Contacts of the helix formed by residues 336 - 353 (chain C) in PDB entry 3Q29
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 336 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLN* 4.8 16.3 + - - +
170C PHE* 3.7 18.4 - - + -
179C ILE* 3.1 42.3 - - + +
334C ILE* 3.3 28.9 - - + -
335C PRO* 1.3 94.2 - - - +
337C MET* 1.3 62.3 + - - +
338C SER 3.4 0.7 - - - -
339C ALA* 3.6 9.2 + - - +
340C PHE* 3.2 20.8 + - - +
369C SER 4.7 8.4 - - - +
374C VAL* 5.2 10.1 - - + -
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Residues in contact with MET 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASP* 3.9 17.3 - - + +
67C ARG* 5.7 1.1 - - + -
169C ALA* 5.0 1.6 - - - -
170C PHE* 3.5 21.3 - - + -
259C PHE* 6.0 0.7 - - - -
331C MET* 5.7 0.7 - - + -
332C PRO* 3.2 50.0 - - + +
334C ILE* 3.0 48.7 + - + +
335C PRO 3.0 0.4 - - - -
336C GLN* 1.3 77.3 - - - +
338C SER* 1.3 67.5 + - - +
340C PHE* 3.0 18.3 + - - +
341C TRP* 2.9 47.7 + - + +
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Residues in contact with SER 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ARG* 3.3 36.5 + - - +
70C GLY* 6.3 1.8 - - - -
335C PRO 3.5 11.5 + - - -
336C GLN 3.4 0.4 - - - -
337C MET* 1.3 79.5 - - - +
339C ALA* 1.3 57.1 + - - +
341C TRP* 3.9 2.9 + - - +
342C TYR* 3.5 20.8 + - - +
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Residues in contact with ALA 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C PRO 4.7 0.6 + - - -
336C GLN* 3.6 10.8 + - - +
337C MET 3.1 0.4 - - - -
338C SER* 1.3 76.8 - - - +
340C PHE* 1.3 61.6 + - - +
341C TRP 3.4 0.2 - - - -
342C TYR* 3.6 6.4 + - - +
343C ALA* 3.0 30.1 + - - +
368C ASN 4.0 18.5 - - - +
369C SER* 4.7 1.6 - - - -
374C VAL* 4.5 16.8 - - + -
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Residues in contact with PHE 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C TRP* 3.7 22.7 - + - -
169C ALA* 3.4 31.2 - - + -
170C PHE* 4.1 16.4 - + + -
182C VAL* 5.0 1.6 - - + -
184C VAL* 3.5 28.3 - - + -
259C PHE* 4.0 9.6 - + - -
336C GLN 3.2 15.8 + - - +
337C MET* 3.2 22.4 - - - +
339C ALA* 1.3 76.6 - - - +
341C TRP* 1.3 91.6 + + - +
343C ALA* 3.1 3.1 + - - +
344C VAL* 2.9 42.7 + - + +
369C SER* 3.9 19.2 - - - -
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Residues in contact with TRP 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASP* 2.8 25.9 + - - -
67C ARG* 3.9 21.1 - - + +
155C PRO* 3.7 22.0 - - + +
156C TYR* 4.2 11.7 - + - -
159C TRP* 5.2 3.1 - + + -
259C PHE* 3.1 36.3 - + + -
331C MET* 3.6 24.9 - - + -
337C MET* 2.9 35.3 + - + +
338C SER 4.1 0.9 - - - +
340C PHE* 1.3 96.7 - + - +
342C TYR* 1.3 53.9 + - - +
344C VAL* 3.1 3.9 + - + +
345C ARG* 2.7 37.5 + - - +
2D GLC 3.6 46.4 - - - +
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Residues in contact with TYR 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU* 5.7 4.9 - - - -
67C ARG* 5.5 0.2 - - - +
338C SER 3.5 15.0 + - - +
339C ALA* 4.0 7.0 - - - +
340C PHE 3.4 0.2 - - - -
341C TRP* 1.3 78.1 - - - +
343C ALA* 1.3 64.6 + - - +
345C ARG* 3.7 15.4 - - - +
346C THR* 3.1 47.9 + - + -
368C ASN* 5.9 6.7 - - + -
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Residues in contact with ALA 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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339C ALA 3.0 20.0 + - - +
340C PHE 3.3 4.9 - - - +
341C TRP 3.1 0.2 - - - -
342C TYR* 1.3 82.1 - - - +
344C VAL* 1.3 62.8 + - + +
346C THR* 3.4 6.7 + - - -
347C ALA* 3.1 21.7 + - - +
365C ALA* 3.5 31.5 - - - +
368C ASN* 4.1 18.6 - - + +
369C SER* 4.2 5.8 - - - -
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Residues in contact with VAL 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C PRO* 3.6 20.4 - - + -
159C TRP* 4.5 19.1 - - + -
162C ILE* 4.9 4.5 - - + -
184C VAL* 4.4 14.4 - - + -
340C PHE* 2.9 49.7 + - + +
341C TRP* 3.9 3.6 - - + +
343C ALA* 1.3 74.9 - - + +
345C ARG* 1.3 67.2 + - - +
347C ALA* 3.6 7.3 - - + +
348C VAL* 2.9 34.1 + - + +
362C LEU* 5.9 4.5 - - + -
365C ALA* 4.8 4.5 - - + +
369C SER* 6.0 0.4 - - - +
