Contacts of the helix formed by residues 477 - 492 (chain D) in PDB entry 2HVI
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 LEU 477 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472D ARG 3.5 0.2 + - - -
473D LEU* 3.2 39.8 + - + +
475D VAL 3.6 0.4 - - - -
476D GLU* 1.3 82.2 - - - +
478D GLU* 1.3 71.6 + - - +
479D GLN 3.5 0.9 - - - -
480D PRO* 3.4 0.3 - - - +
481D LEU* 3.0 24.9 + - - +
767D LEU* 4.4 15.7 - - + -
769D ARG* 3.8 17.3 - - - +
802D ASP* 4.2 3.8 - - - +
805D LYS* 4.0 21.5 - - + -
806D LYS* 3.6 41.7 - - + +
809D ILE* 3.3 11.4 - - + +
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Residues in contact with GLU 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D LEU* 4.2 19.1 - - + -
399D TYR* 5.3 4.3 - - + -
400D LEU* 4.1 19.5 - - + -
473D LEU* 3.0 17.8 + - + +
474D LEU* 3.9 5.8 - - - +
477D LEU* 1.3 80.1 - - + +
479D GLN* 1.3 58.8 + - - +
481D LEU* 3.3 2.5 + - - +
482D SER* 2.9 26.0 + - - -
608D GLN* 2.8 42.4 + - - +
769D ARG* 2.8 27.7 + - - -
805D LYS* 2.8 39.6 + - - -
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Residues in contact with GLN 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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390D VAL* 4.5 10.6 + - + +
391D SER* 3.1 26.5 + - - +
392D PHE* 3.2 6.2 - - - -
393D ASP* 2.8 32.0 + - + -
396D LEU* 4.3 10.1 - - + -
474D LEU* 2.9 45.1 + - + +
475D VAL* 4.0 18.9 + - - +
478D GLU* 1.3 73.0 - - - +
480D PRO* 1.3 71.3 - - + +
482D SER* 3.1 21.3 + - - -
483D SER* 3.5 8.7 + - - -
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Residues in contact with PRO 480 (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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475D VAL 3.3 26.5 - - - +
476D GLU* 3.6 12.3 - - - +
477D LEU 3.4 12.1 - - - +
479D GLN* 1.3 91.6 - - + +
481D LEU* 1.3 62.1 + - - +
483D SER* 3.3 16.9 + - - +
484D ILE* 3.3 18.9 + - + +
809D ILE* 3.9 22.0 - - + -
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Residues in contact with LEU 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477D LEU 3.0 19.5 + - - +
478D GLU* 3.5 3.8 - - - +
480D PRO* 1.3 74.6 - - - +
482D SER* 1.3 66.2 + - - +
484D ILE* 3.0 13.5 + - + +
485D LEU* 2.8 37.7 + - + +
608D GLN* 3.6 17.0 - - - +
616D LEU* 4.4 4.9 - - + -
805D LYS* 3.6 46.7 - - + +
808D MET* 3.8 45.3 - - + -
809D ILE* 4.1 4.4 - - + +
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Residues in contact with SER 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D SER* 3.9 9.5 + - - -
374D LYS* 3.4 36.4 + - - +
393D ASP* 4.6 0.5 + - - -
396D LEU* 4.2 12.0 - - - +
478D GLU 2.9 13.6 + - - -
479D GLN* 3.1 13.2 + - - -
481D LEU* 1.3 76.6 - - - +
483D SER* 1.3 57.3 + - - +
485D LEU* 3.3 2.1 + - - -
486D ALA* 3.0 26.0 + - - +
608D GLN* 3.6 17.7 + - - -
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Residues in contact with SER 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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381D LYS* 5.4 0.2 - - - -
479D GLN 3.8 8.1 + - - -
480D PRO* 3.3 11.0 + - - +
481D LEU 3.2 0.2 - - - -
482D SER* 1.3 75.7 - - - +
484D ILE* 1.3 66.9 + - - +
486D ALA* 3.3 7.7 + - - +
487D GLU* 3.2 29.3 + - - +
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Residues in contact with ILE 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 PRO* 3.5 12.6 - - + +
481D LEU* 3.0 11.7 + - + +
483D SER* 1.3 79.6 - - - +
485D LEU* 1.3 62.7 + - - +
487D GLU* 3.2 11.9 + - - +
488D MET* 3.0 38.8 + - + +
808D MET* 3.8 13.9 - - + +
809D ILE* 3.6 45.1 - - + +
812D ASN* 3.9 26.2 - - + +
824D LEU* 4.0 19.1 - - + -
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Residues in contact with LEU 485 (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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374D LYS* 3.6 20.9 - - + -
