Contacts of the strand formed by residues 1620 - 1624 (chain D) in PDB entry 5JH5
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 CYS1620 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C TYR* 3.9 25.8 - - + -
1610D ASN* 3.2 11.6 - - - +
1611D LEU 2.7 35.0 + - - +
1613D VAL* 6.2 0.2 - - - -
1617D ARG* 4.7 8.1 - - - -
1618D GLY 4.2 8.3 - - - +
1619D PRO* 1.3 75.0 - - - +
1621D ASN* 1.3 60.6 + - - +
1622D TRP* 3.3 34.0 - - - -
1691D ARG* 4.2 17.3 - - + -
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Residues in contact with ASN1621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ARG 3.7 17.6 + - - -
165C TYR 4.0 2.0 + - - -
166C ASP 2.9 23.7 + - - +
168C GLN* 3.6 26.0 + - - +
1608D CYS* 4.2 9.7 - - - -
1609D TYR 3.4 2.7 - - - +
1610D ASN* 3.2 27.5 + - - +
1620D CYS* 1.3 74.5 - - - +
1622D TRP* 1.3 70.2 + - - +
1691D ARG* 3.7 7.3 - - - +
1692D TYR* 3.0 46.2 + - + +
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Residues in contact with TRP1622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1608D CYS* 3.2 8.5 - - - -
1609D TYR* 2.9 38.1 + - - +
1611D LEU* 3.5 31.6 + - + -
1613D VAL* 3.5 26.1 - - + +
1617D ARG* 3.7 21.3 - - - -
1620D CYS* 3.3 39.9 - - - -
1621D ASN* 1.3 91.5 - - - +
1623D PHE* 1.3 68.8 + - - +
1647D GLU* 3.8 19.7 - - - -
1649D THR* 3.4 25.6 - - + -
1689D LEU* 3.8 20.6 - - + -
1690D VAL 3.4 9.2 - - - +
1691D ARG* 3.5 32.5 - - + -
1692D TYR* 4.2 1.6 - - - +
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Residues in contact with PHE1623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ARG* 3.6 18.4 - - - -
1599D GLU* 4.9 0.9 - - - -
1606D LEU* 4.0 23.6 - - + -
1607D PRO 3.6 17.5 - - - -
1608D CYS* 4.2 5.8 - - + -
1609D TYR* 5.2 0.7 - - - -
1622D TRP* 1.3 75.2 - - - +
1624D LEU* 1.3 60.8 + - - +
1627D ASP* 5.7 0.4 - - + -
1628D VAL* 3.5 22.0 - - + -
1689D LEU* 3.3 12.4 - - - +
1690D VAL* 2.8 34.2 + - + -
1692D TYR* 3.3 37.9 - + - -
1696D LEU* 3.7 29.8 - - + -
1697D LEU* 3.4 22.2 - - + -
1700D LEU* 4.2 11.4 - - + -
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Residues in contact with LEU1624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1607D PRO 4.7 3.6 + - - -
1609D TYR* 4.1 16.9 - - + +
1623D PHE* 1.3 72.4 - - - +
1625D PHE* 1.3 66.3 + - - +
1626D SER* 4.2 10.3 - - - +
1627D ASP* 2.8 45.2 + - - +
1628D VAL* 3.2 11.4 + - - +
1656D PHE* 4.2 13.0 - - + -
1672D PRO* 4.4 22.9 - - + -
1687D VAL* 3.7 31.4 - - + -
1688D GLU 3.8 2.7 - - - +
1689D LEU* 4.1 6.1 - - + -
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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