Contacts of the helix formed by residues 329 - 348 (chain C) in PDB entry 6B0Z
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 PRO 329 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 3.7 30.3 - - + -
327C THR 3.3 8.7 - - - +
328C ASN* 1.3 91.8 - - - +
330C ILE* 1.3 58.9 + - - +
331C ALA 3.3 2.2 - - - -
332C SER* 3.0 8.2 + - - -
333C ILE* 2.9 36.1 + - + +
373C THR* 4.3 0.7 - - + -
394C THR* 5.7 2.0 - - + +
397C PHE* 3.6 34.8 - - + -
398C MET* 3.8 25.8 - - + -
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Residues in contact with ILE 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ILE* 3.6 25.8 - - + -
290C MET* 3.7 22.0 - - + -
328C ASN* 2.9 19.5 + - - +
329C PRO* 1.3 76.3 - - - +
331C ALA* 1.3 58.6 + - - +
333C ILE* 3.1 10.8 + - + +
334C PHE* 2.8 41.5 + - + -
363C SER* 3.6 29.8 - - - +
367C ILE* 3.9 24.7 - - + -
397C PHE* 4.1 20.6 - - + -
401C LEU* 4.6 0.9 - - + -
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ILE* 4.5 9.6 - - - -
289C GLY 3.1 22.4 + - - +
291C MET 3.3 27.6 - - - +
292C THR* 3.7 8.9 + - - -
307C ALA* 3.7 10.1 - - + +
309C HIS* 3.6 23.6 - - + +
328C ASN 4.9 0.2 + - - -
329C PRO 3.3 0.6 - - - -
330C ILE* 1.3 76.1 - - - +
332C SER* 1.3 62.2 + - - +
334C PHE* 3.5 0.6 + - - -
335C ALA* 3.1 18.2 + - - +
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Residues in contact with SER 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C THR* 4.6 8.2 + - - +
22C ILE* 4.2 13.1 - - - +
23C TRP* 4.5 15.2 - - - -
26C ILE* 3.6 19.1 - - - -
307C ALA* 4.2 7.7 - - - +
309C HIS* 4.0 19.1 + - - -
329C PRO* 3.0 11.1 + - - +
331C ALA* 1.3 77.0 - - - +
333C ILE* 1.3 65.3 + - - +
335C ALA* 3.2 15.2 + - - +
336C TRP* 3.3 17.8 - - - -
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Residues in contact with ILE 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ILE* 3.8 22.2 - - + -
30C LEU* 3.7 14.4 - - + -
329C PRO* 2.9 28.2 + - + +
330C ILE* 3.5 13.5 - - + +
332C SER* 1.3 76.6 - - - +
334C PHE* 1.3 61.4 + - + +
336C TRP* 3.0 12.3 + - - +
337C THR* 2.9 26.7 + - + +
359C LEU* 3.8 31.6 - - + -
363C SER* 3.9 13.2 - - - +
398C MET* 4.6 1.8 - - - -
401C LEU* 3.7 30.7 - - + -
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Residues in contact with PHE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ILE* 3.5 40.2 - - + -
292C THR* 4.0 14.1 + - - +
330C ILE* 2.8 38.6 + - + +
331C ALA 4.0 0.9 - - - +
333C ILE* 1.3 80.1 - - + +
335C ALA* 1.3 63.8 + - - +
337C THR* 3.2 6.7 - - - -
338C ARG* 3.0 59.5 + - - +
360C GLU* 3.4 49.4 - - + -
363C SER* 4.0 18.8 - - - -
364C ILE* 4.3 6.7 - - + -
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Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TRP* 4.7 13.7 - - + -
71C VAL* 3.4 7.0 - - + +
292C THR* 3.9 3.3 + - - -
305C ALA* 3.3 22.0 - - - +
306C GLU* 3.5 35.2 - - - +
307C ALA 4.0 1.8 - - - +
331C ALA 3.1 8.2 + - - +
332C SER* 3.3 12.8 - - - +
334C PHE* 1.3 77.6 - - - +
336C TRP* 1.3 59.9 + - - +
339C GLY 3.1 16.8 + - - -
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Residues in contact with TRP 336 (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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10C VAL* 5.1 2.7 - - + -
12C GLU* 4.1 9.2 - - + -
23C TRP* 3.4 46.0 - + - -
26C ILE* 3.7 23.4 - - + +
27C LYS* 3.5 38.6 - - + +
31C ILE* 4.3 31.9 - - + -
32C PHE* 5.7 1.1 - + - -
37C LEU* 4.2 23.1 - - + -
39C LEU* 4.8 8.5 - - + -
71C VAL* 4.0 24.3 - - + +
332C SER 3.3 23.3 + - - -
333C ILE* 3.0 8.5 + - - +
335C ALA* 1.3 77.5 - - - +
337C THR* 1.3 59.8 + - + +
339C GLY* 3.0 3.5 + - - -
340C LEU* 2.8 42.1 + - + +
359C LEU* 5.6 0.4 - - + -
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Residues in contact with THR 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 ILE* 2.9 16.0 + - + +
334C PHE* 3.2 16.3 + - - -
336C TRP* 1.3 74.2 - - + +
338C ARG* 1.3 59.3 + - - +
340C LEU* 4.4 4.0 - - + -
341C ALA* 2.7 31.7 + - - +
355C PHE* 6.1 0.2 - - + -
356C ALA* 3.5 24.1 - - - +
359C LEU* 3.8 35.4 - - + -
360C GLU* 2.7 37.8 + - + +
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Residues in contact with ARG 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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110C GLU* 3.4 35.4 + - - +
112C ILE* 4.9 3.2 - - - +
203C LYS* 4.6 6.9 - - - +
292C THR* 3.3 32.4 - - + +
294C VAL* 5.4 14.1 - - + -
303C VAL* 5.2 1.3 - - - +
305C ALA* 4.3 11.2 - - + -
334C PHE* 3.0 43.3 + - - +
335C ALA 4.1 2.0 - - - +
337C THR* 1.3 81.9 + - - +
