Contacts of the strand formed by residues 1730 - 1736 (chain B) in PDB entry 3P7Z
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 THR1730 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1723B LEU* 3.4 6.1 - - - +
1724B LYS* 2.9 60.8 + - + +
1728B LYS* 3.9 7.9 - - - +
1729B ASP* 1.3 77.9 - - - +
1731B LYS* 1.3 72.8 + - - +
1732B VAL* 3.4 8.9 + - + +
1745B SER* 4.7 6.9 - - - -
1747B GLU* 3.5 14.9 + - - +
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Residues in contact with LYS1731 (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* 6.0 3.1 - - - -
1722B ALA 3.5 9.6 - - - +
1723B LEU* 3.7 10.3 - - + +
1730B THR* 1.3 75.1 + - - +
1732B VAL* 1.3 63.5 - - - +
1745B SER* 3.6 0.3 - - - -
1746B ALA* 2.8 35.6 + - + +
1747B GLU* 3.0 39.3 + - + +
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Residues in contact with VAL1732 (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 3.9 3.5 + - - -
1722B ALA* 2.9 52.6 + - + +
1724B LYS* 4.2 19.3 - - + +
1730B THR* 3.4 17.5 - - + +
1731B LYS* 1.3 81.2 - - - +
1733B SER* 1.3 61.2 + - - +
1734B ILE* 4.3 7.6 - - + -
1743B VAL* 3.6 28.7 - - + -
1744B THR 3.2 8.7 - - - +
1745B SER* 4.0 10.5 - - - +
1746B ALA* 3.8 5.4 - - - +
1791B PHE* 4.3 6.7 - - + -
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Residues in contact with SER1733 (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* 4.4 4.0 - - - -
1719B PHE 3.3 7.4 - - - -
1720B HIS* 3.3 28.6 + - - -
1721B ASN 4.9 0.7 + - - -
1732B VAL* 1.3 74.9 - - - +
1734B ILE* 1.3 62.2 + - - +
1735B LYS* 3.9 20.4 - - - +
1742B GLN 3.4 2.3 - - - +
1743B VAL* 3.3 5.0 - - - -
1744B THR* 2.7 39.7 + - - -
1746B ALA* 4.7 8.2 - - - +
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Residues in contact with ILE1734 (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* 2.8 50.1 + - + +
1722B ALA* 3.8 24.9 - - + -
1732B VAL* 4.3 7.2 - - + -
1733B SER* 1.3 75.0 - - - +
1735B LYS* 1.3 61.7 + - - +
1736B VAL* 4.6 6.1 - - + -
1741B VAL* 4.4 20.0 - - + -
1742B GLN 3.7 2.5 - - - +
1743B VAL* 4.9 6.5 - - + -
1778B PHE* 3.9 31.6 - - + -
1791B PHE* 4.0 18.8 - - + -
1793B HIS* 5.5 0.2 - - + -
1799B ILE* 4.2 25.1 - - + -
1803B ILE* 5.2 0.4 - - + -
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Residues in contact with LYS1735 (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* 4.0 34.6 - - + +
1717B LYS 3.5 4.9 - - - -
1718B VAL* 3.9 28.9 - - + +
1720B HIS* 6.0 1.1 - - - -
1733B SER* 4.4 10.5 - - - +
1734B ILE* 1.3 76.0 - - - +
1736B VAL* 1.3 61.1 + - - +
1737B GLY 3.9 1.1 + - - -
1741B VAL* 3.5 4.4 - - - +
1742B GLN* 2.7 54.9 + - + +
1744B THR* 3.5 30.6 + - - +
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Residues in contact with VAL1736 (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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1715B ASP 4.0 1.2 - - - +
1716B LEU* 3.5 4.0 - - - -
1717B LYS* 2.9 44.2 + - + +
1719B PHE* 4.1 15.3 - - + -
1734B ILE* 4.5 9.6 - - + +
1735B LYS* 1.3 74.3 - - - +
1737B GLY* 1.3 70.6 + - - +
1740B ALA 4.1 1.6 - - - -
1741B VAL* 4.5 4.0 - - + +
1799B ILE* 4.8 1.1 - - + +
1802B SER* 3.2 41.3 - - - +
1803B ILE* 4.1 18.8 - - + +
1806B ILE* 3.9 14.8 - - + -
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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