Contacts of the strand formed by residues 337 - 348 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260E VAL* 3.3 7.6 - - - +
261E ASP 3.0 31.2 + - - +
262E ILE* 3.4 9.3 - - - +
263E VAL* 3.0 31.1 + - + +
308E VAL* 3.7 18.2 - - + -
309E THR 3.9 9.4 - - - +
310E TYR* 4.5 1.1 - - + -
326E THR 2.5 29.1 + - - +
327E ALA 3.3 14.3 + - - -
328E PRO* 3.8 29.0 - - + +
333E THR* 5.7 0.4 + - - -
335E TRP 4.1 1.3 - - - -
336E LYS* 1.3 86.8 + - - +
338E THR* 1.3 66.0 + - - +
339E VAL* 4.1 0.4 - - - -
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Residues in contact with THR 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E TYR* 4.8 0.7 - - - +
190E CYS* 3.3 34.8 + - + -
258E PRO* 3.9 15.9 - - + -
259E LEU 3.3 4.9 - - - +
260E VAL* 4.6 9.7 - - + +
307E LEU 3.9 0.2 - - - +
308E VAL* 3.2 5.5 - - - -
309E THR* 2.9 46.6 + - - -
335E TRP 5.0 1.7 + - - -
337E GLN* 1.3 79.2 + - - +
339E VAL* 1.3 63.0 - - - +
340E PHE* 3.7 20.9 - - + -
393E MET* 4.2 9.2 - - - -
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Residues in contact with VAL 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E ILE* 4.6 6.7 - - + -
228E ASP* 4.7 2.9 - - - +
258E PRO* 3.1 6.9 - - - +
259E LEU* 2.7 49.9 + - + +
261E ASP* 4.6 9.4 - - + +
263E VAL* 4.0 27.4 - - + -
306E ALA* 3.7 23.6 - - + -
307E LEU 3.6 4.5 - - - +
308E VAL* 4.2 6.1 - - + -
338E THR* 1.3 79.3 - - - +
340E PHE* 1.3 63.9 + - - +
341E TYR* 3.9 24.8 + - + +
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Residues in contact with PHE 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E CYS* 4.2 3.1 - - - -
223E VAL* 6.3 0.2 - - + -
258E PRO* 3.6 16.4 - - + -
306E ALA* 3.1 3.3 - - - +
307E LEU* 2.8 50.4 + - + +
309E THR* 3.9 24.9 - - + -
338E THR* 3.7 30.5 - - + -
339E VAL* 1.3 73.9 - - - +
341E TYR* 1.3 65.3 + - - +
342E LEU* 4.6 1.9 - - - +
358E ILE* 5.3 4.0 - - + -
372E PHE* 3.8 45.8 - + + -
374E VAL* 4.8 7.6 - - + -
391E TYR* 3.7 40.0 + + + +
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Residues in contact with TYR 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E ASP* 2.7 29.9 + - + -
231E TYR* 3.5 19.8 - - - -
232E LYS* 3.5 43.7 + - + -
235E LYS* 4.7 1.6 - - + -
236E ILE* 3.9 20.0 - - + -
254E ALA 5.9 0.7 - - - -
255E MET* 3.9 32.2 + - + +
257E GLU 5.5 2.7 + - - -
258E PRO* 5.7 0.8 - - - +
259E LEU* 3.8 34.6 - - + +
305E HIS* 4.0 2.7 - - + -
306E ALA* 4.0 16.4 - - + -
339E VAL* 3.9 13.1 + - + +
340E PHE* 1.3 72.3 - - - +
342E LEU* 1.3 57.8 + - - +
343E GLU* 6.0 0.2 - - - +
389E ASN* 4.5 0.9 + - - -
391E TYR* 2.4 35.0 + - - -
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Residues in contact with LEU 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E LYS* 2.8 27.7 + - - -
255E MET* 3.7 4.0 - - - +
304E VAL* 4.2 26.7 - - + +
305E HIS 3.0 21.7 + - - +
306E ALA* 4.1 5.8 - - - +
307E LEU* 4.6 11.2 - - + -