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Residues in contact with ARG 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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1C SO4 5.0 2.2 + - - -
153C GLN* 2.6 44.1 + - - +
154C GLU* 3.2 24.1 + - - -
155C PRO* 3.7 22.1 - - + +
341C TRP 2.7 23.6 + - - +
342C TYR* 3.7 16.5 - - + +
344C VAL* 1.3 72.9 - - - +
346C THR* 1.3 63.8 + - - +
348C VAL* 3.5 1.9 + - - +
349C ILE* 3.1 43.0 + - + +
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Residues in contact with THR 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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342C TYR* 3.1 38.6 + - + -
343C ALA* 3.7 5.2 - - - -
345C ARG* 1.3 81.6 - - - +
347C ALA* 1.3 59.2 + - - +
349C ILE* 4.1 3.9 - - - +
350C ASN* 3.0 48.5 + - - +
356C GLN* 5.2 1.1 - - - +
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Residues in contact with ALA 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LEU* 4.9 1.8 - - - -
343C ALA 3.1 13.9 + - - +
344C VAL* 3.2 8.3 + - - +
346C THR* 1.3 75.8 - - - +
348C VAL* 1.3 66.8 + - + +
350C ASN* 3.2 0.8 + - - -
351C ALA* 2.9 27.3 + - - +
356C GLN* 5.2 0.7 - - - -
361C ALA* 3.4 37.8 - - + +
362C LEU* 4.1 12.3 - - + -
365C ALA* 3.8 10.3 - - + -
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Residues in contact with VAL 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU* 4.2 16.4 - - + +
155C PRO* 4.4 12.3 - - + -
158C THR* 3.8 23.1 - - + +
162C ILE* 4.1 20.9 - - + -
193C LEU* 4.5 11.2 - - + +
196C LEU* 4.1 17.3 - - + -
344C VAL* 2.9 38.2 + - + +
345C ARG* 4.0 4.0 - - - +
347C ALA* 1.3 72.4 - - + +
349C ILE* 1.3 59.5 + - + +
351C ALA* 3.9 1.0 - - - +
352C ALA* 2.9 34.1 + - + +
362C LEU* 6.3 0.4 - - + -
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Residues in contact with ILE 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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152C LEU 4.2 12.6 - - - +
153C GLN* 3.7 41.5 - - - +
207C ALA* 5.7 0.2 - - - +
345C ARG* 3.1 40.8 + - + +
346C THR* 4.1 4.5 - - - +
348C VAL* 1.3 77.8 - - + +
350C ASN* 1.3 64.5 + - - +
352C ALA* 3.7 6.1 - - - +
353C SER* 2.9 33.7 + - - +
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Residues in contact with ASN 350 (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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346C THR* 3.0 39.0 + - - +
347C ALA* 3.8 2.9 - - - +
349C ILE* 1.3 82.1 - - - +
351C ALA* 1.3 60.3 - - - +
353C SER* 3.7 4.1 + - - -
354C GLY 3.0 21.3 + - - -
355C ARG* 3.0 47.8 + - - +
356C GLN* 2.9 44.7 + - + +
361C ALA* 4.6 0.4 - - + -
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Residues in contact with ALA 351 (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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193C LEU* 4.2 18.4 - - + -
197C VAL* 3.7 34.7 - - + +
347C ALA 2.9 17.2 + - - +
348C VAL 3.9 2.5 - - - +
350C ASN* 1.3 76.4 - - - +
352C ALA* 1.3 64.5 + - - +
354C GLY* 3.0 13.9 + - - -
356C GLN 3.4 14.2 - - - +
358C VAL* 4.4 8.5 - - + -
361C ALA* 4.4 8.2 - - + +
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Residues in contact with ALA 352 (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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152C LEU* 5.7 5.2 - - + +
196C LEU* 5.3 3.1 - - + -
197C VAL* 4.2 8.3 - - - +
200C ILE* 3.6 38.5 - - + +
207C ALA* 3.6 24.4 - - + +
348C VAL* 2.9 23.9 + - + +
349C ILE* 3.7 6.5 - - - +
351C ALA* 1.3 78.3 - - - +
353C SER* 1.3 59.0 + - - +
354C GLY* 3.5 0.3 + - - -
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Residues in contact with SER 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ALA* 4.2 11.6 - - - +
208C ASP* 6.2 0.4 - - - -
349C ILE* 2.9 22.5 + - - +
350C ASN* 3.4 11.3 + - - -
352C ALA* 1.3 76.5 - - - +
354C GLY* 1.3 59.1 + - - +
355C ARG* 3.2 17.9 + - - +
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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
------------------------------------------------------------
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