Contacts of the helix formed by residues 407 - 421 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D SER* 3.3 34.5 - - - +
230D GLY* 4.0 3.1 - - - +
231D THR* 5.0 0.3 - - - +
236D TRP* 5.0 1.1 - - + +
295D PHE* 3.7 31.2 - - + -
330D VAL* 4.2 0.2 - - + -
334D GLU* 3.2 47.6 - - + +
403D GLY* 3.0 7.3 + - - +
405D HIS 3.8 0.2 - - - -
406D ASN* 1.3 81.9 - - + +
408D VAL* 1.3 60.3 + - - +
410D PRO* 3.0 5.9 - - - +
411D VAL* 2.9 36.6 + - + +
447D HIS* 4.3 2.0 - - - +
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Residues in contact with VAL 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D VAL* 3.7 29.6 - - + -
331D VAL 5.1 0.9 - - - +
332D LYS 6.0 0.7 - - - +
334D GLU* 4.1 9.4 - - + -
403D GLY 3.0 19.1 + - - +
404D ASP* 4.1 17.3 - - + +
407D VAL* 1.3 70.4 - - - +
409D CYS* 1.3 65.7 + - - +
411D VAL* 2.8 6.2 + - - +
412D ALA* 2.8 19.8 + - - +
524D LEU* 4.0 30.7 - - + -
525D ARG* 4.2 26.9 - - + +
529D CYS* 4.4 5.2 - - - -
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Residues in contact with CYS 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D ASP* 2.9 25.1 + - - +
405D HIS 5.4 0.7 - - - +
408D VAL* 1.3 74.3 - - - +
410D PRO* 1.3 56.6 - - + +
412D ALA 3.0 1.8 + - - +
413D GLN* 2.6 33.8 + - - +
528D THR* 4.2 0.9 - - - -
529D CYS* 2.1 55.4 - - + -
532D TRP* 3.5 25.8 - - + -
533D ASN* 3.1 28.0 + - - +
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Residues in contact with PRO 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D THR* 3.8 20.1 - - + +
233D ASN* 3.3 16.1 + - - +
234D GLY* 4.1 18.2 - - - -
235D PRO* 4.4 0.7 - - + -
404D ASP 3.3 13.5 - - - +
405D HIS 3.5 10.5 - - - +
406D ASN* 3.2 26.5 - - - +
407D VAL 3.0 11.7 - - - +
409D CYS* 1.3 93.1 - - + +
411D VAL* 1.3 55.6 + - - +
413D GLN* 3.2 3.3 + - + +
414D LEU* 2.8 27.5 + - - +
533D ASN* 4.3 1.8 - - - +
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Residues in contact with VAL 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D GLY 4.6 5.4 - - - +
231D THR* 3.6 19.0 - - + +
328D VAL* 3.2 31.2 - - + +
329D GLY* 3.9 7.4 - - - +
330D VAL* 3.3 30.3 - - + -
407D VAL* 2.9 32.0 + - + +
408D VAL 2.8 7.9 + - - +
410D PRO* 1.3 74.8 - - - +
412D ALA* 1.3 55.4 + - - +
414D LEU* 3.0 3.2 + - - +
415D ALA* 2.6 36.0 + - + +
524D LEU* 4.0 14.6 - - + -
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Residues in contact with ALA 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D VAL 2.8 12.0 + - - +
409D CYS* 3.6 9.6 - - - +
411D VAL* 1.3 79.4 - - - +
413D GLN* 1.3 61.9 + - - +
415D ALA* 3.7 5.3 - - - +
416D GLY* 3.1 22.7 + - - -
503D TYR* 4.5 9.8 + - + +
524D LEU* 3.9 37.0 - - + +
529D CYS* 4.6 7.2 - - + -
533D ASN* 4.6 2.0 - - - +
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Residues in contact with GLN 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ASN* 3.9 15.9 - - - +
313D GLU* 3.7 21.6 + - - +
316D ILE* 4.1 6.0 - - + +
409D CYS 2.6 20.9 + - - +
410D PRO* 3.7 6.3 - - + +
412D ALA* 1.3 72.1 - - - +
414D LEU* 1.3 59.4 + - - +
416D GLY* 4.3 0.4 - - - -
417D ARG* 3.1 53.7 + - - +
533D ASN* 3.7 33.6 + - + +
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Residues in contact with LEU 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ILE* 6.4 0.2 - - + -
