Contacts of the strand formed by residues 337 - 348 (chain H) 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 GLN 337 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260H VAL* 3.3 6.6 - - - +
261H ASP 3.1 30.7 + - - +
262H ILE* 3.3 11.5 - - - +
263H VAL* 3.0 29.3 + - + +
308H VAL* 3.6 17.0 - - + -
309H THR 3.8 4.9 - - - +
310H TYR* 4.4 4.0 - - + -
326H THR 2.6 29.3 + - - +
327H ALA 3.2 15.0 + - - -
328H PRO* 3.5 29.0 - - + +
332H TYR* 6.4 0.2 - - - +
333H THR* 5.6 0.8 + - - +
335H TRP 4.4 0.4 - - - -
336H LYS* 1.3 85.7 + - - +
338H THR* 1.3 66.0 + - - +
339H VAL* 4.9 0.4 - - - -
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Residues in contact with THR 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H TYR* 4.3 3.5 - - - +
190H CYS* 3.3 36.3 + - + -
258H PRO* 3.9 16.6 - - + -
259H LEU 3.4 4.3 - - - +
260H VAL* 4.6 8.3 - - + +
308H VAL* 3.2 5.2 - - - -
309H THR* 2.9 44.2 + - - -
335H TRP 5.0 1.9 + - - -
337H GLN* 1.3 78.5 + - - +
339H VAL* 1.3 63.0 + - - +
340H PHE* 3.8 19.9 - - + -
393H MET* 4.3 9.6 - - - -
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Residues in contact with VAL 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226H ILE* 4.7 6.1 - - + -
228H ASP* 4.8 2.0 - - - +
258H PRO* 3.2 6.9 - - - +
259H LEU* 2.7 50.2 + - + +
261H ASP* 4.7 9.6 - - + +
263H VAL* 3.9 27.1 - - + -
306H ALA* 3.8 22.4 - - + -
307H LEU 3.6 3.8 - - - +
308H VAL* 4.1 7.2 - - + -
338H THR* 1.3 77.4 - - - +
340H PHE* 1.3 64.5 + - - +
341H TYR* 4.0 26.9 + - + +
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Residues in contact with PHE 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H CYS* 4.2 2.7 - - - -
258H PRO* 3.7 17.3 - - + -
306H ALA* 3.2 3.2 - - - +
307H LEU* 2.6 50.6 + - + +
309H THR* 3.7 32.8 - - + -
338H THR* 3.8 22.4 - - + -
339H VAL* 1.3 73.4 - - - +
341H TYR* 1.3 64.7 + - - +
342H LEU* 3.7 2.6 + - - +
358H ILE* 5.2 3.1 - - + -
372H PHE* 3.8 47.3 - + + -
374H VAL* 4.8 9.4 - - + -
391H TYR* 3.8 39.3 + + + +
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Residues in contact with TYR 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228H ASP* 2.7 31.2 + - + -
231H TYR* 3.5 19.1 - - - -
232H LYS* 3.6 40.2 + - + -
235H LYS* 4.7 2.0 - - + -
236H ILE* 3.9 20.9 - - + -
254H ALA 5.9 0.9 - - - -
255H MET* 3.8 31.8 + - - +
257H GLU 5.6 1.8 - - - -
258H PRO* 5.7 0.8 - - + +
259H LEU* 3.8 34.1 - - + +
305H HIS* 4.2 2.9 - - + -
306H ALA* 3.9 19.1 - - + -
339H VAL* 4.0 14.7 + - + +
340H PHE* 1.3 70.6 - - - +
342H LEU* 1.3 56.2 + - - +
389H ASN* 4.6 0.9 + - - -
391H TYR* 2.6 34.6 + - - -
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Residues in contact with LEU 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H LYS* 2.9 21.0 + - - -
255H MET* 3.6 4.1 - - - +
304H VAL* 4.1 29.4 - - + +
305H HIS 3.0 22.5 + - - +
306H ALA* 4.2 5.4 - - - +
307H LEU* 4.7 10.1 - - + -
340H PHE* 4.5 4.5 - - + +
341H TYR* 1.3 75.0 - - - +
343H GLU* 1.3 66.5 + - - +
344H ASP 3.5 14.6 - - - +
346H LEU* 4.2 19.3 - - + -
374H VAL* 5.8 3.4 - - + -
376H LEU* 4.3 22.9 - - + -
389H ASN* 4.1 17.5 - - - +
391H TYR* 4.1 7.0 - - - +
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Residues in contact with GLU 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H LYS* 2.9 18.7 + - - -
237H HIS* 5.1 4.5 - - - -
255H MET* 3.8 22.0 - - + +
256H LYS* 5.6 11.9 - - - -
342H LEU* 1.3 71.3 - - - +
344H ASP* 1.3 72.0 + - - +
387H VAL* 4.2 10.0 - - + +
389H ASN* 3.3 27.8 - - - +
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Residues in contact with ASP 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H LYS* 4.5 2.2 - - - +
342H LEU* 3.5 20.6 - - - +
343H GLU* 1.3 86.6 - - - +
345H TYR* 1.3 69.3 + - + +
346H LEU* 3.9 8.4 + - + +
385H THR* 5.8 7.3 - - + +
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Residues in contact with TYR 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F TYR 2.6 29.3 + - - -
105F HIS* 3.6 13.7 - + - -
107F LYS* 3.6 23.2 + - + +
232H LYS* 4.8 3.6 - - - +
303H TYR* 3.6 34.5 - + - -
304H VAL 3.3 14.1 - - - +
305H HIS* 3.7 36.8 - + + +
344H ASP* 1.3 81.7 - - + +
346H LEU* 1.3 63.8 + - - +
347H THR* 4.0 11.2 + - - -
383H CYS* 5.1 2.3 - - - +
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Residues in contact with LEU 346 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303H TYR* 3.2 9.0 - - - +
304H VAL* 2.9 37.5 + - + +
342H LEU* 4.2 19.7 - - + -
344H ASP* 4.1 10.8 - - + +
345H TYR* 1.3 78.8 - - - +
347H THR* 1.3 61.6 + - - +
348H VAL* 3.7 14.0 + - + -
354H ILE* 4.2 27.8 - - + -
376H LEU* 4.0 23.6 - - + -
378H PHE* 4.3 17.9 - - + -
383H CYS* 4.1 7.2 - - - -
385H THR* 3.9 21.5 - - + +
387H VAL* 6.4 0.2 - - + -
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Residues in contact with THR 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F HIS* 4.1 19.0 + - + +
319F HIS* 3.7 28.0 - - + +
302H ASP 4.1 1.8 - - - -
303H TYR* 3.9 20.4 - - + -
345H TYR* 4.0 11.6 + - - -
346H LEU* 1.3 72.5 - - - +
348H VAL* 1.3 60.3 + - - +
352H GLU* 4.2 1.9 - - - +
378H PHE* 3.8 5.7 - - - -
382H LEU* 3.9 33.5 - - + +
383H CYS* 3.4 26.4 + - - +
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Residues in contact with VAL 348 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F HIS* 3.1 9.9 - - - -
269H VAL* 4.2 10.5 - - + -
298H ILE* 3.6 34.8 - - + -
302H ASP 3.0 46.3 + - - +
303H TYR* 4.8 0.2 - - - -
304H VAL* 4.2 10.3 - - + -
346H LEU* 3.7 24.9 - - + -
347H THR* 1.3 79.2 - - - +
349H ARG* 1.3 61.4 + - - +
352H GLU* 3.7 3.4 - - - -
354H ILE* 5.2 0.2 - - + -
378H PHE* 3.6 24.2 - - + -
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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