Contacts of the helix formed by residues 474 - 491 (chain A) in PDB entry 5LUQ
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 VAL 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A GLY 3.4 0.6 + - - -
473A PRO* 1.3 91.4 - - + +
475A LEU* 1.3 75.2 + - + +
476A ARG* 3.5 2.2 - - - -
477A ASN* 3.3 23.4 + - - +
478A CYS* 3.9 2.8 + - - +
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Residues in contact with LEU 475 (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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432A THR* 3.3 28.3 - - + +
435A LEU* 3.5 32.1 - - + -
436A GLU* 2.6 39.3 - - + +
468A LEU* 3.9 12.1 - - + -
472A GLY* 4.6 11.0 - - - +
474A VAL* 1.3 85.2 - - + +
476A ARG* 1.3 55.7 + - - +
478A CYS* 2.7 32.0 + - + +
479A ILE* 3.0 22.3 + - + -
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Residues in contact with ARG 476 (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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465A PHE* 4.9 8.3 - - + -
468A LEU* 4.9 11.7 - - + +
469A ALA* 4.4 28.7 + - - +
471A LYS 5.4 0.2 + - - -
472A GLY 3.4 10.0 + - - +
473A PRO* 2.8 48.9 + - - +
474A VAL 4.7 2.5 - - - +
475A LEU* 1.3 78.5 - - - +
477A ASN* 1.3 63.4 + - + +
479A ILE* 3.0 23.2 - - + +
480A SER* 3.0 31.6 + - - -
551A PHE* 3.0 55.4 - - + -
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Residues in contact with ASN 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A VAL* 3.3 13.9 - - - +
475A LEU 2.8 1.8 + - - -
476A ARG* 1.3 85.9 - - + +
478A CYS* 1.3 62.1 + - - +
480A SER* 3.0 7.5 + - - -
481A THR* 3.0 23.8 + - - -
551A PHE* 4.4 23.8 - - - +
555A SER* 3.0 30.4 + - - -
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Residues in contact with CYS 478 (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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436A GLU* 4.2 18.8 - - - +
474A VAL 3.9 2.4 + - - +
475A LEU* 2.7 14.1 + - - +
477A ASN* 1.3 70.9 - - - +
479A ILE* 1.3 68.6 + - - +
481A THR* 4.0 7.6 - - - +
482A VAL* 3.1 34.8 + - - +
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Residues in contact with ILE 479 (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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435A LEU* 4.9 0.9 - - + -
436A GLU* 3.8 21.1 + - + +
439A VAL* 3.5 23.3 - - + -
440A VAL* 5.3 2.0 - - + -
465A PHE* 3.5 30.7 - - + -
468A LEU* 4.0 22.4 - - + -
475A LEU* 3.0 30.4 + - + +
476A ARG* 3.0 23.6 - - + +
478A CYS* 1.3 81.7 - - - +
480A SER* 1.3 69.0 + - - +
482A VAL* 3.9 0.4 - - - -
483A VAL* 2.9 31.1 + - + +
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Residues in contact with SER 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A PHE* 4.5 11.6 - - - -
476A ARG 3.0 12.0 + - - -
477A ASN* 3.0 7.8 + - - -
479A ILE* 1.3 77.4 - - - +
481A THR* 1.3 67.1 + - - +
483A VAL* 3.1 11.7 - - - +
484A HIS* 2.9 22.7 + - - +
551A PHE* 5.0 3.1 - - - +
552A SER* 4.4 22.1 + - - -
555A SER* 4.0 17.9 - - - -
556A SER* 5.5 1.1 - - - -
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Residues in contact with THR 481 (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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477A ASN* 3.0 15.6 + - - -
478A CYS* 4.0 8.1 - - - -
480A SER* 1.3 74.1 - - - +
482A VAL* 1.3 77.6 + - + +
484A HIS* 2.8 17.4 + - - +
485A GLN* 2.9 21.4 + - + +
555A SER* 3.7 23.3 + - - -
559A SER* 2.9 31.2 + - - +
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Residues in contact with VAL 482 (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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440A VAL* 5.4 10.3 - - + -
478A CYS* 3.1 28.7 + - - +
479A ILE 4.3 0.4 - - - +
481A THR* 1.3 82.0 - - + +
483A VAL* 1.3 64.7 + - + +
485A GLN* 3.0 16.2 + - + +
486A GLY* 2.9 21.9 + - - +
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Residues in contact with VAL 483 (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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440A VAL* 3.6 32.3 - - + -
