Contacts of the strand formed by residues 1618 - 1623 (chain B) 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 TYR1618 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702B OXN 4.1 5.7 - - - -
1582B ASN* 3.9 2.9 - - - -
1583B PRO* 3.5 17.3 - - + +
1585B PHE* 3.9 15.7 - + + -
1610B LEU* 3.3 40.4 - - + +
1613B TYR* 4.9 4.0 - - + +
1614B TYR* 3.6 27.2 - - + +
1616B LYS 3.3 14.4 - - - +
1617B PRO* 1.3 75.4 - - - +
1619B GLU* 1.3 68.2 + - - +
1620B ILE* 3.9 14.1 - - + -
1649B ALA* 2.8 32.8 + - - +
1652B ASN* 3.2 14.9 + - + -
1653B VAL* 3.4 28.5 - - + +
1654B SER* 2.9 24.0 + - - -
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Residues in contact with GLU1619 (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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1578B SER* 2.6 37.0 + - - -
1580B ALA* 4.1 5.4 - - - +
1582B ASN* 2.8 21.0 + - + -
1583B PRO 2.9 10.6 + - - +
1584B ILE* 3.5 9.5 - - + +
1585B PHE* 2.9 26.7 + - - -
1618B TYR* 1.3 79.9 - - - +
1620B ILE* 1.3 69.3 + - - +
1653B VAL* 5.0 0.2 - - - -
1654B SER* 4.1 6.4 - - - -
1655B ALA* 3.5 24.9 - - - +
1657B TYR* 2.7 36.8 + - + -
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Residues in contact with ILE1620 (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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702B OXN 3.7 54.1 - - - +
1572B PHE* 5.1 4.0 - - + -
1585B PHE* 3.3 15.3 - - + +
1587B TYR* 4.9 4.3 - - + -
1610B LEU* 5.3 0.9 - - + -
1618B TYR* 3.9 21.8 - - + -
1619B GLU* 1.3 79.8 - - - +
1621B VAL* 1.3 68.1 + - - +
1622B VAL* 3.9 23.6 - - + -
1653B VAL* 4.0 14.4 - - + -
1655B ALA 3.0 10.0 + - - +
1656B VAL* 3.3 9.4 - - + +
1657B TYR* 2.8 29.2 + - - -
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Residues in contact with VAL1621 (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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1584B ILE* 3.8 18.6 - - + -
1585B PHE 2.7 9.0 + - - +
1586B TYR* 3.4 40.1 - - + +
1587B TYR 2.9 25.6 + - - -
1620B ILE* 1.3 74.9 - - - +
1622B VAL* 1.3 68.2 + - - +
1623B ASP 3.7 0.7 + - - +
1657B TYR* 3.5 26.9 - - + +
1659B TYR* 4.7 6.7 - - + -
1694B LEU* 5.0 9.2 - - + -
1698B ILE* 4.2 10.1 - - + -
1705B LEU* 4.0 15.0 - - + -
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Residues in contact with VAL1622 (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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702B OXN 3.7 38.6 - - + -
1587B TYR* 3.7 12.3 - - + -
1620B ILE* 3.9 18.4 - - + -
1621B VAL* 1.3 75.3 - - - +
1623B ASP* 1.3 59.4 + - - +
1624B LEU* 3.3 33.9 + - + +
1656B VAL* 4.0 17.7 - - + -
1657B TYR 2.6 13.3 + - - +
1658B ILE* 3.8 10.7 - - + -
1659B TYR* 2.9 29.5 + - - +
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Residues in contact with ASP1623 (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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1586B TYR* 5.6 2.0 - - + -
1587B TYR 2.8 17.0 + - - +
1588B VAL* 3.9 7.0 - - + +
1589B ALA* 3.1 24.0 + - - +
1590B ARG* 3.1 12.4 + - - -
1621B VAL* 3.7 2.9 + - + +
1622B VAL* 1.3 69.1 - - - +
1624B LEU* 1.3 60.6 + - - +
1625B THR* 2.5 32.7 + - - +
1627B THR* 4.3 0.2 + - - -
1659B TYR* 3.6 10.4 - - - -
1705B LEU* 4.1 22.2 - - + -
1706B PRO* 3.5 14.7 - - + +
1709B THR* 2.7 25.0 + - - -
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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