Contacts of the helix formed by residues 332 - 349 (chain C) in PDB entry 6T8G
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330C SER* 3.7 3.8 + - - -
331C TYR* 1.3 78.1 + - - +
333C PRO* 1.4 68.2 - - - +
334C GLU* 2.9 14.4 + - - -
335C SER* 3.2 15.7 + - - -
336C LEU 3.5 4.3 + - - -
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Residues in contact with PRO 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C TYR 4.3 1.8 - - - +
332C SER* 1.4 82.9 - - - +
334C GLU* 1.3 59.5 + - - +
335C SER 3.5 0.2 - - - -
336C LEU* 3.7 20.9 - - + -
337C GLU* 2.9 30.1 + - - +
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Residues in contact with GLU 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C SER* 2.9 6.6 + - - +
333C PRO* 1.3 81.4 - - - +
335C SER* 1.3 63.6 + - - +
337C GLU* 3.7 5.9 - - - +
338C ALA* 3.0 27.1 + - + +
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Residues in contact with SER 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C TYR* 5.7 9.2 - - - -
332C SER 3.2 9.5 + - - -
334C GLU* 1.3 82.7 - - - +
336C LEU* 1.3 57.4 + - - +
338C ALA* 3.3 8.2 + - - +
339C MET* 2.9 32.8 + - - +
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Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C TYR* 4.6 14.1 - - + +
332C SER 3.5 4.2 + - - +
333C PRO* 3.7 24.0 - - + -
334C GLU 3.2 0.6 - - - -
335C SER* 1.3 76.7 - - - +
337C GLU* 1.3 59.8 + - - +
339C MET* 3.3 11.9 + - + +
340C SER* 2.9 31.2 + - - -
359C VAL* 3.7 44.9 - - + +
361C PRO* 4.6 19.5 - - + -
366C THR* 4.3 9.6 - - + -
368C PHE* 4.3 11.7 - - + -
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Residues in contact with GLU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C PRO 2.9 19.0 + - - +
334C GLU* 3.7 5.5 - - - +
336C LEU* 1.3 76.1 - - - +
338C ALA* 1.3 61.5 + - - +
340C SER* 3.3 6.9 + - - -
341C ARG* 3.0 61.1 + - - +
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Residues in contact with ALA 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C GLU* 3.0 15.8 + - + +
335C SER* 3.5 12.8 - - - +
337C GLU* 1.3 83.1 + - - +
339C MET* 1.3 57.5 + - - +
341C ARG* 3.4 4.5 + - - +
342C LEU* 2.9 31.1 + - + +
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Residues in contact with MET 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C TYR* 6.0 3.6 - - + -
335C SER* 2.9 19.3 + - - +
336C LEU* 3.3 13.0 + - + +
338C ALA* 1.3 75.9 - - - +
340C SER* 1.3 58.5 + - - +
342C LEU* 3.3 14.2 + - + +
343C LEU* 2.9 28.1 + - + +
366C THR* 5.4 4.5 - - - -
368C PHE* 3.8 30.1 - - + -
413C ILE* 4.3 22.7 - - + -
415C ASN* 4.7 19.7 - - - +
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Residues in contact with SER 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C LEU 2.9 17.4 + - - -
337C GLU* 3.6 9.1 - - - -
339C MET* 1.3 74.9 - - - +
341C ARG* 1.3 71.2 + - - +
343C LEU* 3.2 5.9 + - - +
344C GLU* 3.0 26.9 + - - +
356C VAL* 4.1 20.5 - - - +
359C VAL* 3.7 13.2 - - - +
368C PHE* 3.5 22.7 - - - -
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Residues in contact with ARG 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C GLU* 3.0 52.7 + - - +
338C ALA* 3.9 4.9 - - - +
340C SER* 1.3 83.8 + - - +
342C LEU* 1.3 57.6 + - - +
