Contacts of the helix formed by residues 453 - 472 (chain A) in PDB entry 5SY1
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 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A LEU* 3.7 2.9 - - - -
452A TRP* 1.4 121.5 - - + +
454A PHE* 1.3 65.0 + - - +
455A TRP 3.5 0.2 - - - -
456A LEU* 3.4 20.1 + - + +
457A THR* 3.8 11.3 - - - +
119B ASN* 5.5 6.3 - - + +
121B GLU* 4.8 20.2 - - + +
122B PHE* 4.2 30.5 - - + +
125B ILE* 4.0 4.3 - - + +
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Residues in contact with PHE 454 (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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451A LEU* 3.0 31.9 + - + +
453A PRO* 1.3 80.2 - - - +
455A TRP* 1.3 84.8 + + - +
456A LEU 3.1 0.4 + - - -
457A THR* 2.9 27.1 + - - -
458A LEU* 3.9 16.5 + - + +
502A MET* 4.5 27.6 - - + -
121B GLU* 5.3 7.6 - - + +
124B MET* 5.1 6.3 - - + -
125B ILE* 3.9 28.7 - - + +
128B LEU* 5.5 7.9 - - + -
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Residues in contact with TRP 455 (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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447A ILE* 6.2 1.8 - - + -
448A ILE* 3.8 42.4 - - + -
451A LEU* 3.3 30.2 + - + +
452A TRP* 4.6 2.4 + - - +
453A PRO 3.5 0.2 - - - -
454A PHE* 1.3 102.6 - + - +
456A LEU* 1.3 63.4 + - - +
457A THR 3.3 0.4 - - - -
458A LEU* 3.9 20.9 + - + +
459A VAL* 3.3 24.6 + - - +
506A VAL* 5.8 3.4 - - + +
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Residues in contact with LEU 456 (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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452A TRP 4.3 8.9 + - - +
453A PRO* 3.4 18.2 + - + +
454A PHE 3.1 1.2 - - - -
455A TRP* 1.3 78.3 - - - +
457A THR* 1.3 58.7 + - + +
459A VAL* 3.0 13.2 + - + +
460A LEU* 2.8 61.8 + - + +
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Residues in contact with THR 457 (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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453A PRO 3.8 13.7 - - - +
454A PHE* 2.9 16.3 + - - -
456A LEU* 1.3 78.1 - - + +
458A LEU* 1.3 70.0 + - - +
460A LEU* 4.2 10.5 - - + +
461A ALA* 3.1 27.0 + - - +
499A VAL* 4.7 4.0 - - - +
122B PHE* 5.4 7.2 - - + -
125B ILE* 3.9 32.9 - - + +
128B LEU* 5.9 1.4 - - - +
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Residues in contact with LEU 458 (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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454A PHE* 3.9 19.7 + - + +
455A TRP* 3.9 29.8 + - + +
456A LEU 3.3 0.6 - - - -
457A THR* 1.3 82.4 + - - +
459A VAL* 1.3 63.1 + - + +
462A ALA* 3.3 22.5 + - - +
499A VAL* 4.4 7.9 - - + +
502A MET* 3.8 35.9 - - + +
503A ILE* 3.7 31.6 - - + +
506A VAL* 4.2 17.5 - - + -
128B LEU* 6.5 0.4 - - + -
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Residues in contact with VAL 459 (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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455A TRP 3.3 15.9 + - - +
456A LEU* 3.0 14.9 + - + +
458A LEU* 1.3 79.1 - - + +
460A LEU* 1.3 62.1 + - + +
462A ALA* 3.1 5.5 + - - +
463A LEU* 2.5 41.7 + - + +
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Residues in contact with LEU 460 (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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456A LEU* 2.8 53.8 + - + +
457A THR* 4.4 9.0 - - + +
458A LEU 3.6 0.2 - - - -
459A VAL* 1.3 78.7 - - + +
461A ALA* 1.3 57.4 + - - +
463A LEU* 3.4 16.0 - - + +
464A ILE* 2.8 29.2 + - - +
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Residues in contact with ALA 461 (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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457A THR 3.1 19.1 + - - +
458A LEU 4.8 1.1 - - - +
460A LEU* 1.3 74.5 - - - +
462A ALA* 1.3 60.9 + - - +
464A ILE* 3.2 11.5 + - - +
465A GLN* 3.1 33.8 + - - +
496A LEU* 4.3 15.4 - - + +
499A VAL* 3.7 26.5 - - + -
503A ILE* 4.9 3.4 - - + -
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Residues in contact with ALA 462 (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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458A LEU 3.3 19.6 + - - +
459A VAL* 3.1 5.0 + - - +
461A ALA* 1.3 76.0 - - - +
463A LEU* 1.3 63.1 + - - +
465A GLN* 3.9 9.8 - - - +
466A HIS* 3.2 35.1 + - + -
503A ILE* 4.2 15.8 - - + +
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Residues in contact with LEU 463 (chain A).
