Contacts of the helix formed by residues 332 - 349 (chain F) in PDB entry 6T8B
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330F SER 4.3 0.6 + - - -
331F TYR* 1.3 75.1 - - - +
333F PRO* 1.3 73.3 - - - +
334F GLU* 3.9 7.7 + - - +
335F SER* 2.6 42.6 + - - -
336F LEU* 3.4 4.6 + - - +
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Residues in contact with PRO 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331F TYR 3.8 2.4 - - - +
332F SER* 1.3 84.7 - - - +
334F GLU* 1.3 59.4 + - - +
336F LEU* 3.3 17.2 + - + +
337F GLU* 2.9 28.9 + - - +
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Residues in contact with GLU 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332F SER* 3.2 9.1 - - - +
333F PRO* 1.3 81.8 - - - +
335F SER* 1.3 57.5 + - - +
337F GLU* 3.3 13.8 + - - +
338F ALA* 2.9 32.9 + - + +
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Residues in contact with SER 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F TYR* 3.9 14.1 - - - +
332F SER* 2.6 35.8 + - - -
334F GLU* 1.3 78.7 - - - +
336F LEU* 1.3 59.1 + - - +
338F ALA* 3.7 6.0 - - - +
339F MET* 2.9 31.6 + - - +
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Residues in contact with LEU 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F TYR* 4.7 23.6 - - + +
332F SER 3.4 13.7 + - - +
333F PRO* 3.3 15.6 + - + +
334F GLU 3.2 0.6 - - - -
335F SER* 1.3 83.6 + - - +
337F GLU* 1.3 59.3 + - - +
339F MET* 3.8 4.2 - - + +
340F SER* 2.9 31.9 + - - -
359F VAL* 3.6 41.6 - - + +
361F PRO* 5.1 12.1 - - + -
366F THR* 4.4 10.3 - - + +
368F PHE* 4.3 13.9 - - + -
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Residues in contact with GLU 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333F PRO 2.9 14.4 + - - +
334F GLU* 3.5 19.3 - - - +
336F LEU* 1.3 76.1 - - - +
338F ALA* 1.3 62.6 + - - +
340F SER* 2.6 22.3 + - - -
341F ARG* 3.0 57.8 + - + +
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Residues in contact with ALA 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334F GLU* 2.9 21.2 + - + +
335F SER* 3.7 7.2 - - - +
337F GLU* 1.3 76.6 - - - +
339F MET* 1.3 57.6 + - - +
341F ARG* 3.3 7.3 + - - +
342F LEU* 2.9 28.6 + - - +
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Residues in contact with MET 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335F SER 2.9 18.5 + - - +
336F LEU* 4.0 2.0 - - + +
338F ALA* 1.3 75.9 - - - +
340F SER* 1.3 57.5 + - - +
342F LEU* 3.3 18.0 + - + +
343F LEU* 2.9 28.1 + - - +
368F PHE* 3.4 27.8 - - + -
392F LEU* 3.7 51.8 - - + +
394F VAL* 5.1 1.6 - - + -
413F ILE* 4.0 19.5 - - + -
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Residues in contact with SER 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F LEU 2.9 16.2 + - - -
337F GLU* 2.6 26.2 + - - -
339F MET* 1.3 74.3 - - - +
341F ARG* 1.3 70.9 + - - +
343F LEU* 3.2 6.1 + - - +
344F GLU* 3.0 32.9 + - - +
356F VAL* 3.6 33.6 - - - +
359F VAL* 4.9 6.4 - - - +
368F PHE* 4.5 8.4 - - - -
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Residues in contact with ARG 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337F GLU* 3.0 47.1 + - + +
338F ALA* 3.7 6.1 - - - +
340F SER* 1.3 95.6 + - - +
342F LEU* 1.3 58.2 + - - +
344F GLU* 3.3 34.3 + - - +
345F ILE* 2.9 37.5 + - + +
356F VAL* 5.1 5.3 + - - +
