Contacts of the strand formed by residues 1605 - 1609 (chain B) in PDB entry 2A73
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 TRP1605 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1498B ILE* 3.6 37.2 - - + +
1500B LYS* 4.3 27.4 - - + +
1505B VAL* 3.6 34.8 - - + -
1509B GLU* 6.0 1.6 - - + -
1510B ARG* 4.3 12.1 - - + -
1513B LYS* 3.7 31.0 - - + -
1581B LEU* 3.8 11.5 - - + +
1582B MET* 3.2 9.2 - - - +
1583B TRP* 2.9 87.2 + + + +
1604B THR* 1.3 69.3 - - - +
1606B VAL* 1.3 61.8 - - - +
1607B GLU* 3.2 26.9 + - - +
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Residues in contact with VAL1606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497B PHE* 4.2 9.4 - - + -
1500B LYS* 2.6 33.6 + - - +
1572B LEU* 4.0 25.4 - - + +
1574B LEU* 3.9 28.5 - - + -
1580B TYR* 4.3 10.3 - - + -
1581B LEU 3.8 1.8 - - - -
1582B MET* 3.9 33.0 - - + -
1600B ILE* 4.2 12.3 - - + -
1604B THR* 3.3 13.9 + - + +
1605B TRP* 1.3 76.4 - - - +
1607B GLU* 1.3 59.6 + - - +
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Residues in contact with GLU1607 (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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1500B LYS* 4.1 14.8 - - - +
1505B VAL* 4.7 2.2 - - - -
1510B ARG* 2.8 40.8 + - - -
1580B TYR* 3.1 13.1 - - - -
1581B LEU* 2.9 41.3 + - + +
1605B TRP* 3.2 25.2 + - - +
1606B VAL* 1.3 78.7 - - - +
1608B HIS* 1.3 64.9 + - - +
1623B GLN* 2.8 26.4 + - - +
1627B LEU* 3.7 9.9 - - - +
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Residues in contact with HIS1608 (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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1575B GLU* 5.6 2.6 + - - -
1578B LYS* 3.8 36.0 + - + -
1579B HIS 3.6 4.8 + - - -
1580B TYR* 3.5 24.1 + - + -
1581B LEU* 4.9 0.4 - - - -
1607B GLU* 1.3 77.7 - - - +
1609B TRP* 1.3 70.7 + - - +
1610B PRO* 3.4 27.0 - - + +
1611B GLU 5.6 0.4 - - - -
1614B GLU* 4.7 10.7 + - - -
1620B ASN* 5.7 2.5 - - - -
1623B GLN* 2.8 33.3 + - - +
1627B LEU* 4.2 2.3 - - - +
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Residues in contact with TRP1609 (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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1524B LYS* 3.3 51.0 - - + +
1545B GLN* 5.5 2.7 - - - -
1547B ILE* 4.8 2.7 - - + -
1579B HIS* 2.7 46.0 + - + +
1580B TYR* 3.8 2.9 - - - +
1581B LEU* 3.6 41.7 - - + -
1607B GLU 3.6 0.8 + - - -
1608B HIS* 1.3 78.6 - - - +
1610B PRO* 1.3 97.2 + - + +
1611B GLU 3.6 0.9 + - - -
1615B CYS* 6.2 0.6 - - - -
1624B CYS* 5.5 3.5 + - - +
1627B LEU* 3.5 39.1 - - + +
1628B GLY* 4.9 1.1 - - - -
1630B PHE* 6.0 0.9 - + - -
1631B THR* 3.1 29.2 - - + -
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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