Contacts of the helix formed by residues 355 - 367 (chain C) in PDB entry 1C2O
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 355 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353C LEU 4.0 0.4 + - - -
354C ILE* 1.3 81.1 - - - +
356C ARG* 1.3 66.1 + - - +
357C ALA* 2.9 10.0 + - - +
358C GLN* 2.8 38.3 + - - +
359C PHE* 3.2 15.6 + - - +
389C GLU 5.8 0.7 - - - -
394C LEU* 3.7 3.3 - - - +
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Residues in contact with ARG 356 (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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355C SER* 1.3 72.4 + - - +
357C ALA* 1.3 52.1 + - - +
359C PHE* 2.7 10.7 + - + +
360C LEU* 2.7 55.1 + - + +
379C VAL* 3.4 18.4 - - - +
383C THR* 2.8 43.7 + - - +
385C TRP* 4.1 11.8 - - - -
388C PRO* 2.6 52.0 + - - +
389C GLU* 4.2 25.5 + - - +
394C LEU* 3.7 26.5 - - + +
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Residues in contact with ALA 357 (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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355C SER* 2.9 5.9 + - - +
356C ARG* 1.3 77.9 - - - +
358C GLN* 1.3 62.9 + - + +
360C LEU* 3.2 16.0 + - + +
361C ALA* 3.0 22.7 + - - +
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Residues in contact with GLN 358 (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 VAL* 5.2 1.9 - - - +
344C PRO* 4.0 20.3 + - + +
345C GLY* 3.6 26.8 - - - +
346C PHE* 5.9 0.2 - - + -
353C LEU 4.7 0.2 - - - +
354C ILE* 3.1 19.1 - - + +
355C SER* 2.8 46.4 + - - +
357C ALA* 1.3 76.5 - - + +
359C PHE* 1.3 53.3 + - - +
361C ALA* 2.8 10.1 + - - +
362C GLY* 2.7 33.7 + - - -
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Residues in contact with PHE 359 (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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354C ILE* 3.3 20.3 - - + +
355C SER 3.2 2.7 + - - +
356C ARG* 2.7 15.9 + - - +
358C GLN* 1.3 75.9 - - - +
360C LEU* 1.3 71.1 + - + -
363C VAL* 3.0 23.6 + - + +
378C VAL 5.3 0.2 - - - -
379C VAL* 3.8 27.4 - - + -
382C TYR* 4.2 24.0 - - + -
383C THR* 4.5 4.5 - - - -
394C LEU* 3.5 41.3 - - + -
397C ALA* 3.5 25.4 - - + -
398C MET* 2.9 48.3 - - + +
401C VAL* 4.7 1.8 - - + -
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Residues in contact with LEU 360 (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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356C ARG* 2.7 60.6 + - + +
357C ALA* 3.5 12.8 - - + +
358C GLN 3.2 0.2 - - - -
359C PHE* 1.3 79.1 - - + +
361C ALA* 1.3 61.8 + - - +
363C VAL* 3.6 9.9 + - - +
364C ARG* 3.4 19.1 - - - +
379C VAL* 3.7 38.8 - - + +
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Residues in contact with ALA 361 (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 PRO* 5.6 9.0 - - + -
357C ALA 3.0 11.8 + - - +
358C GLN* 2.8 14.2 + - - +
360C LEU* 1.3 70.9 - - - +
362C GLY* 1.3 70.5 + - - +
363C VAL 3.1 0.2 - - - -
364C ARG* 2.8 20.2 + - - +
365C ILE* 3.1 18.5 + - + +
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Residues in contact with GLY 362 (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 VAL* 3.8 20.5 - - - +
344C PRO* 6.1 0.2 - - - +
358C GLN 2.7 17.1 + - - -
359C PHE 3.2 0.2 + - - -
361C ALA* 1.3 73.0 - - - +
363C VAL* 1.3 63.8 + - - +
365C ILE* 2.7 19.5 + - - +
366C GLY* 2.7 13.5 + - - -
398C MET* 3.4 24.9 - - - -
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Residues in contact with VAL 363 (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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359C PHE* 3.0 28.1 + - + +
360C LEU 3.7 9.4 - - - +
361C ALA 3.1 0.2 - - - -
362C GLY* 1.3 74.8 - - - +
364C ARG* 1.3 58.4 + - - +
366C GLY* 4.7 0.7 - - - +
367C VAL* 3.0 36.6 + - + +
370C ALA* 5.7 0.2 - - - +
375C ALA* 4.2 23.1 - - + +
378C VAL* 4.1 33.7 - - + -
379C VAL* 4.2 10.5 - - + -
398C MET* 3.0 26.0 - - + +
401C VAL* 4.5 7.0 - - + -
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Residues in contact with ARG 364 (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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292C GLU 4.5 1.4 - - - +
360C LEU 3.4 17.3 - - - +
361C ALA* 2.8 16.5 + - - +
363C VAL* 1.3 72.8 - - - +
365C ILE* 1.3 63.1 + - + +
367C VAL 3.6 3.9 + - - +
368C PRO* 3.3 23.0 - - - +
370C ALA* 3.0 27.5 + - - +
371C SER* 3.5 8.9 + - - +
372C ASP* 2.9 28.5 + - - +
375C ALA* 3.4 30.0 - - - +
379C VAL* 6.4 0.4 - - - -
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Residues in contact with ILE 365 (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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292C GLU* 3.7 36.3 - - + +
293C SER* 3.4 25.4 - - - +
294C ILE* 3.4 26.3 + - + -
342C GLY 3.3 22.7 - - - +
343C VAL* 3.9 13.0 - - + -
344C PRO* 3.7 18.2 - - + -
361C ALA* 3.1 15.9 + - + +
362C GLY* 2.7 13.8 + - - +
364C ARG* 1.3 73.9 - - - +
366C GLY* 1.3 57.3 + - - +
368C PRO* 2.9 20.4 - - - +
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Residues in contact with GLY 366 (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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294C ILE* 3.8 23.1 - - - +
296C ARG* 4.1 5.2 + - - -
362C GLY 2.7 13.8 + - - -
363C VAL* 4.0 1.1 - - - -
365C ILE* 1.3 79.5 - - - +
367C VAL* 1.3 62.1 + - - +
368C PRO* 3.3 5.4 - - - +
398C MET* 5.8 0.9 - - - -
401C VAL* 5.4 2.0 - - - -
402C VAL* 4.4 14.3 - - - +
405C HIS* 3.9 13.7 - - - +
406C ASN* 4.8 4.9 + - - -
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Residues in contact with VAL 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C VAL* 3.0 26.0 + - + +
364C ARG* 3.6 8.3 + - - +
366C GLY* 1.3 79.4 - - - +
368C PRO* 1.3 62.2 - - - +
369C GLN* 3.1 18.4 - - + +
370C ALA* 2.9 43.6 + - + +
378C VAL* 4.7 6.1 - - + -
401C VAL* 3.7 27.6 - - + -
405C HIS* 4.3 9.9 - - + +
532C TRP* 4.2 18.6 - - + -
536C LEU* 5.1 4.7 - - + -
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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