Contacts of the strand formed by residues 1653 - 1659 (chain A) 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 VAL1653 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701A OXN 4.6 11.7 - - - +
1618A TYR* 3.3 39.7 - - + +
1620A ILE* 4.3 12.6 - - + -
1649A ALA 3.4 7.2 - - - +
1650A TYR* 2.9 16.8 + - - +
1651A ASP 3.9 1.8 - - - +
1652A ASN* 1.3 74.7 - - - +
1654A SER* 1.3 58.3 + - - +
1655A ALA* 3.9 11.2 - - - +
1656A VAL* 3.7 31.0 - - + -
1684A ARG* 2.9 30.9 + - + +
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Residues in contact with SER1654 (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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1582A ASN* 3.9 7.6 + - - -
1617A PRO* 3.4 27.9 - - - +
1618A TYR 2.9 10.7 + - - -
1619A GLU* 4.1 16.8 - - - -
1651A ASP 5.2 1.1 - - - -
1652A ASN 2.9 1.9 + - - -
1653A VAL* 1.3 73.0 - - - +
1655A ALA* 1.3 63.4 + - - +
1684A ARG* 3.3 19.7 - - - +
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Residues in contact with ALA1655 (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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1618A TYR 4.1 1.0 + - - -
1619A GLU* 3.5 10.0 - - - +
1620A ILE 2.9 25.5 + - - +
1653A VAL* 3.3 3.6 - - - +
1654A SER* 1.3 83.8 - - - +
1656A VAL* 1.3 67.2 + - - +
1657A TYR* 3.9 33.0 - - + +
1684A ARG* 3.4 13.0 - - - +
1686A VAL* 5.0 5.2 - - + -
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Residues in contact with VAL1656 (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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701A OXN 4.3 25.4 - - + -
1620A ILE* 3.1 18.2 - - + +
1622A VAL* 3.9 24.0 - - + -
1653A VAL* 3.7 20.4 - - + -
1655A ALA* 1.3 76.3 - - - +
1657A TYR* 1.3 62.4 + - - +
1658A ILE* 3.7 8.6 + - + +
1684A ARG* 2.8 10.8 + - + +
1685A LEU* 3.6 25.5 - - + -
1686A VAL 2.8 26.2 + - - -
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Residues in contact with TYR1657 (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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1578A SER* 5.0 0.7 - - - -
1584A ILE* 5.9 4.5 - - + -
1619A GLU* 3.0 34.5 + - + -
1620A ILE 2.7 19.7 + - - +
1621A VAL* 3.5 19.0 - - + +
1622A VAL* 2.7 33.4 + - - +
1655A ALA* 3.9 18.6 - - + +
1656A VAL* 1.3 73.9 - - - +
1658A ILE* 1.3 57.7 + - - +
1659A TYR* 4.0 0.4 - - + -
1686A VAL* 3.2 33.9 - - + +
1688A ILE* 4.0 19.7 - - + -
1694A LEU* 4.0 18.4 - - + -
1697A HIS* 3.3 45.7 + + + +
1698A ILE* 6.0 1.8 - - + -
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Residues in contact with ILE1658 (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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1622A VAL* 3.4 20.2 - - + -
1624A LEU* 3.6 32.1 - - + -
1656A VAL* 4.2 7.4 - - + +
1657A TYR* 1.3 74.2 - - - +
1659A TYR* 1.3 60.0 + - - +
1660A ASN 4.2 0.2 + - - -
1661A CYS* 4.2 5.7 + - + -
1685A LEU* 4.2 27.1 - - + -
1686A VAL 2.7 10.7 + - - +
1687A PHE* 3.6 52.4 - - + +
1688A ILE* 2.8 29.2 + - - +
1752A LEU* 5.4 3.4 - - + -
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Residues in contact with TYR1659 (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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1621A VAL* 5.0 6.1 - - + -
1622A VAL 2.9 14.3 + - - +
1623A ASP* 3.5 16.2 - - - -
1624A LEU* 2.7 32.9 + - - +
1657A TYR* 4.0 0.6 + - + -
1658A ILE* 1.3 73.2 - - - +
1660A ASN* 1.3 95.9 + - - +
1661A CYS 3.5 1.1 - - - -
1688A ILE* 3.9 24.5 - - + -
1689A ASP 3.7 19.7 + - - -
1690A CYS 3.9 0.9 - - - -
1691A PRO* 3.6 38.4 - - + +
1694A LEU* 5.5 2.9 - - + -
1705A LEU* 4.0 26.9 - - + -
1709A THR* 3.4 20.1 + - + +
1713A GLU* 4.0 15.6 + - - +
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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