481D LEU* 2.8 28.0 + - + +
484D ILE* 1.3 72.5 - - - +
486D ALA* 1.3 59.7 + - - +
488D MET* 3.2 20.4 + - + +
489D GLU* 2.8 37.6 + - - +
606D PHE* 3.9 21.8 - - + -
608D GLN* 3.6 35.7 - - + +
616D LEU* 3.9 34.8 - - + -
808D MET* 4.1 9.0 - - + -
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Residues in contact with ALA 486 (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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374D LYS* 3.7 10.9 - - + +
377D ALA* 4.2 13.5 - - + -
378D VAL* 3.7 29.6 - - + +
381D LYS* 4.0 13.6 - - - -
482D SER 3.0 13.8 + - - +
483D SER* 3.5 11.7 - - - +
485D LEU* 1.3 77.1 - - - +
487D GLU* 1.3 60.6 + - - +
489D GLU* 3.5 0.4 + - - -
490D PHE* 3.0 26.5 + - - +
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Residues in contact with GLU 487 (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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381D LYS* 4.1 22.7 + - - +
483D SER* 3.2 17.3 + - - +
484D ILE* 3.6 9.8 - - - +
485D LEU 3.2 0.4 - - - -
486D ALA* 1.3 77.3 - - - +
488D MET* 1.3 58.2 + - + +
490D PHE* 3.8 2.8 - - - +
491D ALA* 2.9 31.7 + - - +
812D ASN* 3.8 21.9 + - - +
816D LYS* 4.6 12.0 + - - -
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Residues in contact with MET 488 (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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484D ILE* 3.0 28.0 + - + +
485D LEU* 3.2 14.1 + - + +
487D GLU* 1.3 78.1 - - + +
489D GLU* 1.3 61.9 + - - +
491D ALA* 3.7 3.0 - - - +
492D GLY* 3.1 21.5 + - - +
606D PHE* 4.0 15.0 - - + -
808D MET* 3.6 31.4 - - + -
824D LEU* 3.5 36.1 - - + +
825D LEU* 3.7 14.2 - - - +
826D LEU* 3.5 41.3 - - - +
827D GLN 3.8 3.4 - - - +
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Residues in contact with GLU 489 (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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327D TYR* 2.5 32.2 + - - -
328D HIS* 3.5 8.5 - - + -
374D LYS* 2.7 30.4 + - - +
378D VAL* 3.5 9.0 - - + +
485D LEU* 2.8 24.3 + - - +
486D ALA 3.9 2.5 - - - +
488D MET* 1.3 72.6 - - - +
490D PHE* 1.3 57.6 + - - +
492D GLY* 3.5 2.1 + - - -
603D HIS* 2.8 32.6 + - - +
604D THR* 3.3 27.8 - - - +
605D ILE* 3.9 0.2 - - - -
606D PHE* 2.9 34.3 + - + +
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Residues in contact with PHE 490 (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 HIS* 4.3 4.4 - - - -
378D VAL* 4.6 2.7 - - + +
381D LYS* 3.6 56.3 - - + -
382D TRP* 3.7 45.5 - + - -
486D ALA 3.0 17.8 + - - +
487D GLU* 3.9 3.6 - - - +
489D GLU* 1.3 75.1 - - - +
491D ALA* 1.3 69.2 + - - +
603D HIS* 2.9 19.0 - - - -
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Residues in contact with ALA 491 (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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487D GLU 2.9 19.1 + - - +
488D MET* 3.7 5.8 - - - +
490D PHE* 1.3 81.9 - - - +
492D GLY* 1.3 66.2 + - - +
601D LYS* 2.9 34.6 + - - +
823D HIS* 4.7 22.9 - - + +
824D LEU 5.1 2.0 - - - +
825D LEU* 4.7 3.6 - - + -
835D GLU* 5.7 0.4 - - - +
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Residues in contact with GLY 492 (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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488D MET 3.1 12.9 + - - -
489D GLU 3.5 4.0 + - - -
490D PHE 3.2 2.2 - - - -
491D ALA* 1.3 83.1 - - - +
493D VAL* 1.3 64.9 + - - -
494D LYS 4.4 0.3 + - - -
601D LYS* 4.5 4.1 + - - +
602D VAL 3.5 12.8 - - - -
603D HIS* 3.5 15.3 - - - -
643D SER* 5.7 1.2 - - - -
825D LEU* 3.4 21.3 - - - +
835D GLU* 5.0 2.1 - - - +
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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