Contacts of the strand formed by residues 1617 - 1621 (chain A) in PDB entry 5V7W
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 PHE1617 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1616A ASN* 1.3 79.1 - - - +
1618A CYS* 1.3 65.4 - - - +
1619A VAL* 3.7 25.6 - - + -
1651A ILE* 4.7 3.4 - - + -
1652A GLN 3.2 14.1 - - - +
1653A ASN* 3.9 6.1 - - + -
1654A PRO* 4.8 0.7 - - - -
1690A PRO* 4.3 11.7 - - + -
1693A ASN* 3.6 45.8 - - + +
1694A ARG* 3.8 37.5 - - + -
1617B PHE* 4.4 1.8 - + - -
1618B CYS* 3.2 4.7 - - - +
1619B VAL* 2.8 65.5 + - + +
1649B GLU* 4.9 0.9 - - - -
1693B ASN* 6.1 0.2 - - - -
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Residues in contact with CYS1618 (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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1617A PHE* 1.3 74.9 - - - +
1619A VAL* 1.3 66.7 + - - +
1620A VAL* 4.1 5.4 - - + -
1650A ARG 3.8 1.0 - - - +
1651A ILE* 3.8 1.0 - - - -
1652A GLN* 2.9 54.5 + - - +
1654A PRO* 6.5 0.2 - - - -
1617B PHE 3.2 7.4 - - - +
1618B CYS* 2.0 46.7 - - - +
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Residues in contact with VAL1619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1617A PHE* 3.7 17.9 - - + -
1618A CYS* 1.3 76.3 - - - +
1620A VAL* 1.3 63.0 + - - +
1649A GLU* 3.2 42.8 - - + +
1650A ARG 3.8 1.8 - - - -
1651A ILE* 4.1 12.6 - - + -
1693A ASN* 4.0 12.3 - - - +
1796A LEU* 6.1 0.7 - - + -
1616B ASN* 3.4 14.1 - - - +
1617B PHE* 2.9 49.2 + - + -
1694B ARG* 2.9 17.2 + - - +
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Residues in contact with VAL1620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1618A CYS* 4.9 3.6 - - + -
1619A VAL* 1.3 79.1 - - - +
1621A GLU* 1.3 71.6 + - - +
1622A LEU* 3.7 4.1 + - + +
1649A GLU* 3.2 3.2 - - - -
1650A ARG* 2.8 60.2 + - + +
1652A GLN* 3.8 33.9 - - + +
1614B GLN* 4.8 1.1 - - - +
1616B ASN* 3.5 22.4 - - + +
1694B ARG* 4.2 0.7 - - - -
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Residues in contact with GLU1621 (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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1620A VAL* 1.3 78.5 - - - +
1622A LEU* 1.3 70.4 + - - +
1623A LEU* 4.0 2.2 + - + +
1624A PRO* 5.9 1.2 - - - +
1646A GLU 5.1 0.3 - - - +
1647A LYS* 3.6 28.6 - - + +
1648A ILE 3.8 10.5 - - - +
1649A GLU* 3.9 13.0 - - + -
1614B GLN* 3.0 37.0 + - - +
1616B ASN* 2.9 17.2 + - - +
1694B ARG* 3.6 29.8 + - - +
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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