 62.2 + - - +
387M VAL* 3.8 19.9 - - + +
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Residues in contact with SER 386 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376M LEU 3.2 5.4 - - - -
377M ASP* 3.5 27.9 + - - -
385M THR* 1.3 75.4 - - - +
387M VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 387 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343M GLU* 4.3 10.5 - - + +
374M VAL 4.4 0.4 - - - -
375M ASP* 3.3 4.5 - - - +
376M LEU* 2.8 44.5 + - + +
377M ASP* 4.5 1.1 + - - +
385M THR* 3.8 27.8 - - + +
386M SER* 1.3 78.8 + - - +
388M SER* 1.3 65.5 + - - +
389M ASN* 3.2 29.8 - - - +
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Residues in contact with SER 388 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373M THR* 3.8 9.2 - - - +
374M VAL 3.5 4.3 - - - -
375M ASP* 2.7 25.5 + - - -
387M VAL* 1.3 77.4 - - - +
389M ASN* 1.3 65.2 + - - +
390M ASP* 4.5 2.7 + - - -
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Residues in contact with ASN 389 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256M LYS* 5.5 9.6 - - - +
341M TYR 4.5 0.2 + - - -
342M LEU* 4.1 23.0 - - - +
343M GLU* 3.5 20.9 - - - +
373M THR* 3.3 3.8 - - - +
374M VAL* 2.8 42.2 + - - +
376M LEU* 6.2 1.8 - - - +
387M VAL* 3.2 28.0 - - - +
388M SER* 1.3 75.8 + - - +
390M ASP* 1.3 65.7 + - - +
391M TYR* 3.5 33.7 + - + +
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Residues in contact with ASP 390 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256M LYS* 3.0 36.6 - - + +
372M PHE 3.5 5.2 - - - +
373M THR* 3.1 26.9 + - - +
388M SER* 4.5 3.0 + - - -
389M ASN* 1.3 76.9 - - - +
391M TYR* 1.3 68.4 + - - +
392M LYS* 6.2 1.3 - - + -
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Residues in contact with TYR 391 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255M MET 3.6 23.3 - - - -
256M LYS* 3.1 13.7 - - + +
257M GLU 4.9 0.2 - - - -
258M PRO* 4.2 16.8 - - + -
340M PHE* 3.7 34.1 + + + +
341M TYR 2.4 33.5 + - - -
342M LEU* 4.1 5.9 - - - +
371M ASP* 3.6 0.9 - - - +
372M PHE* 2.8 43.8 + - + +
374M VAL* 3.9 25.7 - - + +
389M ASN* 3.5 40.5 + - + -
390M ASP* 1.3 78.4 - - - +
392M LYS* 1.3 67.3 + - - +
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Residues in contact with LYS 392 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256M LYS* 2.9 12.3 + - + +
257M GLU* 3.6 10.6 - - - +
258M PRO* 3.4 15.3 - - - +
363M ASN* 3.3 30.3 - - - +
369M ASP* 6.0 3.3 + - + +
370M LEU 3.3 5.4 - - - +
371M ASP* 3.7 15.5 + - - +
372M PHE* 5.3 0.2 - - - -
390M ASP* 6.2 1.8 - - + -
391M TYR* 1.3 79.2 - - - +
393M MET* 1.3 63.9 + - - +
394M ARG 3.5 4.6 + - - +
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Residues in contact with MET 393 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189M TYR* 3.9 17.9 - - + -
190M CYS* 4.0 25.4 - - - -
193M TYR* 3.4 52.4 - - + -
258M PRO* 3.7 26.2 - - + +
260M VAL* 4.5 9.2 - - + -
338M THR* 4.2 12.3 - - - -
369M ASP* 3.7 14.0 - - - +
370M LEU* 2.9 22.6 + - + +
372M PHE* 3.8 14.3 - - + -
392M LYS* 1.3 70.9 - - - +
394M ARG* 1.3 83.1 - - + +
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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