Contacts of the helix formed by residues 316 - 330 (chain C) in PDB entry 1Q57
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 MET 316 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314C SER 3.0 4.5 + - - +
315C GLY* 1.3 69.2 - - - -
317C VAL* 1.3 77.1 + - - +
318C MET 2.8 4.7 - - - -
319C SER* 2.8 13.8 + - - +
320C THR* 2.7 59.7 + - - +
504C ARG* 5.4 5.4 - - - -
535C TYR* 3.0 53.8 - - + +
522D ARG* 5.0 17.7 - - + +
524D THR 4.9 11.0 - - - +
525D GLY* 5.2 11.9 - - - +
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Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C SER* 5.3 2.2 - - - +
315C GLY* 3.5 18.2 - - - +
316C MET* 1.3 95.4 - - + +
318C MET* 1.3 56.7 + - - +
320C THR* 4.2 3.8 - - - -
321C PHE* 3.0 28.8 + - - +
502C LEU* 4.3 7.5 - - + +
504C ARG* 3.5 39.0 - - + +
514C VAL* 4.0 38.8 - - + -
535C TYR* 6.0 1.8 - - + -
542C LEU* 3.4 19.9 - - + +
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Residues in contact with MET 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C VAL* 3.7 27.1 - - + +
311C THR* 3.8 0.4 - - - -
312C SER* 3.0 47.7 + - - +
313C GLY 3.8 4.0 - - - +
315C GLY 3.4 10.4 - - - +
316C MET 2.8 1.2 - - - -
317C VAL* 1.3 80.5 - - - +
319C SER* 1.3 61.6 + - - +
321C PHE* 3.3 2.7 + - - +
322C VAL* 3.2 19.6 + - - +
463C ILE* 3.4 35.2 - - + +
464C CYS 3.7 2.9 - - - +
465C HIS* 3.3 33.4 - - + +
502C LEU* 3.9 13.0 - - + +
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Residues in contact with SER 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C GLY 4.1 1.7 + - - -
316C MET* 2.8 20.8 + - - +
318C MET* 1.3 75.8 - - - +
320C THR* 1.3 56.9 + - - -
322C VAL* 4.1 2.4 - - - +
323C ARG* 3.0 50.2 + - - +
344C GLU* 5.3 1.0 + - - -
424C ASP* 2.6 31.3 + - - -
463C ILE* 4.3 2.8 - - - +
465C HIS* 5.8 3.8 + - - -
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Residues in contact with THR 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C MET* 2.7 43.8 + - - +
317C VAL 3.7 4.5 - - - -
319C SER* 1.3 70.0 - - - +
321C PHE* 1.3 59.5 + - - +
322C VAL 3.1 1.6 - - - -
323C ARG* 2.9 7.6 + - - +
324C GLN* 2.6 53.9 + - - +
356C LEU* 4.8 8.3 - - + -
535C TYR* 4.6 2.2 - - + -
540C GLY 3.5 22.7 - - - +
542C LEU* 3.9 11.0 - - + +
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Residues in contact with PHE 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C PHE* 4.4 15.3 - + - -
290C SER 4.2 10.1 - - - -
295C ILE* 4.6 20.4 - - + -
310C VAL* 4.2 20.6 - - + -
317C VAL 3.0 15.9 + - - +
318C MET* 3.6 4.3 - - - +
320C THR* 1.3 81.9 - - - +
322C VAL* 1.3 65.0 + - - +
324C GLN* 3.2 5.6 + - + +
325C GLN* 2.8 56.1 + - + +
500C ILE* 4.6 15.3 - - + -
502C LEU* 3.6 19.5 - - + -
516C VAL* 5.6 0.4 - - + -
533C MET* 3.0 37.7 - - + -
542C LEU* 3.9 9.0 - - + -
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Residues in contact with VAL 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C VAL* 3.8 21.1 - - + -
318C MET 3.2 5.4 + - - +
319C SER* 4.4 4.5 - - - +
320C THR 3.1 0.6 - - - -
321C PHE* 1.3 80.9 - - + +
323C ARG* 1.3 59.6 + - - +
325C GLN* 3.4 6.4 + - + +
326C ALA* 3.0 26.9 + - - +
341C MET* 5.5 3.1 - - - -
422C ILE* 3.0 39.9 - - + +
424C ASP* 5.2 3.8 - - - +
461C VAL* 4.8 7.2 - - + -
463C ILE* 3.2 39.3 - - + -
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Residues in contact with ARG 323 (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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319C SER* 3.0 41.7 + - - +
320C THR* 2.9 11.8 + - - +
322C VAL* 1.3 80.3 - - - +
324C GLN* 1.3 67.1 + - - +
326C ALA* 3.4 7.4 - - + +
327C LEU* 2.9 24.1 + - - +
339C LEU* 6.4 1.8 - - + -
341C MET* 2.9 37.6 - - - +
344C GLU* 2.7 34.3 + - - -
349C THR* 4.6 3.4 - - - -
352C ASP* 4.4 25.0 + - + +
353C LEU* 4.1 21.5 - - + +