344C GLU* 2.7 33.2 + - - +
345C ILE* 3.0 35.6 + - + +
356C VAL* 4.1 30.1 + - - +
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Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C ALA* 2.9 19.5 + - + +
339C MET* 3.4 14.8 - - + +
340C SER 3.2 0.2 - - - -
341C ARG* 1.3 77.7 - - - +
343C LEU* 1.3 56.8 + - - +
345C ILE* 3.4 5.2 + - - +
346C LYS* 2.9 44.9 + - + +
391C SER 5.2 1.6 - - - +
392C LEU* 3.7 28.7 - - + -
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C MET* 2.9 17.1 + - + +
340C SER* 3.2 4.9 + - - +
342C LEU* 1.3 75.6 - - + +
344C GLU* 1.3 61.7 + - - +
346C LYS* 3.8 4.7 - - - +
347C LEU* 2.9 52.9 + - + +
354C VAL* 4.4 1.1 - - + -
356C VAL* 4.0 18.4 - - + -
368C PHE* 5.1 10.5 - - + -
370C ILE* 3.8 17.3 - - + -
388C LEU* 5.1 4.3 - - + -
392C LEU* 4.7 14.4 - - + -
411C ILE* 4.4 20.0 - - + -
413C ILE* 3.7 30.3 - - + -
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Residues in contact with GLU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340C SER 3.0 13.1 + - - +
341C ARG* 2.7 45.1 + - - +
343C LEU* 1.3 78.7 - - - +
345C ILE* 1.3 61.9 + - + +
348C LYS* 2.9 32.4 + - + +
354C VAL* 3.6 36.3 - - + +
355C SER* 5.4 1.0 - - - -
356C VAL* 4.4 9.0 - - + -
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Residues in contact with ILE 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C ARG* 3.0 24.1 + - + +
342C LEU* 3.8 5.8 - - - +
344C GLU* 1.3 81.2 - - + +
346C LYS* 1.3 55.5 + - + +
348C LYS* 2.8 13.2 + - + +
349C GLU* 2.7 56.8 + - + +
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Residues in contact with LYS 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B GLN* 5.9 2.8 - - - +
374B ALA* 5.7 2.2 - - - +
407B THR* 6.2 2.2 - - - +
342C LEU* 2.9 43.4 + - + +
343C LEU 4.2 1.6 - - - +
345C ILE* 1.3 74.1 - - + +
347C LEU* 1.3 60.4 + - - +
349C GLU* 3.3 35.7 + - - +
350C PHE* 3.2 27.9 - - - -
388C LEU* 4.3 8.9 - - + +
390C ARG* 5.1 3.0 - - - +
391C SER* 3.5 38.8 + - - +
392C LEU* 4.3 11.4 - - + -
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Residues in contact with LEU 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C LEU* 2.9 30.8 + - + +
346C LYS* 1.3 77.0 - - - +
348C LYS* 1.3 59.6 + - - +
349C GLU 3.1 1.8 - - - -
350C PHE* 2.9 31.1 + - + +
352C VAL* 3.3 27.9 - - + +
354C VAL* 3.8 16.8 - - + -
370C ILE* 3.7 29.2 - - + -
381C ILE* 4.6 9.0 - - + -
384C LEU* 4.1 20.2 - - + -
388C LEU* 3.8 32.3 - - + -
411C ILE* 4.9 4.9 - - + -
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Residues in contact with LYS 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C GLU* 2.9 22.3 + - + +
345C ILE* 2.8 14.7 + - + +
347C LEU* 1.3 72.4 - - - +
349C GLU* 1.3 60.7 + - - +
350C PHE 3.0 10.7 - - - +
352C VAL 3.5 15.8 + - - +
353C GLU* 4.3 30.6 + - + +
354C VAL* 4.5 2.9 - - + +
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Residues in contact with GLU 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B ALA* 3.4 34.5 - - + +
375B GLY* 3.6 16.8 + - - +
345C ILE* 2.7 33.0 + - + +
346C LYS* 3.3 50.9 + - - +
348C LYS* 1.3 74.5 - - - +
350C PHE* 1.3 64.0 + - + +
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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