Contacts of the helix formed by residues 491 - 507 (chain A) in PDB entry 3S51
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 PRO 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A THR 5.0 12.8 - - - +
453A SER* 6.2 1.6 - - - -
489A PHE 4.3 2.9 - - - +
490A LEU* 1.3 94.0 - - + +
492A LEU* 1.3 67.9 + - - +
493A GLN* 4.5 7.0 - - + +
494A THR* 2.8 38.4 + - - +
495A VAL* 3.1 8.9 + - - +
530A ASP* 5.3 1.3 - - - +
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Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A LEU 3.6 2.2 + - - -
491A PRO* 1.3 71.1 - - - +
493A GLN* 1.3 64.1 + - - +
495A VAL* 3.0 4.4 + - + -
496A GLN* 2.9 46.9 + - - +
530A ASP* 3.8 21.6 + - - +
533A LYS* 3.6 39.3 - - + +
534A SER* 3.5 41.5 + - - +
537A ALA* 4.4 3.1 - - + -
603A MET* 4.9 4.3 - - - -
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Residues in contact with GLN 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A LEU* 5.4 11.4 - - - +
457A ASN* 3.2 36.5 + - - +
460A LEU* 4.5 2.8 - - - +
491A PRO* 3.1 6.1 + - + +
492A LEU* 1.3 78.6 - - - +
494A THR* 1.3 62.3 + - - +
496A GLN* 3.7 8.1 + - - +
497A GLY* 3.3 17.3 + - - -
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Residues in contact with THR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL* 3.6 36.2 + - + +
456A ILE* 4.7 11.1 - - + +
460A LEU* 3.8 10.6 - - + +
490A LEU* 4.0 20.4 - - + -
491A PRO* 2.8 32.0 + - + +
493A GLN* 1.3 77.3 - - - +
495A VAL* 1.3 54.8 + - - +
497A GLY* 3.1 2.3 + - - -
498A LEU* 2.7 36.1 + - + +
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Residues in contact with VAL 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LEU* 3.3 57.4 - - + +
490A LEU* 3.9 15.5 - - + +
491A PRO 3.5 12.6 - - - +
492A LEU* 3.0 7.1 + - + +
494A THR* 1.3 76.0 - - - +
496A GLN* 1.3 57.7 + - - +
498A LEU* 3.6 7.5 - - + +
499A LEU* 2.9 46.2 + - + +
534A SER* 3.8 24.7 - - - +
537A ALA* 5.7 0.7 - - + -
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Residues in contact with GLN 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU* 2.9 37.1 + - - +
493A GLN* 4.0 7.3 - - - +
495A VAL* 1.3 74.7 - - - +
497A GLY* 1.3 57.4 + - - +
499A LEU* 3.2 6.4 + - - +
500A LYS* 2.7 63.6 + - + +
537A ALA* 3.5 29.4 - - + +
603A MET* 5.1 8.5 - - - +
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Residues in contact with GLY 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 4.0 22.9 - - - +
493A GLN 3.3 7.3 + - - -
494A THR 3.1 5.9 + - - -
496A GLN* 1.3 77.0 - - - +
498A LEU* 1.3 61.5 + - - +
500A LYS* 4.0 5.6 - - - +
501A ALA* 3.1 27.9 + - - +
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU* 4.4 10.1 - - + -
448A VAL* 4.3 13.5 - - + -
449A VAL* 5.1 0.2 - - + -
460A LEU* 3.9 13.3 - - + +
463A PHE* 3.5 35.0 - - + -
480A VAL* 6.3 0.4 - - + -
483A THR* 3.2 33.2 - - + -
484A PHE* 4.8 11.0 - - + -
490A LEU* 4.2 19.7 - - + -
494A THR* 2.7 19.9 + - + +
495A VAL* 3.6 8.1 - - + +
497A GLY* 1.3 73.6 - - - +
499A LEU* 1.3 63.4 + - + +
501A ALA* 3.9 1.5 - - - +
502A VAL* 3.0 27.9 + - + +
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Residues in contact with LEU 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A PHE* 4.0 17.3 - - + -
487A LEU* 4.2 7.6 - - + -
495A VAL* 2.9 39.6 + - + +
496A GLN* 3.7 4.7 - - + +
498A LEU* 1.3 74.7 - - + +
500A LYS* 1.3 69.3 + - - +
502A VAL* 3.0 16.8 + - + +
503A GLN* 3.2 12.8 + - - +
506A LEU* 5.6 0.9 - - + -
516A LEU* 4.0 35.7 - - + -
537A ALA* 4.3 4.9 - - + +
538A GLY* 3.5 34.5 - - - +
541A LEU* 3.5 18.6 - - + +
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Residues in contact with LYS 500 (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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496A GLN* 2.7 54.4 + - + +
497A GLY* 4.0 5.2 - - - +