443A ILE* 3.5 46.7 - - + +
465A PHE* 5.2 1.6 - - + -
479A ILE* 2.9 23.5 + - + +
480A SER* 3.1 26.7 - - - +
482A VAL* 1.3 75.7 - - - +
484A HIS* 1.3 61.6 + - + +
486A GLY* 3.8 1.8 + - - +
487A LEU* 3.5 20.3 + - - +
534A LEU* 6.2 3.8 - - + -
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Residues in contact with HIS 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A SER 2.9 18.4 + - - +
481A THR* 2.8 7.2 + - - +
483A VAL* 1.3 78.3 - - + +
485A GLN* 1.3 66.5 + - + +
487A LEU* 3.2 6.2 + - + +
488A ILE* 2.9 39.6 + - + +
531A PHE* 5.5 2.9 - + - -
534A LEU* 4.3 24.6 - - + +
556A SER* 3.1 31.3 - - - -
559A SER* 6.0 0.4 - - - -
616A LYS* 3.1 41.2 - - + +
619A ASP* 5.3 6.7 - - - -
620A PHE* 5.9 1.6 - - - -
623A PHE* 4.9 15.4 - + - -
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Residues in contact with GLN 485 (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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481A THR* 2.9 19.3 + - + +
482A VAL* 3.1 18.6 - - + +
484A HIS* 1.3 76.4 - - - +
486A GLY* 1.3 63.5 + - - +
488A ILE* 3.2 11.2 - - - +
489A ARG* 2.8 29.6 + - - +
559A SER* 3.1 33.2 + - - -
563A LEU* 3.4 35.7 - - - +
612A LEU* 5.3 2.2 - - + +
616A LYS* 4.9 0.2 + - - -
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Residues in contact with GLY 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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444A ASP* 5.1 12.3 - - - -
482A VAL* 2.9 13.9 + - - +
483A VAL* 3.8 2.2 + - - -
485A GLN* 1.3 74.9 - - - +
487A LEU* 1.3 62.1 + - - +
489A ARG* 4.2 2.8 - - - +
490A ILE* 2.9 29.1 + - - +
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Residues in contact with LEU 487 (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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443A ILE* 5.5 3.4 - - + -
444A ASP* 5.2 3.7 + - - -
446A PHE* 3.5 17.0 - - + -
483A VAL 3.5 12.9 + - - +
484A HIS* 3.2 13.1 + - - +
486A GLY* 1.3 75.5 - - - +
488A ILE* 1.3 71.3 + - + +
490A ILE* 3.0 25.6 - - - +
491A CYS* 3.0 7.8 + - - -
527A TYR* 4.8 2.2 - - + +
530A LEU* 3.4 41.0 - - + +
531A PHE* 3.4 33.7 - - + -
534A LEU* 3.5 28.7 - - + -
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Residues in contact with ILE 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 HIS* 3.2 28.0 - - + +
485A GLN* 3.2 23.6 - - - +
487A LEU* 1.3 83.3 - - + +
489A ARG* 1.3 59.1 + - - +
491A CYS* 3.0 23.2 - - - +
527A TYR* 5.5 3.1 - - + -
531A PHE* 5.8 1.6 - - + -
563A LEU* 3.3 31.6 - - + -
612A LEU* 2.9 33.1 - - + +
615A ALA* 4.9 3.8 - - + -
616A LYS* 3.4 39.0 - - + +
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Residues in contact with ARG 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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485A GLN* 2.8 17.6 + - + +
486A GLY* 4.2 2.7 - - - +
488A ILE* 1.3 76.1 - - - +
490A ILE* 1.3 59.1 + - - +
491A CYS 2.8 9.7 + - - -
492A SER* 3.1 31.6 + - - +
608A PRO* 4.3 19.5 + - - -
611A ASN* 3.5 25.6 - - - +
612A LEU* 3.5 28.0 - - + +
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Residues in contact with ILE 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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444A ASP* 5.0 9.2 - - - +
486A GLY 2.9 17.6 + - - +
487A LEU* 3.0 23.1 - - - +
489A ARG* 1.3 76.6 - - - +
491A CYS* 1.3 63.4 + - - +
492A SER* 2.9 18.0 + - - +
525A LYS* 4.8 31.9 - - + +
530A LEU* 4.4 15.0 - - + -
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Residues in contact with CYS 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 LEU 3.0 8.5 + - - +
488A ILE 3.0 21.8 - - - +
489A ARG 2.8 1.8 + - - -
490A ILE* 1.3 75.2 - - - +
492A SER* 1.3 58.1 + - - +
493A LYS 2.7 28.9 + - - +
494A PRO* 4.9 5.4 - - - -
495A VAL* 5.0 0.2 - - - +
525A LYS 4.6 3.9 - - - +
527A TYR* 3.6 39.4 + - + +
530A LEU* 6.1 0.9 - - - -
611A ASN 4.3 11.0 - - - +
612A LEU* 4.8 0.2 - - - -
615A ALA* 3.3 29.4 - - + -
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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