Contacts of the helix formed by residues 688 - 693 (chain A) in PDB entry 5IY6
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 688 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A ILE* 1.3 78.6 - - - +
689A ILE* 1.3 61.3 + - - -
690A GLY 3.1 2.9 - - - -
691A ASP* 2.5 34.8 + - - +
692A SER* 3.7 5.2 + - - -
981B LEU* 4.3 12.4 - - - +
1025B ASN* 3.9 15.1 + - - -
1042B PHE* 4.0 10.8 - - - -
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Residues in contact with ILE 689 (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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688A GLY* 1.3 69.6 - - - -
690A GLY* 1.3 58.3 + - - +
692A SER* 2.7 35.3 + - - +
693A ILE* 3.2 19.6 + - + +
828A LEU* 5.1 12.3 - - + -
978B ILE* 4.4 14.1 - - + +
981B LEU* 3.7 31.4 - - + +
982B ILE* 5.1 4.7 - - + +
985B LEU* 4.3 25.6 - - + -
1008B VAL* 5.2 9.0 - - + -
1012B SER* 5.5 2.7 - - - +
1023B ARG* 4.4 16.4 + - - +
1042B PHE* 4.4 20.0 - - + -
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Residues in contact with GLY 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A GLY 3.1 1.6 - - - -
689A ILE* 1.3 78.5 - - - +
691A ASP* 1.3 55.9 + - - +
693A ILE* 3.0 35.6 + - - +
764A ASN* 4.8 0.7 + - - -
1023B ARG* 3.9 23.7 - - - +
1025B ASN* 4.2 7.9 - - - +
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Residues in contact with ASP 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ILE* 3.3 18.3 - - + -
688A GLY* 2.5 39.6 + - - +
690A GLY* 1.3 76.8 - - - +
692A SER* 1.3 57.8 + - - +
693A ILE 3.3 3.1 + - - +
760A LEU* 4.5 6.2 - - - +
764A ASN* 2.6 52.4 + - - +
765A ASN* 3.0 26.4 + - - -
766A PHE* 4.5 10.8 - - + +
785A ILE* 4.5 1.9 - - - +
1025B ASN* 5.0 2.1 + - - +
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Residues in contact with SER 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A GLY 4.1 6.2 + - - -
689A ILE* 2.7 21.5 + - - +
691A ASP* 1.3 79.2 - - - +
693A ILE* 1.3 61.7 + - - +
694A ALA 3.6 1.9 + - - -
784A VAL* 5.5 4.8 - - - +
785A ILE* 3.8 29.1 - - - +
828A LEU* 4.0 34.2 - - - +
978B ILE* 4.9 15.6 - - - +
981B LEU* 5.2 2.3 - - - +
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Residues in contact with ILE 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A ILE* 3.3 24.7 - - + +
690A GLY* 3.0 18.7 + - - +
691A ASP 4.4 3.5 - - - +
692A SER* 1.3 81.1 - - - +
694A ALA* 1.3 74.2 + - - +
759A SER 4.9 1.9 - - - +
760A LEU* 4.5 9.2 - - - +
764A ASN* 5.2 1.4 + - - -
828A LEU* 5.6 4.5 - - + -
1008B VAL* 5.2 9.2 - - + -
1023B ARG* 3.2 47.8 - - - +
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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