Contacts of the strand formed by residues 1675 - 1678 (chain A) in PDB entry 5A31
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 GLU1675 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966A PRO* 5.7 1.8 - - - -
980A ARG* 3.6 13.9 - - - +
982A ASP* 4.5 7.3 - - - +
983A LEU* 5.0 9.8 - - + +
1667A LYS* 3.8 3.8 - - - +
1668A VAL* 2.8 58.6 + - + +
1674A TRP* 1.3 76.8 - - - +
1676A LEU* 1.3 73.0 + - - +
1677A LEU* 5.0 4.2 - - + +
1697A LEU* 4.0 19.8 - - - +
1698A TYR 3.2 23.3 - - - +
1699A VAL* 3.8 14.5 - - + +
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Residues in contact with LEU1676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966A PRO* 6.3 0.4 - - - +
983A LEU* 6.1 0.9 - - - +
1665A GLN* 3.6 21.5 - - - +
1667A LYS* 3.9 29.4 - - + +
1668A VAL* 6.2 0.2 - - - -
1675A GLU* 1.3 87.7 - - - +
1677A LEU* 1.3 77.9 + - - +
1678A ILE* 4.1 17.5 - - + +
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Residues in contact with LEU1677 (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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1619A LEU* 5.4 0.9 - - + -
1665A GLN* 4.0 2.3 - - - +
1666A ILE* 2.4 67.6 + - + +
1667A LYS* 4.3 0.2 - - - +
1668A VAL* 6.3 0.6 - - + +
1675A GLU* 5.0 7.2 - - + +
1676A LEU* 1.3 80.2 - - - +
1678A ILE* 1.3 87.4 + - - +
1679A ASP* 4.6 0.4 - - - +
1686A HIS* 3.7 27.8 - - + +
1687A LEU* 3.9 30.5 - - + -
1690A ILE* 4.6 6.7 - - + -
1697A LEU* 4.5 22.2 - - + -
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Residues in contact with ILE1678 (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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1664A LYS 4.8 0.2 - - - +
1665A GLN* 4.1 17.9 - - + +
1676A LEU* 4.2 15.7 - - + -
1677A LEU* 1.3 85.2 - - - +
1679A ASP* 1.3 81.2 + - - +
1680A LEU* 4.2 8.9 + - + +
1684A THR 5.0 2.8 + - - -
1686A HIS* 5.2 3.8 - - - +
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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
------------------------------------------------------------
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