Contacts of the helix formed by residues 1634 - 1645 (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 LYS1634 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602B POP 2.9 24.7 - - - +
1594B THR* 3.7 31.8 - - + +
1595B GLY* 6.1 1.1 - - - -
1632B ARG* 3.7 15.7 + - - +
1633B PHE* 1.3 71.2 - - - +
1635B THR* 1.3 67.6 + - - +
1636B ASP* 3.2 4.7 - - + +
1637B PHE* 2.8 15.0 + - + +
1638B LEU* 2.7 20.0 + - - -
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Residues in contact with THR1635 (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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602B POP 3.2 33.4 + - - -
1633B PHE 3.7 1.4 + - - -
1634B LYS* 1.3 70.3 - - - +
1636B ASP* 1.3 70.0 + - - +
1638B LEU* 3.3 5.0 + - - +
1639B SER* 3.2 23.9 + - - +
1671B TYR* 4.7 0.5 - - - -
1672B HIS* 3.4 26.9 - - + +
1675B LEU* 4.8 5.3 - - + +
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Residues in contact with ASP1636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1634B LYS* 3.2 3.8 - - + +
1635B THR* 1.3 86.3 - - - +
1637B PHE* 1.3 62.2 + - - +
1639B SER* 3.1 9.5 + - - -
1640B LYS* 3.1 22.9 + - - +
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Residues in contact with PHE1637 (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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1592B PHE* 4.1 15.3 - + - -
1599B GLY* 3.5 32.5 - - - -
1602B LEU* 4.5 4.5 - - + -
1603B ILE* 3.3 32.5 - - + -
1633B PHE* 3.7 38.8 - + + -
1634B LYS* 2.8 21.4 + - + +
1636B ASP* 1.3 73.3 - - - +
1638B LEU* 1.3 65.2 + - - +
1640B LYS* 3.1 21.7 + - + +
1641B TRP* 3.1 47.5 + + - -
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Residues in contact with LEU1638 (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 4.9 9.0 - - + -
1633B PHE* 4.2 19.2 - - + +
1634B LYS 2.7 14.7 + - - +
1635B THR* 3.5 9.9 - - - +
1637B PHE* 1.3 75.1 - - - +
1639B SER* 1.3 61.6 + - - +
1641B TRP* 3.3 17.7 + - + +
1642B PHE* 3.4 25.5 - - + -
1668B TYR* 3.1 29.6 - - + +
1672B HIS* 3.7 33.7 - - + +
1675B LEU* 4.1 15.9 - - + -
1676B LEU* 4.2 16.2 - - + -
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Residues in contact with SER1639 (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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1635B THR* 3.2 9.1 + - - +
1636B ASP* 3.1 18.0 + - - -
1638B LEU* 1.3 75.7 - - - +
1640B LYS* 1.3 65.1 + - - +
1642B PHE* 3.1 15.1 + - - +
1643B VAL* 3.5 18.0 - - - +
1675B LEU* 3.6 26.4 - - - +
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Residues in contact with LYS1640 (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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1600B ASP* 2.7 32.6 + - - -
1603B ILE* 3.9 17.3 - - + -
1636B ASP 3.1 16.0 + - - +
1637B PHE* 3.1 20.8 + - + +
1639B SER* 1.3 76.4 + - - +
1641B TRP* 1.3 63.5 + - - +
1643B VAL* 2.9 31.2 + - + +
1644B VAL* 3.1 24.6 + - + +
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Residues in contact with TRP1641 (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 3.9 28.5 - + + -
1587B TYR* 5.8 1.6 - + - -
1602B LEU* 3.3 26.0 - - + -
1603B ILE* 4.1 19.3 - - + +
1606B VAL* 3.5 33.9 - - + -
1633B PHE* 3.4 31.0 - + - -
1637B PHE* 3.1 54.2 + + - -
1638B LEU* 3.3 10.3 - - + +
1640B LYS* 1.3 77.4 - - - +
1642B PHE* 1.3 60.1 + - + +
1644B VAL* 3.8 5.1 - - + +
1645B PHE* 3.5 49.6 - + - -
1650B TYR* 2.5 29.2 + - - -
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Residues in contact with PHE1642 (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 5.4 18.6 - + - -
1638B LEU* 3.4 33.4 - - + -
1639B SER* 3.1 9.7 + - - +
1640B LYS 3.1 1.2 - - - -
1641B TRP* 1.3 81.4 - - + +
1643B VAL* 1.3 61.8 + - + +
1650B TYR* 3.2 35.7 + + - -
1675B LEU* 4.0 22.0 - - + -
1676B LEU* 4.5 15.3 - - + -
1678B GLY* 5.9 6.1 - - - -
1679B LEU* 4.7 24.9 - - + -
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Residues in contact with VAL1643 (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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1639B SER* 3.5 13.5 - - - +
1640B LYS* 2.9 36.1 + - + +
1642B PHE* 1.3 84.1 - - + +
1644B VAL* 1.3 72.0 + - + +
1645B PHE 3.6 9.0 - - - +
1650B TYR* 4.0 0.4 - - - -
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Residues in contact with VAL1644 (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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1603B ILE* 3.8 24.5 - - + -
1607B LEU* 5.6 2.0 - - - +
1640B LYS* 3.6 37.7 - - + +
1641B TRP* 3.8 5.2 - - - +
1643B VAL* 1.3 78.5 - - + +
1645B PHE* 1.3 90.8 + - + +
1646B PRO* 3.8 3.1 - - - +
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Residues in contact with PHE1645 (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 4.2 11.2 - - - -
1603B ILE* 4.2 8.7 - - + -
1606B VAL* 3.6 25.6 - - + -
1607B LEU* 3.5 44.9 - - + -
1610B LEU* 4.6 7.6 - - + -
1614B TYR* 4.3 10.5 - + - -
1641B TRP* 3.5 32.3 - + - -
1643B VAL 3.6 7.1 - - - +
1644B VAL* 1.3 91.9 - - + +
1646B PRO* 1.3 75.8 - - + +
1647B GLY 3.7 0.2 + - - -
1649B ALA* 4.0 8.5 - - + -
1650B TYR* 3.1 46.6 + + + +
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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