340E PHE 4.6 3.1 - - - +
341E TYR* 1.3 77.4 - - - +
343E GLU* 1.3 59.8 + - - +
344E ASP 3.4 12.1 - - - +
346E LEU* 4.2 26.0 - - + -
374E VAL* 5.8 2.5 - - + -
376E LEU* 4.2 24.5 - - + -
389E ASN* 4.0 18.6 - - - +
391E TYR* 4.2 4.7 - - - +
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Residues in contact with GLU 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E LYS* 3.1 15.8 + - - -
237E HIS* 5.2 4.3 - - - -
255E MET* 3.8 22.6 - - + +
256E LYS* 5.6 11.9 - - - -
342E LEU* 1.3 71.5 - - - +
344E ASP* 1.3 71.1 + - - +
387E VAL* 4.1 11.3 - - + +
388E SER 5.4 0.2 - - - +
389E ASN* 3.4 27.7 - - - +
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Residues in contact with ASP 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E LYS* 4.6 1.8 - - - +
342E LEU* 3.5 21.9 - - - +
343E GLU* 1.3 87.4 - - - +
345E TYR* 1.3 70.7 + - + +
346E LEU* 3.8 7.9 + - + +
385E THR* 5.9 5.4 - - + +
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Residues in contact with TYR 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E LYS* 4.8 3.3 - - - +
237E HIS* 6.4 0.2 - - - -
303E TYR* 3.7 34.1 - + - -
304E VAL 3.2 15.0 - - - +
305E HIS* 3.6 36.3 - + + +
344E ASP* 1.3 82.5 - - - +
346E LEU* 1.3 64.0 + - - +
347E THR* 3.9 10.7 + - - -
383E CYS* 4.8 3.1 - - - -
104G TYR 2.8 26.9 + - - -
105G HIS* 3.5 18.1 - + + -
107G LYS* 3.8 17.5 + - + +
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Residues in contact with LEU 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E TYR* 3.2 8.0 - - - +
304E VAL* 2.8 38.2 + - + +
342E LEU* 4.2 19.7 - - + -
344E ASP* 4.1 9.9 - - + +
345E TYR* 1.3 79.2 - - - +
347E THR* 1.3 61.3 - - - +
348E VAL* 3.7 14.4 + - + -
354E ILE* 4.2 27.8 - - + -
376E LEU* 4.1 23.8 - - + -
378E PHE* 4.4 17.5 - - + -
383E CYS* 4.0 7.4 - - - -
385E THR* 4.1 20.4 - - + +
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Residues in contact with THR 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302E ASP 4.1 2.2 - - - -
303E TYR* 3.7 19.7 - - + -
345E TYR* 3.9 10.8 + - - -
346E LEU* 1.3 71.2 - - - +
348E VAL* 1.3 61.0 + - - +
352E GLU* 4.3 1.7 - - - +
378E PHE* 3.9 12.1 - - - -
382E LEU* 3.8 30.8 - - + +
383E CYS* 3.5 17.9 + - - +
105G HIS 5.2 0.3 + - - -
108G HIS* 4.1 19.6 + - + +
319G HIS* 3.5 33.7 - - + +
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Residues in contact with VAL 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E VAL* 4.1 11.2 - - + -
298E ILE* 3.6 35.4 - - + -
301E ASN* 3.5 0.5 - - - -
302E ASP 3.1 46.7 + - - +
303E TYR* 4.8 0.2 - - - -
304E VAL* 4.1 10.8 - - + -
346E LEU* 3.7 24.2 - - + +
347E THR* 1.3 77.0 - - - +
349E ARG* 1.3 63.9 + - - +
352E GLU* 3.8 2.9 - - - -
378E PHE* 3.6 24.7 - - + -
319G HIS* 3.1 9.4 - - - -
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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