Contacts of the strand formed by residues 1717 - 1725 (chain B) in PDB entry 2D4Q
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 LYS1717 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1715B ASP 5.0 3.1 - - - +
1716B LEU* 1.3 74.9 - - - +
1718B VAL* 1.3 59.9 + - - +
1719B PHE* 4.0 15.9 - - + -
1734B ILE 3.8 1.7 - - - +
1735B LYS* 3.6 1.4 - - - -
1736B VAL* 2.9 41.4 + - + +
1802B SER* 3.9 21.0 + - - +
1805B HIS* 6.0 4.2 - - - -
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Residues in contact with VAL1718 (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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1716B LEU* 3.7 23.5 + - + +
1717B LYS* 1.3 74.9 - - - +
1719B PHE* 1.3 69.0 + - - +
1720B HIS* 3.6 40.9 + - + +
1733B SER* 4.6 2.5 - - - -
1734B ILE 3.7 2.5 - - - -
1735B LYS* 4.2 32.3 - - + +
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Residues in contact with PHE1719 (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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1717B LYS* 4.0 20.4 - - + -
1718B VAL* 1.3 80.1 - - - +
1720B HIS* 1.3 63.1 + - - +
1722B ALA* 4.5 1.7 - - - +
1732B VAL 4.3 0.9 - - - +
1733B SER* 3.4 1.7 - - - -
1734B ILE* 2.9 45.0 + - + +
1736B VAL* 4.2 14.4 - - + -
1793B HIS* 3.9 22.4 - - + +
1795B GLU* 4.6 12.8 - - + -
1798B ALA* 4.0 21.3 - - + -
1799B ILE* 3.6 52.3 - - + -
1802B SER* 4.1 10.5 - - - -
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Residues in contact with HIS1720 (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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1718B VAL* 3.6 28.5 + - + +
1719B PHE* 1.3 72.6 - - - +
1721B ASN* 1.3 76.7 + - - +
1722B ALA 3.3 0.4 - - - -
1733B SER* 3.1 25.1 + - - +
1735B LYS* 5.9 1.8 - - - -
1793B HIS* 2.7 33.5 - - - -
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Residues in contact with ASN1721 (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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1720B HIS* 1.3 86.3 - - - +
1722B ALA* 1.3 62.8 + - - +
1723B LEU* 5.4 0.5 - - - +
1731B LYS* 6.3 2.0 - - - -
1732B VAL 3.7 6.1 + - - +
1733B SER* 4.6 1.2 + - - -
1792B MET 4.6 1.2 - - - +
1793B HIS* 3.7 9.9 + - + -
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Residues in contact with ALA1722 (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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1719B PHE 4.5 3.6 - - - +
1720B HIS 3.3 1.2 - - - -
1721B ASN* 1.3 81.2 - - - +
1723B LEU* 1.3 62.3 + - - +
1731B LYS* 3.6 6.2 - - - +
1732B VAL* 2.9 40.0 + - + +
1734B ILE* 3.8 31.0 - - + -
1791B PHE* 5.1 0.9 - - + -
1792B MET 3.4 10.5 - - - +
1793B HIS* 3.6 15.3 - - + +
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Residues in contact with LEU1723 (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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1721B ASN 5.4 0.2 - - - +
1722B ALA* 1.3 76.6 - - - +
1724B LYS* 1.3 62.5 + - - +
1725B LEU* 3.5 26.6 + - + +
1729B ASP* 3.7 26.0 - - + +
1730B THR* 3.4 24.9 - - - +
1731B LYS* 4.0 12.6 - - + +
1791B PHE* 3.3 6.7 - - - -
1792B MET* 2.9 51.0 + - + +
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Residues in contact with LYS1724 (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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1663B SER* 5.3 3.4 + - - -
1723B LEU* 1.3 72.4 - - - +
1725B LEU* 1.3 69.7 + - - +
1726B ALA* 5.1 8.1 - - + -
1729B ASP* 3.2 7.8 - - - +
1730B THR* 2.8 57.0 + - + +
1732B VAL* 4.2 11.1 - - + +
1743B VAL* 5.1 8.7 - - + +
1760B ASP* 4.6 13.5 + - - -
1762B TYR* 4.8 4.2 + - - -
1789B LEU* 4.3 29.3 - - - +
1790B THR 3.6 8.5 - - - +
1791B PHE* 3.7 25.8 - - + -
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Residues in contact with LEU1725 (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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1723B LEU* 3.7 20.9 - - + +
1724B LYS* 1.3 76.3 - - - +
1726B ALA* 1.3 64.3 + - - +
1729B ASP* 3.2 28.7 - - - +
1777B GLN* 3.7 11.7 - - - +
1790B THR* 2.9 44.2 + - + +
1792B MET* 3.6 35.9 - - + -
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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