Contacts of the helix formed by residues 332 - 349 (chain E) in PDB entry 6T8O
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 SER 332 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330E SER* 3.1 12.0 + - - -
331E TYR* 1.3 74.1 - - - +
333E PRO* 1.3 68.0 - - - +
334E GLU* 3.3 20.4 + - - +
335E SER* 2.9 32.7 + - - -
336E LEU* 3.0 25.1 + - - +
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Residues in contact with PRO 333 (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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331E TYR 4.1 3.6 - - - +
332E SER* 1.3 86.9 - - - +
334E GLU* 1.3 57.3 + - + +
336E LEU* 3.8 14.6 - - + +
337E GLU* 2.9 29.1 + - - +
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Residues in contact with GLU 334 (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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332E SER* 3.3 20.5 + - - +
333E PRO* 1.3 80.1 - - + +
335E SER* 1.3 61.7 + - - +
337E GLU* 3.4 8.1 + - - +
338E ALA* 2.9 28.8 + - - +
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Residues in contact with SER 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E TYR 5.6 0.2 - - - -
332E SER* 2.9 26.9 + - - -
334E GLU* 1.3 78.0 + - - +
336E LEU* 1.3 62.3 + - - +
338E ALA* 3.4 6.3 + - - +
339E MET* 2.9 30.3 + - - +
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Residues in contact with LEU 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E TYR* 4.0 24.0 - - + +
332E SER 3.0 15.6 + - - +
333E PRO* 3.8 12.8 - - + +
335E SER* 1.3 77.6 - - - +
337E GLU* 1.3 57.1 + - - +
339E MET* 3.4 5.0 + - + +
340E SER* 2.9 33.7 + - - -
359E VAL* 3.8 36.0 - - + +
361E PRO* 4.8 18.8 - - + -
366E THR* 4.4 15.7 - - + +
368E PHE* 4.7 6.5 - - + -
415E ASN* 5.9 2.9 - - - +
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Residues in contact with GLU 337 (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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333E PRO 2.9 18.3 + - - +
334E GLU* 3.7 7.9 - - - +
335E SER 3.3 0.2 - - - -
336E LEU* 1.3 74.1 - - - +
338E ALA* 1.3 65.1 + - - +
340E SER* 3.3 6.0 + - - -
341E ARG* 3.0 76.0 + - - +
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Residues in contact with ALA 338 (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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334E GLU 2.9 17.4 + - - +
335E SER* 3.8 7.0 - - - +
337E GLU* 1.3 82.2 + - - +
339E MET* 1.3 56.0 + - - +
341E ARG* 3.4 5.3 + - - +
342E LEU* 2.9 29.4 + - - +
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Residues in contact with MET 339 (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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335E SER 2.9 19.1 + - - +
336E LEU* 3.7 6.5 - - + +
338E ALA* 1.3 73.2 - - - +
340E SER* 1.3 61.7 + - - +
342E LEU* 3.4 22.5 + - + +
343E LEU* 2.9 28.1 + - - +
368E PHE* 3.6 29.6 - - + -
392E LEU* 4.8 14.8 - - - +
394E VAL* 6.0 2.0 - - + -
413E ILE* 4.6 21.8 - - + -
416E GLU* 4.9 15.7 - - + +
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Residues in contact with SER 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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336E LEU 2.9 23.2 + - - -
337E GLU* 3.3 8.2 + - - -
339E MET* 1.3 77.0 - - - +
341E ARG* 1.3 67.6 + - - +
343E LEU* 3.3 3.1 + - - -
344E GLU* 3.0 32.4 + - - +
356E VAL* 3.5 29.6 - - - +
359E VAL* 3.4 24.1 - - - +
368E PHE* 4.4 6.8 - - - -
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Residues in contact with ARG 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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337E GLU* 3.0 45.7 + - - +
338E ALA* 3.9 5.6 - - - +
340E SER* 1.3 93.5 - - - +
342E LEU* 1.3 58.1 + - - +
344E GLU* 3.3 32.0 + - - +
