Contacts of the helix formed by residues 413 - 420 (chain D) in PDB entry 3R2A
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 GLY 413 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394C GLU* 5.4 9.2 - - - -
397C TYR* 3.8 24.1 + - - -
401C GLU* 5.7 0.7 - - - -
411D GLN* 3.4 2.0 - - - +
412D PRO* 1.3 78.4 - - - +
414D ARG* 1.3 64.4 + - - +
415D PHE 3.3 2.9 - - - -
416D ALA* 3.5 4.5 + - - -
417D LYS* 3.0 23.0 + - - +
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Residues in contact with ARG 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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360D MET* 3.1 46.2 + - + +
361D GLN 4.1 4.0 + - - -
362D MET* 4.5 0.8 - - - +
366D GLU* 1.5 60.7 + - - -
404D CYS* 4.3 11.4 - - + -
408D TYR* 3.5 37.6 + - + +
411D GLN* 3.2 41.0 + - + +
412D PRO 3.4 1.4 - - - -
413D GLY* 1.3 75.3 - - - +
415D PHE* 1.3 66.7 + - - +
417D LYS* 3.0 9.8 + - + +
418D LEU* 2.8 25.1 + - + +
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Residues in contact with PHE 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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401C GLU* 5.2 4.5 - - - +
415C PHE* 5.1 13.0 - + - -
416C ALA* 4.3 17.9 - - + -
397D TYR* 3.6 29.6 - + + -
400D LEU* 3.7 19.7 - - + -
401D GLU* 3.6 57.2 - - + +
404D CYS* 4.6 9.0 - - + +
412D PRO 4.6 6.4 + - - +
413D GLY 3.3 0.6 - - - -
414D ARG* 1.3 78.3 - - - +
416D ALA* 1.3 65.0 + - - +
418D LEU* 3.0 17.5 + - + +
419D LEU* 3.2 33.2 + - + +
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Residues in contact with ALA 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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397C TYR* 3.4 38.6 - - + -
401C GLU* 6.4 0.2 - - - -
415C PHE* 4.0 21.3 - - + -
419C LEU* 4.0 13.0 - - + +
413D GLY* 3.5 4.3 + - - +
414D ARG 3.3 0.4 - - - -
415D PHE* 1.3 81.9 - - - +
417D LYS* 1.3 63.3 + - - +
419D LEU* 3.4 4.1 + - - +
420D LEU* 3.1 27.6 + - - +
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Residues in contact with LYS 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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390C GLU* 1.4 47.7 + - - +
394C GLU* 4.1 13.9 + - - +
397C TYR* 3.8 14.4 + - - +
356D LYS* 5.4 6.5 - - - +
359D ASP* 6.5 0.2 - - - -
360D MET* 4.2 32.1 - - + +
413D GLY 3.0 15.1 + - - +
414D ARG* 3.0 14.5 + - + +
416D ALA* 1.3 80.4 - - - +
418D LEU* 1.3 62.5 + - - +
420D LEU* 3.4 12.6 + - + +
421D ARG* 3.8 12.5 + - - +
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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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360D MET* 3.6 17.5 - - + -
362D MET* 3.2 33.7 - - + -
366D GLU* 3.8 30.1 - - + +
370D LEU* 3.6 24.1 - - + +
400D LEU* 4.6 13.7 - - + -
404D CYS* 3.6 31.0 - - - -
414D ARG* 2.8 18.3 + - + +
415D PHE* 3.0 7.4 + - + +
417D LYS* 1.3 77.2 - - - +
419D LEU* 1.3 63.9 + - + +
421D ARG* 3.2 20.3 + - - +
422D LEU 4.2 0.9 + - - -
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Residues in contact with LEU 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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415C PHE* 6.4 0.4 - - + -
416C ALA* 3.8 34.3 - - + -
419C LEU* 4.5 20.6 - - + +
420C LEU* 4.0 27.3 - - + +
423C PRO* 5.4 1.0 - - - +
370D LEU* 4.7 5.8 - - + -
373D ILE* 4.4 17.7 - - + -
397D TYR* 5.0 1.3 - - + -
400D LEU* 5.7 1.6 - - + -
415D PHE* 3.2 32.4 + - + +
416D ALA* 3.8 8.3 - - - +
418D LEU* 1.3 81.9 - - + +
420D LEU* 1.3 61.6 + - - +
421D ARG 3.1 0.7 - - - -
422D LEU* 3.2 33.1 + - + +
423D PRO* 3.5 3.5 - - - +
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Residues in contact with LEU 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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373C ILE* 4.3 9.0 - - + -
393C ARG* 3.8 34.5 + - - +
397C TYR* 3.2 40.2 - - + -
419C LEU* 4.4 18.2 - - + +
422C LEU* 4.0 27.4 - - + -
426C ARG* 5.6 0.2 + - - -
416D ALA 3.1 13.4 + - - +
417D LYS* 3.9 9.0 - - + +
418D LEU 3.2 0.8 - - - -
419D LEU* 1.3 76.5 - - - +
421D ARG* 1.3 71.6 + - - +
422D LEU 3.2 0.9 - - - -
423D PRO* 2.9 21.8 - - + +
424D ALA* 4.3 1.4 + - - +
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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