Contacts of the strand formed by residues 384 - 393 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378G PHE 3.1 13.0 - - - +
379G LYS* 3.2 38.4 - - + +
380G GLY 5.0 1.6 - - - +
383G CYS* 1.3 79.4 - - - +
385G THR* 1.3 76.1 + - - +
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Residues in contact with THR 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344G ASP* 5.8 6.7 - - + +
346G LEU* 4.0 23.3 - - + +
376G LEU* 4.4 6.3 - - - +
377G ASP* 3.6 0.5 - - - -
378G PHE* 2.9 34.5 + - - +
383G CYS* 5.4 5.0 - - + -
384G GLU* 1.3 87.7 - - - +
386G SER* 1.3 62.9 + - - +
387G VAL* 3.8 19.3 - - + +
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Residues in contact with SER 386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376G LEU 3.3 5.4 - - - -
377G ASP* 3.4 25.5 + - - -
385G THR* 1.3 75.8 - - - +
387G VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 387 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343G GLU* 4.3 10.5 - - + +
374G VAL 3.8 0.6 - - - +
375G ASP* 3.2 5.0 - - - +
376G LEU* 2.7 46.4 + - + +
377G ASP* 4.3 1.1 + - - +
385G THR* 3.8 25.6 - - + +
386G SER* 1.3 80.0 + - - +
388G SER* 1.3 65.5 + - - +
389G ASN* 3.3 29.6 - - - +
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Residues in contact with SER 388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373G THR* 3.8 10.4 - - - +
374G VAL 3.6 0.4 - - - -
375G ASP* 2.6 27.6 + - - -
387G VAL* 1.3 77.2 - - - +
389G ASN* 1.3 64.5 + - - +
390G ASP* 4.3 4.2 + - - +
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Residues in contact with ASN 389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G LYS* 5.4 8.8 - - - +
341G TYR 4.5 0.2 + - - -
342G LEU* 4.2 22.6 - - - +
343G GLU* 3.4 22.5 + - - +
373G THR* 3.3 4.7 - - - +
374G VAL* 2.9 38.7 + - + +
376G LEU* 6.3 1.0 - - - +
387G VAL* 3.3 26.8 - - - +
388G SER* 1.3 74.8 - - - +
390G ASP* 1.3 65.2 + - - +
391G TYR* 3.6 33.7 + - + +
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Residues in contact with ASP 390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G LYS* 2.9 35.8 - - + +
372G PHE 3.4 6.7 - - - +
373G THR* 3.0 25.0 + - - +
388G SER* 4.3 4.1 + - - +
389G ASN* 1.3 77.0 - - - +
391G TYR* 1.3 68.8 - - - +
392G LYS* 6.3 1.3 - - + -
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Residues in contact with TYR 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255G MET 3.3 27.6 - - - -
256G LYS* 3.0 14.1 - - + +
257G GLU 4.4 0.7 - - - -
258G PRO* 4.1 17.9 - - + -
340G PHE* 3.7 28.2 + + + +
341G TYR 2.3 40.9 + - - -
342G LEU* 4.2 5.7 - - - +
371G ASP* 3.7 0.7 - - - -
372G PHE* 2.9 40.5 + - + +
374G VAL* 3.9 24.3 - - + +
389G ASN* 3.6 38.7 + - + -
390G ASP* 1.3 77.3 - - - +
392G LYS* 1.3 70.5 + - - +
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Residues in contact with LYS 392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G LYS* 2.7 15.7 + - + +
257G GLU* 3.6 10.4 - - - +
258G PRO* 3.4 14.7 - - - +
363G ASN* 3.3 31.1 - - - +
369G ASP* 5.9 3.7 - - + +
370G LEU 3.3 5.2 - - - +
371G ASP* 3.5 16.0 + - - +
372G PHE* 5.3 0.2 - - - -
390G ASP* 6.3 1.1 - - + -
391G TYR* 1.3 79.3 - - - +
393G MET* 1.3 61.6 + - - +
394G ARG 3.4 4.7 + - - +
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Residues in contact with MET 393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G TYR* 3.9 17.9 - - + -
190G CYS* 4.1 25.4 - - - -
193G TYR* 3.5 50.6 - - + -
258G PRO* 3.8 25.6 - - + +
260G VAL* 4.5 9.4 - - + -
338G THR* 4.4 10.5 - - - -
369G ASP* 3.7 13.0 - - - +
370G LEU* 2.8 25.3 + - + +
372G PHE* 3.9 9.6 - - + -
392G LYS* 1.3 71.9 - - - +
394G ARG* 1.3 87.2 + - + +
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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