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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459A VAL* 2.5 25.0 + - + +
460A LEU* 3.4 20.6 - - + +
462A ALA* 1.3 74.3 - - - +
464A ILE* 1.3 64.9 + - + +
466A HIS* 3.4 4.7 + - + +
467A VAL* 2.9 58.4 + - + +
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Residues in contact with ILE 464 (chain A).
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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460A LEU 2.8 16.3 + - - +
461A ALA* 3.3 18.8 - - + +
463A LEU* 1.3 83.0 - - + +
465A GLN* 1.3 61.6 + - - +
467A VAL* 4.1 12.6 - - + +
468A ALA* 3.3 30.1 + - + +
492A LEU* 4.7 11.6 - - + +
496A LEU* 4.2 19.5 - - + -
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Residues in contact with GLN 465 (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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461A ALA* 3.1 21.2 + - - +
462A ALA* 4.2 9.3 - - - +
463A LEU 3.2 0.6 - - - -
464A ILE* 1.3 76.8 - - - +
466A HIS* 1.3 63.4 + - - +
468A ALA* 5.0 0.8 - - - +
469A SER* 3.2 23.6 + - - -
473A PHE* 5.8 0.5 - - - -
492A LEU* 5.3 4.3 - - + -
493A SER* 6.3 0.2 - - - +
496A LEU* 3.5 29.2 - - + +
500A ASN* 3.0 41.3 + - - +
503A ILE* 5.1 2.0 - - - +
397B VAL* 3.6 33.4 - - + +
400B MET* 4.4 28.7 + - + +
405B TYR* 5.7 0.7 + - - -
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Residues in contact with HIS 466 (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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462A ALA* 3.2 28.1 + - + +
463A LEU* 3.4 6.3 + - + +
465A GLN* 1.3 78.3 - - - +
467A VAL* 1.3 65.8 + - + +
469A SER* 3.5 2.2 + - - -
470A ARG* 3.4 23.0 + - - +
393B ARG* 3.9 26.0 + - - +
394B PRO* 4.8 13.9 - - + -
397B VAL* 3.8 36.7 - - + +
543B ARG* 6.1 1.3 - - - -
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Residues in contact with VAL 467 (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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463A LEU* 2.9 50.0 + - + +
464A ILE* 4.6 10.1 - - + -
466A HIS* 1.3 78.8 - - + +
468A ALA* 1.3 64.8 + - - +
469A SER 3.2 0.9 + - - -
470A ARG* 3.6 1.4 + - - -
471A PHE* 3.4 43.6 + - + +
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Residues in contact with ALA 468 (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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464A ILE* 3.3 27.5 + - + +
465A GLN 5.0 0.2 - - - +
467A VAL* 1.3 81.0 - - - +
469A SER* 1.3 56.5 + - - +
471A PHE* 5.2 0.2 - - - -
472A LEU* 3.2 40.3 + - + +
473A PHE* 3.2 25.0 - - + -
492A LEU* 4.6 8.7 - - + -
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Residues in contact with SER 469 (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 GLN 3.2 20.9 + - - -
466A HIS* 3.8 4.9 - - - -
467A VAL 3.1 1.0 - - - -
468A ALA* 1.3 78.0 - - - +
470A ARG* 1.3 61.0 + - - +
473A PHE* 3.3 17.4 + - - -
474A ILE* 3.0 33.5 + - - +
393B ARG* 3.9 19.8 + - - +
396B LEU* 3.4 24.0 - - - +
397B VAL* 4.6 6.1 - - - -
400B MET* 5.7 2.2 - - - -
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Residues in contact with ARG 470 (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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466A HIS 3.4 8.1 + - - +
467A VAL* 4.4 2.0 - - - +
469A SER* 1.3 79.3 - - - +
471A PHE* 1.3 78.5 + - + +
474A ILE* 3.9 17.5 - - - +
393B ARG* 3.7 36.6 - - + +
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Residues in contact with PHE 471 (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 VAL* 3.4 35.9 + - + +
468A ALA* 5.2 0.4 - - - -
469A SER 3.2 0.2 - - - -
470A ARG* 1.3 96.6 - - + +
472A LEU* 1.3 73.3 + - + +
474A ILE 5.2 1.8 - - - -
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Residues in contact with LEU 472 (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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468A ALA* 3.2 26.6 + - + +
471A PHE* 1.3 94.0 - - + +
473A PHE* 1.3 76.8 + - + +
474A ILE 3.8 1.9 - - - +
475A ARG* 5.7 1.4 - - - +
485A ASN* 4.0 16.1 + - - +
71B LEU* 5.3 15.5 - - + -
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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