Contacts of the helix formed by residues 407 - 421 (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 VAL 407 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C SER* 3.3 34.1 - - - +
230C GLY* 4.0 3.6 - - - +
231C THR* 5.0 0.2 - - - +
236C TRP* 5.0 1.1 - - + +
295C PHE* 3.7 31.2 - - + -
330C VAL* 4.2 0.4 - - + -
334C GLU* 3.2 47.6 - - + +
403C GLY* 3.0 7.5 + - - +
405C HIS 3.8 0.2 - - - -
406C ASN* 1.3 82.2 - - + +
408C VAL* 1.3 59.0 + - - +
410C PRO* 3.0 5.4 - - - +
411C VAL* 2.9 36.9 + - + +
447C HIS* 4.3 2.0 - - - +
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Residues in contact with VAL 408 (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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330C VAL* 3.7 30.7 - - + -
331C VAL 5.1 1.3 - - - +
332C LYS 6.0 0.2 - - - +
334C GLU* 4.1 9.2 - - + -
403C GLY 3.0 18.7 + - - +
404C ASP* 4.1 16.6 - - + +
407C VAL* 1.3 69.4 - - - +
409C CYS* 1.3 64.9 + - - +
411C VAL* 2.8 6.1 + - - +
412C ALA* 2.8 19.4 + - - +
524C LEU* 4.0 29.8 - - + -
525C ARG* 4.2 26.9 - - + +
529C CYS* 4.3 5.6 - - - -
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Residues in contact with CYS 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C ASP* 3.0 25.3 + - - +
405C HIS 5.4 0.4 - - - +
408C VAL* 1.3 73.6 - - - +
410C PRO* 1.3 56.9 - - + +
412C ALA 3.0 1.4 + - - +
413C GLN* 2.6 33.8 + - - +
528C THR* 4.2 1.1 - - - -
529C CYS* 2.1 55.2 - - + -
532C TRP* 3.5 26.9 - - + -
533C ASN* 3.1 28.2 + - - +
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Residues in contact with PRO 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C THR* 3.8 20.0 - - - +
233C ASN* 3.3 16.2 + - - +
234C GLY* 4.1 17.9 - - - -
235C PRO* 4.4 0.2 - - + -
404C ASP 3.3 12.6 - - - +
405C HIS 3.5 11.4 - - - +
406C ASN 3.2 26.2 - - - +
407C VAL 3.0 11.9 - - - +
408C VAL 3.3 0.2 - - - -
409C CYS* 1.3 92.2 - - + +
411C VAL* 1.3 55.1 + - - +
413C GLN* 4.3 3.4 - - + +
414C LEU* 2.8 28.2 + - - +
533C ASN* 4.3 1.5 - - - +
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Residues in contact with VAL 411 (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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230C GLY 4.6 5.2 - - - +
231C THR* 3.6 19.0 - - + +
328C VAL* 3.2 30.8 - - + +
329C GLY* 3.9 7.6 - - - +
330C VAL* 3.3 30.1 - - + -
407C VAL* 2.9 32.7 + - + +
408C VAL 2.8 7.2 + - - +
410C PRO* 1.3 74.8 - - - +
412C ALA* 1.3 55.9 + - - +
414C LEU* 3.0 2.8 + - - +
415C ALA* 2.6 35.3 + - + +
524C LEU* 4.0 14.1 - - + -
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Residues in contact with ALA 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C VAL 2.8 10.9 + - - +
409C CYS* 3.6 9.9 - - - +
411C VAL* 1.3 79.4 - - - +
413C GLN* 1.3 63.4 + - - +
415C ALA* 3.7 5.3 - - - +
416C GLY* 3.1 21.8 + - - -
503C TYR* 4.5 9.4 + - + +
524C LEU* 3.9 36.1 - - + +
529C CYS* 4.6 8.1 - - + -
533C ASN* 4.6 1.8 - - - +
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Residues in contact with GLN 413 (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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233C ASN* 3.9 15.3 - - - +
313C GLU* 3.7 22.4 + - - +
316C ILE* 4.1 5.8 - - + +
409C CYS 2.6 19.6 + - - +
410C PRO* 3.2 6.7 + - + +
412C ALA* 1.3 72.7 - - - +
414C LEU* 1.3 58.6 + - - +
416C GLY* 4.3 0.2 - - - -
417C ARG* 3.1 53.2 + - - +
533C ASN* 3.7 34.4 + - + +
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Residues in contact with LEU 414 (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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213C ILE* 6.4 0.2 - - + -