356C LEU* 4.0 15.7 - - + -
424C ASP* 3.4 5.1 + - - -
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Residues in contact with GLN 324 (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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290C SER* 4.9 15.3 - - - +
291C GLY* 5.1 1.4 - - - -
320C THR* 2.6 33.5 + - - +
321C PHE* 3.3 10.5 - - + +
323C ARG* 1.3 70.6 - - - +
325C GLN* 1.3 62.8 + - - +
327C LEU* 2.9 30.7 + - - +
328C GLN* 3.3 10.0 + - + +
356C LEU* 4.1 7.7 - - + +
541C TRP* 2.9 45.0 - - + +
542C LEU* 2.7 49.9 + - - +
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Residues in contact with GLN 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C PHE* 3.1 21.7 - - + +
290C SER* 2.2 54.2 + - - +
321C PHE* 2.8 41.3 + - + +
322C VAL* 3.5 11.7 - - + +
323C ARG 3.2 0.2 - - - -
324C GLN* 1.3 76.4 - - - +
326C ALA* 1.3 65.5 + - - +
328C GLN* 4.6 0.6 - - - +
329C TRP* 3.0 70.6 + - + +
422C ILE* 5.2 0.9 - - + -
461C VAL* 6.3 2.0 - - + -
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Residues in contact with ALA 326 (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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322C VAL 3.0 11.3 + - - +
323C ARG* 3.4 13.5 - - - +
325C GLN* 1.3 77.2 - - - +
327C LEU* 1.4 67.2 + - - +
329C TRP* 4.2 0.9 - - - -
330C GLY 3.1 13.5 + - - -
337C VAL* 3.4 12.5 - - + +
339C LEU* 3.9 20.2 - - + -
353C LEU* 4.9 3.8 - - + -
391C PHE* 3.2 15.1 - - + -
422C ILE* 3.5 22.4 - - + +
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Residues in contact with LEU 327 (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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323C ARG 2.9 16.2 + - - +
324C GLN* 2.9 15.8 + - - +
326C ALA* 1.4 78.8 - - - +
328C GLN* 1.3 71.5 + - + +
330C GLY 2.9 6.8 + - - -
331C THR* 3.1 10.5 + - + +
353C LEU* 4.1 18.6 - - + +
356C LEU* 4.1 5.4 - - + +
357C HIS* 3.6 43.3 - - + +
385C LEU* 3.7 30.7 - - + -
391C PHE* 3.4 11.8 - - + -
541C TRP* 3.9 22.9 - - + -
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Residues in contact with GLN 328 (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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290C SER* 4.7 22.0 - - - +
324C GLN* 3.3 9.9 + - + +
325C GLN 4.6 1.1 - - - +
327C LEU* 1.3 83.6 - - - +
329C TRP* 1.4 56.3 + - + +
331C THR* 2.7 18.1 + - - -
332C ALA* 2.6 44.6 + - + +
333C MET* 3.3 4.9 + - + -
357C HIS* 5.5 2.5 - - - -
359C ARG* 3.6 15.8 - - - +
541C TRP* 3.5 32.6 - - + -
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Residues in contact with TRP 329 (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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287C LEU* 3.4 38.7 - - + +
288C LEU 3.6 21.6 + - - +
289C PHE* 4.1 21.8 - + - -
290C SER* 5.9 2.2 - - - -
302C ALA* 4.4 16.6 - - + -
308C ILE* 5.9 0.2 - - + -
325C GLN* 3.0 59.5 + - + +
326C ALA* 3.9 7.0 - - - +
327C LEU 2.9 2.6 + - - -
328C GLN* 1.4 73.0 - - + +
330C GLY* 1.3 58.1 + - - +
331C THR 3.2 0.2 - - - -
333C MET* 2.8 41.7 - - + +
335C LYS* 3.3 13.2 + - + +
337C VAL* 4.1 6.7 - - + -
420C VAL* 3.6 40.6 - - + -
422C ILE* 4.8 1.3 - - + -
459C VAL* 5.0 0.4 - - + -
461C VAL* 3.9 16.6 - - + -
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Residues in contact with GLY 330 (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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326C ALA 3.1 3.4 + - - -
327C LEU 2.9 7.6 + - - -
329C TRP* 1.3 77.0 - - - +
331C THR* 1.3 71.5 + - - +
333C MET 3.6 3.4 - - - -
334C GLY 5.2 0.4 - - - -
335C LYS 3.1 16.4 - - - -
337C VAL* 3.9 3.3 - - - +
390C THR* 3.2 24.4 + - - +
391C PHE* 3.4 17.2 - - - -
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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