Contacts of the helix formed by residues 477 - 492 (chain A) in PDB entry 6UR2
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A ARG 3.5 0.8 + - - +
473A LEU* 3.1 41.3 + - + +
475A VAL 3.7 0.2 - - - -
476A GLU* 1.3 79.3 - - - +
478A GLU* 1.3 67.9 + - - +
479A GLN 3.5 1.1 - - - -
480A PRO* 3.4 1.3 - - - +
481A LEU* 3.0 25.8 + - - +
767A LEU* 4.0 23.8 - - + -
769A ARG* 3.8 17.5 - - - +
802A ASP* 4.1 5.6 - - - +
805A LYS* 4.2 16.8 - - + -
806A LYS* 3.8 36.8 - - + +
809A ILE* 3.2 16.1 - - + +
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Residues in contact with GLU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 3.6 20.5 - - + +
399A TYR* 5.4 1.6 - - + -
400A LEU* 4.0 20.2 - - + -
473A LEU* 3.0 21.6 + - + +
474A LEU* 4.1 6.5 - - - +
477A LEU* 1.3 73.5 - - + +
479A GLN* 1.3 60.1 + - - +
481A LEU* 3.6 2.3 + - - +
482A SER 3.0 13.5 + - - -
608A GLN* 2.6 56.9 + - - +
769A ARG* 2.8 40.5 + - - -
805A LYS* 3.1 22.8 + - - -
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Residues in contact with GLN 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A SER* 5.8 1.1 - - - +
390A VAL* 4.6 10.4 + - + +
391A SER* 3.3 24.7 + - - +
392A PHE* 3.3 5.7 - - - -
393A ASP* 2.7 41.9 + - + -
396A LEU* 4.2 5.4 - - + -
474A LEU* 3.0 44.7 + - + +
475A VAL* 3.8 20.5 + - - +
478A GLU* 1.3 73.9 - - - +
480A PRO* 1.4 69.0 - - + +
482A SER* 3.1 18.6 + - - -
483A SER* 3.5 7.4 + - - -
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Residues in contact with PRO 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A VAL 3.3 26.9 - - - +
476A GLU* 3.6 15.7 - - - +
477A LEU 3.4 13.0 - - - +
479A GLN* 1.4 91.4 - - + +
481A LEU* 1.3 59.6 + - - +
483A SER* 3.4 10.6 + - - +
484A ILE* 3.3 25.6 + - + +
809A ILE* 4.3 19.7 - - + -
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A LEU 3.0 19.9 + - - +
478A GLU* 3.6 6.5 - - - +
479A GLN 3.2 0.2 - - - -
480A PRO* 1.3 73.4 - - - +
482A SER* 1.3 56.5 + - - +
484A ILE* 3.0 10.2 + - + +
485A LEU* 2.8 49.6 + - + +
608A GLN* 3.8 12.6 - - - +
616A LEU* 4.4 2.9 - - + -
805A LYS* 3.4 49.6 - - + +
808A MET* 4.0 42.6 - - + -
809A ILE* 4.3 8.5 - - + +
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Residues in contact with SER 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A SER* 3.6 16.7 + - - -
374A LYS* 3.5 25.2 + - - +
393A ASP* 4.7 0.2 + - - -
396A LEU* 4.0 12.2 - - - +
478A GLU 3.0 13.8 + - - -
479A GLN* 3.1 12.8 + - - -
481A LEU* 1.3 76.8 - - - +
483A SER* 1.3 56.8 + - - +
485A LEU* 3.4 5.0 + - - +
486A ALA* 2.9 29.3 + - - +
608A GLN* 3.5 17.0 + - - -
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Residues in contact with SER 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LYS* 5.1 0.9 + - - -
479A GLN 3.5 5.9 + - - -
480A PRO* 3.4 13.1 + - - +
481A LEU 3.2 0.2 - - - -
482A SER* 1.3 79.0 + - - +
484A ILE* 1.3 62.2 + - - +
486A ALA* 3.2 9.8 + - - +
487A GLU* 3.1 28.3 + - - +
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Residues in contact with ILE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A PRO* 3.3 14.1 + - + +
481A LEU* 3.0 10.9 + - + +
483A SER* 1.3 73.2 - - - +
485A LEU* 1.3 68.1 + - - +
487A GLU* 3.2 14.5 + - - +
488A MET* 3.0 30.2 + - + +
808A MET* 3.7 31.2 - - + +
809A ILE* 3.7 24.0 - - + +
812A ASN* 4.0 24.7 - - + +
824A LEU* 3.9 25.6 - - + -