214C LEU* 5.5 0.7 - - + -
227C LEU* 3.7 30.1 - - + -
231C THR* 3.9 15.3 - - + -
232C PRO* 4.1 8.5 - - + -
233C ASN* 3.6 11.2 - - - +
316C ILE* 3.2 42.0 - - + -
328C VAL* 4.9 11.0 - - + -
410C PRO 2.8 16.6 + - - +
411C VAL* 3.6 3.1 - - - +
413C GLN* 1.3 77.0 - - - +
415C ALA* 1.3 67.5 + - - +
417C ARG* 3.1 0.9 + - - +
418C LEU* 2.7 53.0 + - + +
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Residues in contact with ALA 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C VAL* 5.2 8.4 - - + +
411C VAL* 2.6 25.1 + - + +
412C ALA* 3.7 7.2 - - - +
414C LEU* 1.3 73.1 - - - +
416C GLY* 1.3 58.8 + - - +
418C LEU* 3.4 4.7 - - - +
419C ALA* 2.8 30.0 + - - +
425C VAL* 3.8 20.1 - - + +
427C ALA* 5.4 3.6 - - + -
503C TYR* 3.9 28.5 - - + -
524C LEU* 5.9 1.1 - - + -
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Residues in contact with GLY 416 (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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412C ALA 3.1 11.6 + - - -
413C GLN 4.3 0.4 - - - -
415C ALA* 1.3 79.6 - - - +
417C ARG* 1.3 60.9 + - - +
419C ALA* 3.9 1.7 - - - +
420C ALA* 2.9 28.2 + - - +
503C TYR* 3.6 19.6 - - - -
505C THR* 4.4 10.5 - - - +
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Residues in contact with ARG 417 (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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316C ILE* 3.2 41.5 - - + +
317C ASN* 2.8 46.7 + - - +
413C GLN* 3.1 39.6 + - - +
414C LEU 3.8 2.5 - - - +
416C GLY* 1.3 74.9 - - - +
418C LEU* 1.3 62.6 + - - +
420C ALA* 3.7 5.6 + - - +
421C GLN* 2.7 46.2 + - - +
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Residues in contact with LEU 418 (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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213C ILE* 5.3 7.2 - - + -
316C ILE* 5.0 2.0 - - + -
321C PHE* 3.3 43.5 - - + +
324C LEU* 5.0 3.6 - - + -
326C VAL* 4.1 28.5 - - + -
328C VAL* 5.4 1.6 - - + -
414C LEU* 2.7 50.0 + - + +
415C ALA* 3.4 5.2 - - - +
417C ARG* 1.3 75.7 - - - +
419C ALA* 1.3 70.2 + - - +
421C GLN* 2.7 14.6 + - - +
422C GLY 3.1 8.1 + - - -
423C ALA* 3.1 24.5 + - + -
425C VAL* 3.8 5.4 - - + -
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Residues in contact with ALA 419 (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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415C ALA 2.8 19.5 + - - +
416C GLY* 3.9 3.1 - - - +
418C LEU* 1.3 72.3 - - - +
420C ALA* 1.3 64.3 + - - +
422C GLY* 2.9 17.0 + - - -
423C ALA 3.8 15.1 + - - +
425C VAL* 3.6 7.3 - - + +
503C TYR* 3.9 25.6 - - + +
504C THR* 4.5 1.8 - - + -
505C THR* 4.4 17.3 - - - +
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Residues in contact with ALA 420 (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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416C GLY 2.9 17.8 + - - +
417C ARG* 3.9 11.2 - - - +
419C ALA* 1.3 76.5 - - - +
421C GLN* 1.3 65.8 + - - +
422C GLY 3.7 0.2 + - - -
505C THR* 4.2 22.3 + - + -
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Residues in contact with GLN 421 (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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316C ILE 3.8 3.9 + - - -
317C ASN 3.1 19.2 - - - +
318C THR* 4.1 3.5 - - - -
319C GLY 2.8 25.8 - - - +
320C ASP* 4.6 3.5 - - - +
321C PHE* 3.6 17.0 + - + -
322C GLN* 3.6 17.9 + - - +
417C ARG* 2.7 45.8 + - - +
418C LEU 2.7 13.4 + - - +
420C ALA* 1.3 78.5 - - - +
422C GLY* 1.3 54.9 + - - -
423C ALA 3.7 0.4 - - - -
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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