499A LEU* 1.3 73.2 - - - +
501A ALA* 1.3 63.4 + - - +
503A GLN* 2.9 35.5 + - - +
504A PRO* 4.4 0.9 - - - +
537A ALA* 5.0 3.6 + - - +
541A LEU* 3.5 30.8 - - + +
544A LYS* 3.5 26.9 - - - +
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Residues in contact with ALA 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 4.4 3.4 - - + +
463A PHE* 4.2 10.5 - - + -
464A SER* 3.4 44.2 + - - +
467A ILE* 3.9 15.7 - - - +
468A MET* 5.9 0.7 - - - +
497A GLY 3.1 16.7 + - - +
498A LEU 3.9 2.5 - - - +
500A LYS* 1.3 80.3 - - - +
502A VAL* 1.3 60.3 + - - +
503A GLN 3.1 1.6 + - - -
504A PRO* 3.4 12.6 - - - +
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Residues in contact with VAL 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A PHE* 3.9 20.2 - - + -
467A ILE* 4.1 8.7 - - + -
480A VAL* 3.4 32.1 - - + -
484A PHE* 4.0 20.4 - - + -
498A LEU* 3.0 17.3 + - + +
499A LEU* 3.0 12.5 + - + +
501A ALA* 1.3 76.2 - - - +
503A GLN* 1.3 67.2 + - - +
504A PRO* 3.4 0.9 - - - -
505A LEU* 3.0 23.3 + - + +
506A LEU* 3.5 23.9 + - + -
512A MET* 4.9 2.2 - - - -
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Residues in contact with GLN 503 (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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499A LEU 3.2 4.8 + - - +
500A LYS* 2.9 34.1 + - - +
501A ALA 3.1 0.2 - - - -
502A VAL* 1.3 78.6 - - - +
504A PRO* 1.3 65.2 - - + +
506A LEU* 2.7 31.0 + - - +
507A LYS* 3.3 14.2 + - + +
541A LEU* 3.6 26.0 - - + +
544A LYS* 5.1 5.9 - - - +
545A ASN* 2.7 39.4 + - - +
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Residues in contact with PRO 504 (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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467A ILE* 4.2 12.6 - - + -
468A MET* 3.9 33.4 - - + -
471A PRO* 4.2 19.3 - - + -
500A LYS 4.4 0.9 - - - +
501A ALA 3.4 14.4 - - - +
502A VAL 3.6 0.9 - - - -
503A GLN* 1.3 94.5 - - + +
505A LEU* 1.3 59.0 + - - +
507A LYS* 3.9 13.3 + - + +
508A ILE* 3.6 25.1 - - - +
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Residues in contact with LEU 505 (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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467A ILE* 3.8 33.4 - - + -
471A PRO* 3.4 39.0 - - + +
474A LEU* 3.6 33.0 - - + +
475A GLN* 4.1 3.4 - - - +
480A VAL* 4.1 11.4 - - + -
502A VAL* 3.0 14.2 + - + +
503A GLN 3.0 1.0 - - - -
504A PRO* 1.3 76.3 - - - +
506A LEU* 1.3 59.8 + - - +
507A LYS 3.2 0.4 - - - -
508A ILE* 2.9 7.0 + - + +
509A SER* 2.8 32.1 + - - -
512A MET* 3.7 27.4 - - + -
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Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A PHE* 4.9 0.7 - - + -
499A LEU* 5.1 0.4 - - + +
502A VAL* 3.8 24.0 - - + -
503A GLN* 2.7 17.7 + - - +
505A LEU* 1.3 73.7 - - - +
507A LYS* 1.3 57.3 + - + +
508A ILE 3.0 5.7 + - - -
509A SER 3.5 15.2 - - - +
512A MET* 3.9 21.1 - - + +
513A ARG* 3.9 29.5 + - + +
516A LEU* 3.8 30.3 - - + -
541A LEU* 4.2 23.1 - - + -
542A LEU* 4.5 9.0 - - + -
545A ASN* 5.2 0.9 - - - +
546A PHE* 3.5 26.1 - - + -
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Residues in contact with LYS 507 (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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503A GLN* 3.3 10.2 + - + +
504A PRO* 4.1 14.4 - - + +
505A LEU 3.2 1.2 - - - -
506A LEU* 1.3 75.5 - - + +
508A ILE* 1.3 62.6 + - + +
545A ASN* 3.4 44.6 + - + +
546A PHE* 4.1 7.4 - - + -
563A VAL* 4.1 17.6 + - - +
564A THR 3.8 20.8 + - - -
565A GLN* 4.8 0.7 - - - +
566A VAL* 3.9 31.4 - - + +
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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
------------------------------------------------------------
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