Contacts of the helix formed by residues 487 - 496 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ASP* 3.2 26.2 - - - -
67A ASN* 4.9 0.7 - - - -
68A GLN 4.3 4.3 - - - -
69A ARG* 5.5 0.2 - - - -
76A SER* 3.4 27.2 + - - -
486B ARG* 1.3 73.2 - - - +
488B SER* 1.3 63.6 + - - -
489B LEU 3.1 1.9 + - - +
490B PHE* 3.3 26.6 + - - -
491B LEU* 3.7 3.3 + - - +
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Residues in contact with SER 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLN 4.2 3.2 + - - -
69A ARG* 2.3 61.9 + - - +
70A GLY* 3.5 27.5 + - - +
71A LEU* 4.6 1.6 + - - +
473B PHE* 3.9 14.5 - - - -
485B ASN* 5.0 2.9 - - - -
486B ARG 2.7 12.8 + - - -
487B GLY* 1.3 73.2 - - - -
489B LEU* 1.3 60.1 + - - -
491B LEU* 3.5 3.3 + - - +
492B LEU* 3.4 12.1 + - - +
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 3.9 25.6 - - + -
399A TRP* 3.4 35.7 - - + -
400A MET* 4.1 16.3 - - + +
473B PHE* 3.5 51.1 - - + -
484B ASN* 5.2 9.9 - - + +
485B ASN 4.6 5.8 - - - +
486B ARG* 4.2 3.3 - - - -
487B GLY 3.1 4.7 - - - +
488B SER* 1.3 77.5 - - - +
490B PHE* 1.3 69.7 + - + +
491B LEU 3.1 0.2 - - - -
492B LEU* 3.2 2.6 + - - +
493B SER* 3.1 20.5 + - - +
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Residues in contact with PHE 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP* 5.2 4.0 - - - -
76A SER* 3.4 17.0 - - - +
77A PRO* 4.0 3.4 - - + +
78A VAL 4.8 3.4 - - - +
79A ASN* 3.2 29.8 - - + -
80A PHE* 3.5 46.7 - + + -
81A LEU* 3.8 33.4 - - + -
399A TRP* 4.3 9.2 - + - -
486B ARG* 4.0 18.8 - - + -
487B GLY* 3.3 33.9 - - - -
488B SER 3.4 0.2 - - - -
489B LEU* 1.3 80.1 - - + +
491B LEU* 1.3 62.7 + - - +
493B SER* 3.2 16.6 + - - -
494B TYR* 3.7 7.3 + - - +
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Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 3.9 32.5 - - + +
74A LEU* 4.8 14.1 - - + -
75A LEU 4.4 8.1 - - - +
76A SER* 4.1 3.3 + - - -
77A PRO* 3.7 26.2 - - + -
136A TYR* 3.8 23.1 - - + +
487B GLY 3.7 6.2 + - - +
488B SER* 3.5 12.3 + - - +
489B LEU 3.1 0.6 - - - -
490B PHE* 1.3 79.0 - - - +
492B LEU* 1.3 58.4 + - - +
494B TYR* 3.0 20.8 + - + +
495B ILE* 3.0 37.2 + - + +
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 4.5 15.5 - - - +
400A MET* 3.7 22.7 - - + -
464B ILE* 4.7 15.0 - - + +
465B GLN* 5.3 0.9 - - - -
468B ALA* 4.6 13.0 - - + -
473B PHE* 4.1 21.8 - - + -
488B SER 3.4 9.1 + - - +
489B LEU* 3.2 9.6 + - - +
491B LEU* 1.3 79.8 - - - +
493B SER* 1.3 59.4 + - - +
494B TYR 3.2 3.3 + - - -
495B ILE* 4.5 13.2 - - + +
496B LEU* 3.4 46.0 + - + +
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Residues in contact with SER 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A PHE* 3.9 12.3 - - - -
94A TYR* 4.1 8.9 + - - -
274A LYS* 4.2 14.0 + - - -
399A TRP* 4.6 4.2 - - - -
400A MET* 4.1 34.0 - - - +
401A GLY* 4.8 5.6 + - - +
465B GLN* 6.3 0.2 - - - +
489B LEU 3.1 13.1 + - - -
490B PHE* 3.2 17.3 + - - -
492B LEU* 1.3 74.7 - - - +
494B TYR* 1.3 56.2 + - - +
496B LEU* 4.5 6.4 - - - +
497B PHE* 4.6 10.9 + - - +
500B ASN* 5.7 1.8 + - - +
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Residues in contact with TYR 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 4.4 12.8 - - + -
80A PHE* 5.0 4.0 - + + -
93A VAL* 3.4 16.7 - - + +
94A TYR* 3.2 32.1 - + - +
97A LEU* 3.3 32.2 - - + +
132A PRO* 3.7 31.6 + - + +
135A TYR 4.1 10.0 + - - -
136A TYR* 4.2 22.7 - + - -
139A LEU* 3.5 26.3 - - + +
490B PHE 3.7 10.8 - - - +
491B LEU* 3.0 10.8 + - + +
493B SER* 1.3 80.2 + - - +
495B ILE* 1.3 68.5 + - + +
496B LEU 3.2 1.3 + - - -
497B PHE* 3.5 15.5 + - - +
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Residues in contact with ILE 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 6.2 1.8 - - - +
128A LEU 4.6 2.3 - - - +
129A LEU* 3.9 30.5 - - + +
132A PRO* 4.1 20.5 - - + +
133A THR* 5.5 6.5 - - - +
136A TYR* 6.4 0.4 - - + -
491B LEU* 3.0 43.5 + - + +
492B LEU* 3.7 13.9 + - + +
494B TYR* 1.3 78.9 - - + +
496B LEU* 1.3 62.4 + - + +
497B PHE 3.2 4.6 + - - -
498B LEU 4.7 0.3 + - - -
499B VAL* 4.9 0.7 - - - +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 4.6 9.4 - - + -
400A MET* 5.0 0.7 - - + -
461B ALA* 4.3 22.0 - - + +
464B ILE* 4.2 13.2 - - + -
465B GLN* 3.5 32.5 - - + +
492B LEU* 3.4 39.2 + - + +
493B SER* 4.9 3.8 - - - -
494B TYR 3.2 0.6 - - - -
495B ILE* 1.3 82.1 - - + +
497B PHE* 1.3 60.0 + - - -
498B LEU 3.6 0.9 - - - -
499B VAL* 3.9 17.9 - - + -
500B ASN* 2.7 42.8 + - - +
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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