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Residues in contact with LEU 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F ALA 2.9 17.6 + - - +
339F MET* 3.6 22.7 - - + +
340F SER 3.2 0.2 - - - -
341F ARG* 1.3 76.6 - - - +
343F LEU* 1.3 56.0 + - - +
345F ILE* 3.8 7.6 - - + +
346F LYS* 2.9 53.4 + - + +
391F SER 5.5 0.9 - - - +
392F LEU* 3.7 26.2 - - + +
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Residues in contact with LEU 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339F MET 2.9 14.8 + - - +
340F SER* 3.2 8.7 + - - +
342F LEU* 1.3 75.5 - - - +
344F GLU* 1.3 62.8 + - - +
346F LYS* 3.8 1.1 - - - -
347F LEU* 2.9 39.2 + - + +
354F VAL* 5.4 0.2 - - + -
356F VAL* 4.2 4.7 - - + -
368F PHE* 3.6 37.9 - - + -
370F ILE* 3.8 21.3 - - + -
388F LEU* 3.7 30.7 - - + -
392F LEU* 3.9 22.1 - - + +
411F ILE* 4.2 9.2 - - + -
413F ILE* 4.1 8.3 - - + -
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Residues in contact with GLU 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F SER 3.0 18.0 + - - +
341F ARG* 3.3 36.2 + - - +
343F LEU* 1.3 75.5 - - - +
345F ILE* 1.3 61.5 + - + +
347F LEU* 3.4 1.6 + - - +
348F LYS* 2.9 30.8 + - - +
354F VAL* 4.2 25.1 + - + +
355F SER* 3.4 9.3 - - - -
356F VAL* 2.8 41.3 + - + +
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Residues in contact with ILE 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F ARG* 2.9 25.1 + - + +
342F LEU* 3.8 9.0 - - + +
343F LEU 3.2 0.2 - - - -
344F GLU* 1.3 79.4 - - + +
346F LYS* 1.3 63.9 + - + +
348F LYS* 3.2 8.5 + - + +
349F GLU* 2.9 51.4 + - + +
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Residues in contact with LYS 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371E GLN* 5.9 2.0 - - - +
374E ALA* 5.7 2.2 - - - +
407E THR* 5.5 4.8 - - - +
342F LEU* 2.9 36.0 + - + +
345F ILE* 1.3 78.2 - - + +
347F LEU* 1.3 61.7 + - - +
349F GLU* 3.0 38.5 + - - +
350F PHE* 3.8 24.9 - - - -
388F LEU* 4.1 17.7 - - + +
391F SER* 3.4 35.4 - - - +
392F LEU* 3.8 17.5 - - + -
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Residues in contact with LEU 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F LEU* 2.9 25.9 + - + +
344F GLU 3.8 2.7 - - - +
346F LYS* 1.3 75.0 - - - +
348F LYS* 1.3 52.9 + - - +
349F GLU 3.0 4.5 - - - -
350F PHE* 2.6 33.2 + - + +
351F GLY 3.6 0.7 + - - -
352F VAL* 2.9 28.2 - - + +
354F VAL* 3.6 35.4 - - + -
370F ILE* 4.2 0.9 - - + -
381F ILE* 4.6 5.8 - - + -
384F LEU* 3.8 21.8 - - + -
388F LEU* 3.6 29.2 - - + -
411F ILE* 3.9 24.2 - - + -
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Residues in contact with LYS 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344F GLU 2.9 18.7 + - - +
345F ILE* 3.2 8.7 + - + +
347F LEU* 1.3 74.1 - - - +
349F GLU* 1.3 60.8 + - + +
350F PHE 3.1 0.9 + - - -
351F GLY* 3.4 18.7 + - - +
352F VAL 3.1 10.2 + - - +
353F GLU* 3.4 45.2 + - + +
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Residues in contact with GLU 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374E ALA* 3.6 33.0 - - + +
375E GLY* 3.6 13.4 + - - +
345F ILE* 2.9 33.8 + - + +
346F LYS* 3.0 41.4 + - - +
347F LEU 3.0 0.8 + - - -
348F LYS* 1.3 77.4 - - - +
350F PHE* 1.3 69.1 + - + +
351F GLY 3.4 0.6 + - - -
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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