214D LEU* 5.5 0.9 - - + -
227D LEU* 3.7 30.3 - - + -
231D THR* 3.9 15.0 - - + -
232D PRO* 4.1 8.7 - - + -
233D ASN* 3.6 12.1 - - - +
316D ILE* 3.2 41.1 - - + -
328D VAL* 4.9 10.3 - - + -
410D PRO 2.8 16.3 + - - +
411D VAL* 3.6 3.1 - - - +
413D GLN* 1.3 76.5 - - - +
415D ALA* 1.3 67.3 + - - +
417D ARG* 3.1 1.2 + - - +
418D LEU* 2.7 52.3 + - + +
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Residues in contact with ALA 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D VAL* 5.2 8.7 - - + +
411D VAL* 2.6 25.0 + - + +
412D ALA* 3.3 7.2 + - - +
414D LEU* 1.3 74.6 - - - +
416D GLY* 1.3 59.4 + - - +
418D LEU* 3.1 4.7 + - - +
419D ALA* 2.8 29.6 + - - +
425D VAL* 3.8 19.6 - - + +
427D ALA* 5.4 3.8 - - + -
503D TYR* 3.9 28.5 - - + -
524D LEU* 5.9 1.6 - - + -
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Residues in contact with GLY 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412D ALA 3.1 11.0 + - - -
413D GLN 4.3 0.2 - - - -
415D ALA* 1.3 81.3 - - - +
417D ARG* 1.3 61.7 + - - +
419D ALA* 3.9 1.7 - - - +
420D ALA* 2.9 27.6 + - - +
503D TYR* 3.6 19.0 - - - -
505D THR* 4.4 11.2 - - - +
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Residues in contact with ARG 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D ILE* 3.2 41.7 - - + +
317D ASN* 2.8 45.6 - - - +
413D GLN* 3.1 38.2 + - - +
414D LEU 3.1 2.7 + - - +
416D GLY* 1.3 75.0 - - - +
418D LEU* 1.3 64.4 + - - +
420D ALA* 3.7 6.0 + - - +
421D GLN* 2.7 46.1 + - - +
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Residues in contact with LEU 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ILE* 5.3 7.4 - - + -
316D ILE* 5.0 2.0 - - + -
321D PHE* 3.3 43.0 - - + +
324D LEU* 5.0 4.0 - - + -
326D VAL* 4.1 28.3 - - + -
328D VAL* 5.4 1.6 - - + -
414D LEU* 2.7 49.1 + - + +
415D ALA* 3.4 5.4 - - - +
417D ARG* 1.3 75.5 - - - +
419D ALA* 1.3 69.4 + - - +
421D GLN* 2.7 14.9 + - - +
422D GLY 3.1 8.3 + - - -
423D ALA* 3.1 25.1 + - + +
425D VAL* 3.8 4.7 - - + -
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Residues in contact with ALA 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415D ALA 2.8 18.4 + - - +
416D GLY 3.9 3.1 - - - +
418D LEU* 1.3 71.6 - - - +
420D ALA* 1.3 63.0 + - - +
422D GLY* 2.9 16.3 + - - -
423D ALA 3.8 15.3 + - - +
425D VAL* 3.6 7.3 - - + +
503D TYR* 3.9 25.8 - - + +
504D THR* 4.5 1.6 - - + -
505D THR* 4.4 17.9 - - - +
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Residues in contact with ALA 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416D GLY 2.9 18.4 + - - +
417D ARG* 3.9 10.8 - - - +
419D ALA* 1.3 75.7 - - - +
421D GLN* 1.3 66.4 + - - +
422D GLY 3.7 0.3 + - - -
505D THR* 4.2 22.0 + - + +
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Residues in contact with GLN 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D ILE 3.8 4.5 + - - -
317D ASN 3.1 18.6 - - - +
318D THR* 4.1 4.0 - - - -
319D GLY 2.8 26.6 - - - +
320D ASP* 4.6 3.2 - - - +
321D PHE* 3.6 17.2 + - + -
322D GLN* 3.6 18.1 + - - +
417D ARG* 2.7 46.3 + - - +
418D LEU 2.7 13.1 + - - +
420D ALA* 1.3 77.1 - - - +
422D GLY* 1.3 55.1 + - - -
423D ALA 3.7 0.7 - - - -
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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