Contacts of the helix formed by residues 411 - 417 (chain D) in PDB entry 1CX2
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 ASN 411 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D PRO* 3.6 19.7 - - + +
282D ASN* 4.2 6.1 - - - +
283D LEU* 3.1 60.7 - - + +
285D PHE* 4.1 4.7 - - - -
409D TYR 3.8 0.4 + - - -
410D ASN* 1.3 76.8 + - - +
412D SER* 1.3 67.2 + - - +
413D ILE 3.0 2.9 + - - -
414D LEU* 3.4 10.7 + - - +
415D LEU* 3.1 37.9 + - - +
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Residues in contact with SER 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D ASN* 3.2 6.3 + - - -
411D ASN* 1.3 80.3 - - - +
413D ILE* 1.3 58.0 + - - +
415D LEU* 4.2 9.2 - - - +
416D GLU* 2.5 66.4 + - - +
681D NAG 4.9 8.7 - - - -
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Residues in contact with ILE 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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296D PRO* 4.7 3.1 - - + -
397D ILE* 5.3 0.2 - - + -
402D TYR* 4.0 17.7 - - + -
406D GLN 3.3 27.6 - - - +
407D PHE* 3.6 42.0 - - + -
410D ASN* 3.2 28.1 + - + +
411D ASN 3.0 2.2 + - - -
412D SER* 1.3 79.2 - - - +
414D LEU* 1.3 58.1 + - - +
416D GLU* 3.7 1.2 - - - +
417D HIS* 2.9 41.4 + - - +
422D PHE* 3.8 13.5 - - + -
681D NAG 3.2 22.1 + - - +
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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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262D TYR* 4.5 19.1 + - + -
285D PHE* 5.0 4.9 - - + -
296D PRO* 4.3 8.7 - - + +
299D MET* 3.8 37.9 - - + +
300D MET* 3.9 15.7 - - + +
303D THR* 4.5 1.8 - - - +
410D ASN 4.6 2.6 + - - +
411D ASN 3.4 7.0 + - - +
412D SER 3.3 0.2 - - - -
413D ILE* 1.3 75.6 - - - +
415D LEU* 1.3 63.9 + - + +
418D GLY* 2.9 31.9 + - - +
419D LEU* 3.6 27.1 - - + -
422D PHE* 3.6 36.8 - - + -
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Residues in contact with LEU 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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257D ILE* 3.5 40.4 - - + -
262D TYR* 3.9 27.3 + - + -
282D ASN 5.5 1.3 - - - +
285D PHE* 3.8 18.6 - - + -
411D ASN* 3.1 44.5 + - - +
412D SER* 3.3 7.1 + - - +
414D LEU* 1.3 80.7 - - + +
416D GLU* 1.3 70.0 - - - +
418D GLY* 4.2 3.8 + - - -
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Residues in contact with GLU 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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402D TYR* 6.2 0.2 - - - +
412D SER* 2.5 50.8 + - - +
413D ILE* 3.7 2.7 - - - +
415D LEU* 1.3 80.1 - - - +
417D HIS* 1.3 70.6 + - + +
418D GLY* 3.4 0.5 + - - -
681D NAG 5.7 4.5 - - - +
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Residues in contact with HIS 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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397D ILE* 3.0 32.8 + - + +
398D GLU 5.2 1.9 + - - -
399D ASP 5.6 0.6 + - - -
400D GLN* 4.0 9.4 + - - +
402D TYR* 2.8 47.7 + + - -
413D ILE* 2.9 28.0 + - + +
416D GLU* 1.3 80.6 - - + +
418D GLY* 1.3 59.7 + - - +
421D GLN* 3.2 37.6 + - + +
422D PHE* 4.0 4.3 - - + -
681D NAG 5.2 0.2 - - - -
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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
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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