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Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LYS* 3.7 14.8 - - + -
481A LEU* 2.8 30.4 + - + +
482A SER 3.6 4.7 - - - +
484A ILE* 1.3 71.8 - - - +
486A ALA* 1.3 57.4 + - - +
488A MET* 3.2 22.6 + - + +
489A GLU* 2.9 34.3 + - - +
606A PHE* 4.1 23.6 - - + -
608A GLN* 3.7 35.0 - - + +
616A LEU* 3.8 35.7 - - + -
808A MET* 4.1 10.3 - - + -
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Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LYS* 3.8 10.3 - - + +
377A ALA* 4.3 12.8 - - + -
378A VAL* 3.6 27.1 - - + +
381A LYS* 4.0 14.4 - - - -
482A SER 2.9 14.2 + - - +
483A SER* 3.2 12.1 + - - +
485A LEU* 1.3 75.9 - - - +
487A GLU* 1.3 63.1 + - - +
489A GLU* 3.3 2.0 + - - +
490A PHE* 3.0 26.0 + - - +
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Residues in contact with GLU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LYS* 3.8 23.0 + - - +
483A SER* 3.1 20.6 + - - +
484A ILE* 3.2 13.2 + - - +
486A ALA* 1.3 75.4 - - - +
488A MET* 1.3 57.5 + - + +
490A PHE* 3.8 3.5 - - - +
491A ALA* 2.9 31.6 + - - +
812A ASN* 3.2 26.7 + - - -
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Residues in contact with MET 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A ILE* 3.0 25.4 + - + +
485A LEU* 3.2 15.2 + - + +
487A GLU* 1.3 72.2 - - + +
489A GLU* 1.3 65.1 + - - +
491A ALA* 3.6 3.4 + - - +
492A GLY* 3.2 20.8 + - - +
604A THR* 6.0 0.2 - - - +
606A PHE* 4.2 14.8 - - + -
808A MET* 3.7 29.4 - - + -
824A LEU* 3.5 38.4 - - + +
825A LEU* 3.3 39.0 - - - +
826A LEU* 3.7 19.5 - - - +
827A GLN* 3.8 3.8 - - + +
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Residues in contact with GLU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A TYR* 2.6 31.8 + - - -
328A HIS* 3.7 12.7 + - + -
374A LYS* 3.0 24.6 + - - +
378A VAL* 3.7 4.2 - - + +
485A LEU 2.9 18.3 + - - +
486A ALA 3.6 4.0 - - - +
488A MET* 1.3 77.0 - - - +
490A PHE* 1.3 58.2 + - - +
492A GLY* 3.4 5.0 + - - -
603A HIS* 2.9 31.2 + - - +
604A THR* 3.4 18.2 - - - +
605A ILE* 3.8 4.5 - - - -
606A PHE* 2.7 44.0 + - + +
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Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A HIS* 4.2 4.9 - - - -
378A VAL* 4.8 4.5 - - + -
381A LYS* 3.7 55.2 - - + -
382A TRP* 3.7 41.7 - + - -
486A ALA 3.0 17.3 + - - +
487A GLU* 3.9 3.8 - - - +
489A GLU* 1.3 73.7 - - - +
491A ALA* 1.3 68.4 + - - +
601A LYS* 4.8 0.9 + - - -
603A HIS* 2.9 22.1 + - - -
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A GLU 2.9 18.7 + - - +
488A MET* 3.6 9.0 - - - +
490A PHE* 1.3 78.9 - - - +
492A GLY* 1.3 65.4 + - - +
601A LYS* 2.6 36.5 + - - +
823A HIS* 4.4 24.7 - - + +
824A LEU 4.8 0.7 - - - +
825A LEU* 4.5 3.4 - - + -
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Residues in contact with GLY 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A MET 3.2 10.3 + - - -
489A GLU* 3.8 3.6 - - - -
490A PHE 3.3 2.2 + - - -
491A ALA* 1.3 82.0 - - - +
493A VAL* 1.3 64.5 + - - -
601A LYS* 4.6 3.8 - - - -
602A VAL 3.4 13.2 - - - -
603A HIS* 3.7 15.9 - - - -
643A SER* 5.7 1.4 - - - -
825A LEU* 3.3 23.7 - - - +
835A 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
------------------------------------------------------------
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