345E ILE* 3.0 37.0 + - + +
356E VAL* 5.0 4.9 + - - +
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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
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338E ALA 2.9 18.1 + - - +
339E MET* 3.7 18.4 - - + +
340E SER 3.3 0.2 - - - -
341E ARG* 1.3 76.4 - - - +
343E LEU* 1.3 56.0 + - - +
345E ILE* 3.8 8.5 - - + -
346E LYS* 2.9 58.8 + - + +
391E SER 5.4 0.2 - - - +
392E LEU* 3.8 25.8 - - + +
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Residues in contact with LEU 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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339E MET* 2.9 16.9 + - - +
340E SER* 3.6 6.3 - - - +
342E LEU* 1.3 73.7 - - - +
344E GLU* 1.3 62.1 + - + +
346E LYS* 3.9 1.9 - - - +
347E LEU* 3.0 51.5 + - + +
354E VAL* 5.1 2.7 - - + -
356E VAL* 3.9 19.1 - - + -
368E PHE* 3.6 28.0 - - + -
370E ILE* 3.9 14.8 - - + -
388E LEU* 5.2 2.5 - - + -
392E LEU* 4.7 16.5 - - + +
411E ILE* 4.0 19.3 - - + -
413E ILE* 3.7 17.7 - - + -
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Residues in contact with GLU 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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340E SER 3.0 17.9 + - - +
341E ARG* 3.6 36.1 + - - +
343E LEU* 1.3 79.6 - - + +
345E ILE* 1.3 62.4 + - + +
347E LEU* 3.5 2.6 + - - +
348E LYS* 2.9 29.9 + - - +
354E VAL* 3.5 22.4 + - - +
355E SER* 3.4 11.4 - - - -
356E VAL* 2.7 37.9 + - + +
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Residues in contact with ILE 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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341E ARG* 3.0 20.5 + - + +
342E LEU* 4.0 10.3 - - + +
344E GLU* 1.3 80.6 - - + +
346E LYS* 1.3 61.3 + - + +
348E LYS* 3.1 11.5 + - + +
349E GLU* 2.9 43.1 + - + +
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Residues in contact with LYS 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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371D GLN* 5.6 6.3 - - - +
342E LEU* 2.9 39.4 + - + +
343E LEU 4.1 2.5 - - - +
345E ILE* 1.3 79.1 - - + +
347E LEU* 1.3 60.7 + - - +
349E GLU* 3.8 34.6 + - - +
350E PHE* 3.2 27.4 - - - -
388E LEU* 4.3 6.5 - - + +
391E SER* 3.3 47.0 + - - +
392E LEU* 3.9 12.8 - - + -
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Residues in contact with LEU 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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343E LEU* 3.0 34.1 + - + +
344E GLU 4.2 0.7 - - - +
346E LYS* 1.3 75.8 - - - +
348E LYS* 1.3 64.0 + - - +
349E GLU 3.2 0.4 - - - -
350E PHE* 3.3 11.2 + - + +
352E VAL* 2.9 42.9 - - + +
354E VAL* 3.7 28.3 - - + -
370E ILE* 5.6 0.2 - - + -
381E ILE* 5.0 12.3 - - + +
384E LEU* 4.8 16.8 - - + -
388E LEU* 3.8 34.1 - - + -
411E ILE* 4.0 18.8 - - + -
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Residues in contact with LYS 348 (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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344E GLU 2.9 19.9 + - - +
345E ILE* 3.1 16.1 + - + +
347E LEU* 1.3 74.1 - - - +
349E GLU* 1.3 60.9 + - - +
350E PHE 2.9 13.0 - - - +
352E VAL 3.5 5.2 - - - +
353E GLU* 3.8 45.0 - - + +
354E VAL 5.6 0.4 - - - +
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Residues in contact with GLU 349 (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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374D ALA* 3.6 38.4 - - + +
375D GLY* 3.4 19.9 + - - +
345E ILE* 2.9 29.2 + - + +
346E LYS* 3.8 44.0 + - - +
347E LEU 3.2 0.4 - - - -
348E LYS* 1.3 78.7 - - - +
350E PHE* 1.3 65.2 + - + +
391E SER* 5.4 1.9 - - - -
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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