Contacts of the helix formed by residues 473 - 484 (chain D) in PDB entry 4Z2C
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 473 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459D ILE* 5.9 0.8 - - - +
460D LEU* 4.2 22.0 + - + +
469D LYS* 3.1 13.2 + - + +
470D ILE 3.4 16.0 + - - +
471D LEU 4.3 1.2 - - - +
472D ALA* 1.3 75.8 - - - +
474D GLU* 1.3 64.5 + - - +
475D GLU* 3.0 19.2 + - - +
476D ILE* 2.9 45.7 + - + +
477D ARG* 3.4 20.1 + - - +
5F A 4.2 17.0 + - - -
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Residues in contact with GLU 474 (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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472D ALA 3.3 3.0 + - - +
473D ASN* 1.3 72.7 - - - +
475D GLU* 1.3 65.0 + - + +
477D ARG* 3.3 17.9 + - - +
478D SER* 2.9 28.6 + - - -
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Residues in contact with GLU 475 (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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453D LEU* 5.3 0.2 - - - +
454D PRO 4.0 5.0 - - - +
455D ILE* 4.0 10.9 - - + -
456D ARG* 3.6 48.2 + - - +
459D ILE* 5.7 12.8 - - + -
473D ASN* 3.0 14.9 + - - +
474D GLU* 1.3 77.8 - - + +
476D ILE* 1.3 61.2 + - + +
478D SER* 2.4 31.2 + - - -
479D LEU* 2.9 15.5 + - - +
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Residues in contact with ILE 476 (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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459D ILE* 5.9 3.1 - - + -
460D LEU* 4.4 15.7 - - + +
462D VAL* 4.0 26.7 - - + -
470D ILE* 4.0 19.7 - - + +
473D ASN* 2.9 35.4 + - + +
475D GLU* 1.3 74.8 - - + +
477D ARG* 1.3 58.5 + - - +
479D LEU* 3.2 5.8 + - - +
480D PHE* 2.9 60.6 + - + -
487D PHE* 4.9 7.4 - - + -
521D LEU* 3.8 24.7 - - + -
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Residues in contact with ARG 477 (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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471D LEU 2.6 30.2 + - - +
472D ALA* 3.5 20.0 + - - +
473D ASN 3.4 12.6 + - - +
474D GLU* 3.3 23.3 + - - +
475D GLU 3.2 0.6 - - - -
476D ILE* 1.3 79.7 - - - +
478D SER* 1.3 53.8 + - - +
480D PHE* 3.8 5.8 - - - +
481D THR* 2.4 46.2 + - - +
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Residues in contact with SER 478 (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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413D PRO* 4.7 15.7 - - - +
453D LEU* 4.1 21.6 - - - +
454D PRO 5.1 0.3 + - - -
474D GLU 2.9 12.8 + - - -
475D GLU* 2.4 37.7 + - - -
477D ARG* 1.3 76.1 - - - +
479D LEU* 1.3 58.4 + - - +
481D THR* 3.7 6.1 - - - -
482D ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 479 (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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429D LEU* 6.0 1.8 - - + -
431D ILE* 4.2 24.5 - - + -
453D LEU* 4.3 15.5 - - + -
475D GLU 2.9 12.3 + - - +
476D ILE* 3.2 10.1 + - - +
478D SER* 1.3 78.2 + - - +
480D PHE* 1.3 58.9 + - + +
482D ALA* 3.5 3.0 + - - +
483D MET* 2.9 38.0 + - + +
501D LEU* 5.3 3.4 - - + -
518D LEU* 5.9 2.0 - - + -
521D LEU* 5.0 13.7 - - + -
522D ILE* 6.2 1.6 - - + -
526D MET* 4.9 14.8 - - - -
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Residues in contact with PHE 480 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476D ILE* 2.9 48.3 + - + +
477D ARG* 4.0 5.8 - - - +
479D LEU* 1.3 76.5 - - + +
481D THR* 1.3 64.3 + - - +
483D MET* 4.6 3.1 - - - -
484D GLY* 3.2 19.4 + - - -
485D THR* 3.9 10.8 + - + -
486D GLY* 3.1 35.4 + - - -
487D PHE* 3.5 33.2 - + + -
488D GLY 5.4 0.2 - - - -
491D PHE* 6.2 1.1 - - + -
521D LEU* 4.3 11.9 - - + -
525D TYR* 3.2 30.3 - - + -
526D MET* 3.5 26.5 - - + -
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Residues in contact with THR 481 (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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413D PRO* 4.4 21.1 - - + -
477D ARG* 2.4 33.0 + - - +
478D SER* 3.7 7.8 - - - -
479D LEU 3.3 0.2 - - - -
480D PHE* 1.3 76.8 - - - +
482D ALA* 1.3 63.5 + - - +
484D GLY* 3.4 11.1 + - - -
497D ARG* 4.3 5.2 + - - -
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Residues in contact with ALA 482 (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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413D PRO* 5.1 0.9 - - + +
416D LEU* 4.0 31.4 - - + -
429D LEU* 5.0 6.5 - - + -
453D LEU* 4.5 10.1 - - + -
478D SER 2.9 18.3 + - - +
479D LEU* 3.8 4.3 - - - +
481D THR* 1.3 76.0 - - - +
483D MET* 1.3 66.6 + - + +
484D GLY 3.2 0.3 + - - -
497D ARG* 2.9 31.8 + - - +
498D TYR* 3.6 13.0 - - + -
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Residues in contact with MET 483 (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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429D LEU* 5.1 2.0 - - + -
479D LEU* 2.9 24.5 + - + +
480D PHE* 4.3 4.3 - - - +
482D ALA* 1.3 76.9 - - + +
484D GLY* 1.3 62.2 + - - +
485D THR* 3.2 21.0 + - - +
496D ALA* 3.5 14.8 - - + -
497D ARG* 3.0 26.1 + - - -
498D TYR* 4.2 31.0 - - + +
501D LEU* 4.1 32.1 - - + -
526D MET* 4.0 22.4 - - + -
529D ILE* 3.9 25.4 - - + -
534D TYR* 6.1 0.4 - - + -
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Residues in contact with GLY 484 (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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480D PHE 3.2 11.3 + - - -
481D THR* 3.8 8.5 - - - -
482D ALA 3.1 4.9 - - - -
483D MET* 1.3 78.1 - - - +
485D THR* 1.3 62.4 + - - +
486D GLY 3.6 1.1 - - - -
495D LYS* 3.0 23.3 - - - +
497D ARG* 4.2 11.9 - - - -
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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