Contacts of the helix formed by residues 487 - 496 (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 GLY 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486A ARG* 1.3 73.8 - - - +
488A SER* 1.3 62.1 + - - -
489A LEU 3.1 2.2 + - - +
490A PHE* 3.3 29.6 + - - -
491A LEU* 3.7 4.2 + - - +
66B ASP* 3.3 26.9 - - - -
67B ASN* 5.1 0.2 - - - -
68B GLN 4.2 4.7 - - - -
69B ARG* 5.3 0.3 - - - -
76B SER* 3.7 22.4 + - - -
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Residues in contact with SER 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A PHE* 3.9 14.8 - - - -
485A ASN* 5.0 3.6 - - - -
486A ARG 2.7 12.5 + - - -
487A GLY* 1.3 73.0 - - - -
489A LEU* 1.3 59.2 + - - -
491A LEU* 3.5 2.3 + - - +
492A LEU* 3.4 10.2 + - - +
68B GLN 4.2 3.4 + - - -
69B ARG* 2.4 61.6 + - - +
70B GLY* 3.5 28.3 + - - +
71B LEU* 4.6 2.8 + - - +
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Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A PHE* 3.5 49.6 - - + -
484A ASN* 5.2 9.0 - - + +
485A ASN 4.6 5.4 - - - +
486A ARG* 4.2 4.0 - - - -
487A GLY 3.1 5.4 - - - +
488A SER* 1.3 76.9 - - - +
490A PHE* 1.3 69.9 + - + +
491A LEU 3.1 0.7 - - - -
492A LEU* 3.2 3.1 + - - +
493A SER* 3.1 19.8 + - - +
396B LEU* 3.7 27.6 - - + -
399B TRP* 3.6 32.1 - - + -
400B MET* 4.0 18.1 - - + +
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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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486A ARG* 4.0 19.3 - - + -
487A GLY* 3.3 34.5 - - - +
488A SER 3.4 0.2 - - - -
489A LEU* 1.3 80.1 - - + +
491A LEU* 1.3 62.3 + - - +
493A SER* 3.2 16.2 + - - -
494A TYR* 3.7 11.3 + - - +
66B ASP* 5.2 4.7 - - - -
76B SER* 3.5 18.4 - - - +
77B PRO* 4.2 2.9 - - + +
78B VAL 5.1 2.2 - - - +
79B ASN* 3.4 27.8 - - - -
80B PHE* 3.7 39.7 - + + -
81B LEU* 3.8 32.8 - - + -
399B TRP* 4.3 10.1 - + - -
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Residues in contact with LEU 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 GLY 3.7 5.8 + - - +
488A SER 3.5 10.5 + - - +
489A LEU 3.1 0.4 - - - -
490A PHE* 1.3 79.4 - - - +
492A LEU* 1.3 57.8 + - - +
494A TYR* 3.0 19.9 + - + +
495A ILE* 3.0 37.4 + - + +
69B ARG* 3.7 38.4 - - + +
74B LEU* 4.9 13.0 - - + -
75B LEU 4.5 7.9 - - - +
76B SER* 4.3 3.7 + - - -
77B PRO* 3.9 23.8 - - + -
136B TYR* 4.0 19.5 - - + +
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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
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464A ILE* 4.7 13.9 - - + +
465A GLN* 5.3 2.5 - - - -
468A ALA* 4.6 13.9 - - + -
473A PHE* 4.1 21.5 - - + -
488A SER 3.4 9.9 + - - +
489A LEU* 3.2 9.2 + - - +
491A LEU* 1.3 80.1 - - - +
493A SER* 1.3 58.1 + - - +
494A TYR 3.1 3.3 + - - -
495A ILE* 3.7 14.3 + - + +
496A LEU* 3.4 45.6 + - + +
69B ARG* 4.5 14.8 - - - +
400B MET* 3.8 20.4 - - + -
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Residues in contact with SER 493 (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* 6.3 0.2 - - - +
489A LEU 3.1 12.3 + - - -
490A PHE* 3.2 17.2 + - - -
492A LEU* 1.3 75.5 - - - +
494A TYR* 1.3 56.1 + - - +
496A LEU* 4.5 4.2 - - - -
497A PHE* 4.6 11.8 + - - +
500A ASN* 5.7 2.9 + - - +
80B PHE* 4.1 10.9 - - - -
94B TYR* 4.3 7.5 + - - -
274B LYS* 4.3 14.0 + - - -
399B TRP* 4.5 5.1 - - - -
400B MET* 3.9 36.3 - - - +
401B GLY* 4.8 5.1 + - - -
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Residues in contact with TYR 494 (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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490A PHE 3.7 10.3 - - - +
491A LEU* 3.0 10.8 + - + +
493A SER* 1.3 79.5 + - - +
495A ILE* 1.3 71.8 + - + +
496A LEU 3.2 1.1 - - - -
497A PHE* 3.5 15.5 + - - +
77B PRO* 4.4 12.8 - - + -
80B PHE* 5.0 3.8 - + + -
93B VAL* 3.7 14.8 - - + +
94B TYR* 3.2 30.5 - + - +
97B LEU* 3.4 31.8 - - + +
132B PRO* 3.7 33.8 + - + +
135B TYR 4.2 8.8 + - - -
136B TYR* 4.1 23.3 - + - -
139B LEU* 3.7 24.7 - - + +
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Residues in contact with ILE 495 (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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491A LEU* 3.0 42.7 + - + +
492A LEU* 3.7 14.6 + - + +
494A TYR* 1.3 81.3 - - + +
496A LEU* 1.3 62.7 + - + +
497A PHE 3.2 4.6 + - - -
498A LEU 4.7 1.2 + - - -
499A VAL* 4.9 0.3 - - - +
69B ARG* 5.9 2.9 - - - +
128B LEU 4.7 1.6 - - - +
129B LEU* 3.7 32.6 - - + +
132B PRO* 4.4 16.0 - - + +
133B THR* 5.7 5.4 - - - +
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ALA* 4.3 21.8 - - + +
464A ILE* 4.2 12.8 - - + -
465A GLN* 3.5 32.8 - - + +
492A LEU* 3.4 40.1 + - + +
493A SER* 4.9 2.9 - - - -
494A TYR 3.2 1.2 - - - -
495A ILE* 1.3 81.9 - - + +
497A PHE* 1.3 60.2 + - - -
498A LEU 3.6 1.1 - - - -
499A VAL* 3.9 19.1 - - + -
500A ASN* 2.7 42.8 + - - +
129B LEU* 4.7 7.6 - - + -
400B MET* 5.1 0.2 - - + -
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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