339C GLY* 1.3 62.4 + - - +
341C ALA* 3.9 6.1 - - + +
342C HIS* 3.1 22.9 + - - +
360C GLU* 2.9 31.7 + - - -
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Residues in contact with GLY 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C VAL* 3.4 27.5 - - - +
70C GLY 5.2 0.4 - - - -
71C VAL* 4.1 9.4 - - - -
303C VAL* 5.1 3.8 - - - -
305C ALA* 4.2 5.9 - - - +
335C ALA 3.1 11.8 + - - -
336C TRP 3.0 6.7 + - - -
338C ARG* 1.3 74.8 - - - +
340C LEU* 1.3 60.4 + - - +
342C HIS* 3.2 4.5 + - - +
343C ARG* 2.8 24.1 + - - +
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Residues in contact with LEU 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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10C VAL* 4.2 14.1 - - + -
31C ILE* 4.7 18.2 - - + -
35C VAL* 5.2 1.8 - - + -
37C LEU* 3.9 31.4 - - + -
71C VAL* 6.1 0.7 - - + -
336C TRP* 2.8 36.9 + - + +
337C THR* 3.8 6.5 - - + +
339C GLY* 1.3 68.8 - - - +
341C ALA* 1.3 61.1 + - - +
343C ARG* 3.1 5.4 + - - +
344C ALA* 2.8 32.3 + - - +
352C LEU* 3.8 21.5 - - + +
355C PHE* 4.1 30.7 - - + -
356C ALA* 4.1 9.4 - - + -
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Residues in contact with ALA 341 (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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337C THR 2.7 21.9 + - - +
338C ARG* 3.9 8.1 - - + +
340C LEU* 1.3 73.0 - - - +
342C HIS* 1.3 57.7 + - - +
344C ALA* 3.4 6.1 + - - +
345C LYS* 3.0 27.2 + - - +
353C ALA* 5.2 5.4 - - + +
356C ALA* 3.9 14.0 - - + +
357C ASN* 5.9 3.1 - - - +
360C GLU* 5.5 2.7 - - - +
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Residues in contact with HIS 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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68C ASN 3.9 0.2 - - - -
69C VAL* 3.5 20.4 - - + -
300C GLY 4.4 5.4 - - - -
301C LYS* 2.3 37.5 + - - -
303C VAL* 3.3 42.4 - - + +
338C ARG 3.1 17.6 + - - +
339C GLY 3.6 3.6 - - - +
340C LEU 3.2 0.2 - - - -
341C ALA* 1.3 74.8 - - - +
343C ARG* 1.3 63.9 + - - +
345C LYS* 3.2 33.9 + - - +
346C LEU* 3.1 44.1 + - + +
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Residues in contact with ARG 343 (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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7C GLY 3.3 21.8 - - - +
9C SER* 2.5 59.2 + - - +
10C VAL* 4.1 9.4 - - + -
67C HIS 3.0 24.2 + - - -
68C ASN* 4.9 2.6 - - - +
69C VAL* 3.9 18.1 - - + +
339C GLY 2.8 13.3 + - - +
340C LEU* 3.1 12.5 + - - +
342C HIS* 1.3 77.6 - - - +
344C ALA* 1.3 61.0 - - - +
346C LEU* 3.4 26.4 + - - +
347C ASP* 3.1 57.2 + - - +
352C LEU* 3.9 4.0 - - + -
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Residues in contact with ALA 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C LEU 2.8 19.2 + - - +
341C ALA 3.8 3.4 - - - +
343C ARG* 1.3 71.7 - - - +
345C LYS* 1.3 61.3 + - - +
348C ASN* 2.8 27.5 + - - -
349C ASN* 3.0 25.4 + - - +
352C LEU* 3.9 7.6 - - + -
353C ALA* 3.3 41.1 - - + +
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Residues in contact with LYS 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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202C SER* 3.9 27.2 + - - +
300C GLY 5.9 0.4 - - - -
341C ALA 3.0 13.5 + - - +
342C HIS* 3.2 42.8 + - - +
344C ALA* 1.3 78.5 - - - +
346C LEU* 1.3 66.5 + - + +
348C ASN* 3.6 13.0 + - - +
353C ALA* 5.6 0.4 - - - +
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Residues in contact with LEU 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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68C ASN* 4.1 16.8 - - + +
69C VAL* 4.4 0.2 - - + -
300C GLY 5.1 2.2 - - - +
301C LYS* 3.8 22.2 - - + +
342C HIS* 3.1 49.6 + - + +
343C ARG* 3.4 33.7 - - - +
345C LYS* 1.3 83.2 - - + +
347C ASP* 1.3 60.1 + - - +
348C ASN* 3.4 14.0 + - - -
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Residues in contact with ASP 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLY 4.3 5.7 - - - +
8C GLY* 4.6 5.2 - - - -
9C SER 5.1 0.3 + - - -
343C ARG* 3.1 55.8 + - - +
345C LYS 3.3 0.2 - - - -
346C LEU* 1.3 78.8 - - - +
348C ASN* 1.3 74.2 + - - +
349C ASN* 3.2 16.5 + - + +
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Residues in contact with ASN 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 ALA 2.8 9.5 + - - -
345C LYS 3.6 7.9 + - - +
346C LEU 3.4 16.5 + - - -
347C ASP* 1.3 78.1 + - - +
349C ASN* 1.3 57.9 - - - +
350C LYS* 3.3 13.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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