Contacts of the helix formed by residues 1598 - 1611 (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 ASN1598 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1562B GLU* 4.2 10.7 + - - +
1596B GLN 3.8 2.4 + - - -
1597B ILE* 1.3 77.0 - - - +
1599B GLY* 1.3 67.8 + - - +
1600B ASP* 3.2 19.8 + - - +
1601B LEU* 2.9 67.0 + - + +
1602B LEU 3.3 8.3 + - - -
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Residues in contact with GLY1599 (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* 5.1 4.7 - - - -
1597B ILE 3.4 5.2 + - - -
1598B ASN* 1.3 72.4 + - - +
1600B ASP* 1.3 62.3 + - - +
1602B LEU* 3.0 7.6 + - - +
1603B ILE* 3.0 24.4 + - - +
1637B PHE* 3.5 31.4 - - - -
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Residues in contact with ASP1600 (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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1598B ASN* 3.2 15.3 + - - +
1599B GLY* 1.3 73.9 - - - +
1601B LEU* 1.3 58.4 + - + +
1603B ILE* 3.2 9.1 + - - +
1604B TYR* 2.8 32.9 + - - +
1637B PHE* 5.7 0.2 - - - -
1640B LYS* 2.7 36.4 + - - -
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Residues in contact with LEU1601 (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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1562B GLU* 3.4 44.4 - - + +
1563B PHE* 3.7 30.7 - - + +
1566B LEU* 3.7 12.8 - - + -
1597B ILE* 5.4 0.7 - - + -
1598B ASN* 2.9 33.8 + - + +
1600B ASP* 1.3 78.0 - - + +
1602B LEU* 1.3 57.5 + - - +
1604B TYR* 3.6 8.1 - - + +
1605B HIS* 2.8 30.7 + - - +
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Residues in contact with LEU1602 (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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1566B LEU* 3.5 16.3 - - + +
1571B ILE* 4.2 35.0 - - + -
1572B PHE* 5.2 0.4 - - + -
1587B TYR* 4.6 8.7 - - + -
1592B PHE* 4.3 23.6 - - + -
1597B ILE* 4.5 6.1 - - + -
1598B ASN 3.3 5.9 + - - +
1599B GLY* 3.0 11.3 + - - +
1601B LEU* 1.3 77.9 - - - +
1603B ILE* 1.3 57.2 + - - +
1605B HIS* 3.2 2.4 + - - +
1606B VAL* 2.8 46.0 + - + +
1633B PHE* 4.5 8.1 - - + -
1637B PHE* 4.5 5.2 - - + -
1641B TRP* 3.3 35.2 - - + -
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Residues in contact with ILE1603 (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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1599B GLY 3.0 16.3 + - - +
1600B ASP* 3.5 12.1 - - - +
1602B LEU* 1.3 75.9 - - - +
1604B TYR* 1.3 58.3 + - - +
1606B VAL* 3.3 2.4 + - - +
1607B LEU* 2.8 30.6 + - + +
1637B PHE* 3.3 31.4 - - + -
1640B LYS* 3.9 33.4 - - + -
1641B TRP* 4.1 20.0 - - + +
1644B VAL* 3.8 32.3 - - + -
1645B PHE* 4.2 8.3 - - + -
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Residues in contact with TYR1604 (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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1563B PHE* 3.2 28.0 - + - -
1600B ASP 2.8 17.9 + - - +
1601B LEU* 3.6 8.3 - - + +
1603B ILE* 1.3 75.4 - - - +
1605B HIS* 1.3 58.6 + - - +
1607B LEU* 3.2 16.7 + - + +
1608B LEU* 2.9 76.2 + - + +
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Residues in contact with HIS1605 (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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1563B PHE* 3.4 31.8 - + + -
1566B LEU* 4.0 24.9 + - + -
1567B LYS* 3.8 31.3 - - + +
1571B ILE* 3.7 18.8 - - + +
1572B PHE* 3.1 33.0 + - + +
1601B LEU 2.8 20.6 + - - +
1602B LEU* 3.7 4.1 + - - +
1604B TYR* 1.3 69.7 - - - +
1606B VAL* 1.3 65.0 + - - +
1608B LEU* 4.1 1.7 - - - +
1609B THR* 2.7 46.6 + - - -
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Residues in contact with VAL1606 (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 4.1 5.2 - - - +
1572B PHE* 3.8 42.6 - - + -
1587B TYR* 5.5 2.0 - - + -
1602B LEU* 2.8 33.5 + - + +
1603B ILE 3.6 3.8 - - - +
1605B HIS* 1.3 76.3 - - - +
1607B LEU* 1.3 58.7 + - - +
1609B THR* 3.0 3.5 + - - -
1610B LEU* 2.8 39.3 + - + +
1641B TRP* 3.5 25.6 - - + -
1645B PHE* 3.6 20.2 - - + -
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Residues in contact with LEU1607 (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* 2.8 19.5 + - + +
1604B TYR* 3.2 24.2 + - + +
1606B VAL* 1.3 77.0 - - - +
1608B LEU* 1.3 64.3 + - + +
1610B LEU* 3.7 0.8 - - - +
1611B LYS* 2.8 40.6 + - + +
1614B TYR* 3.9 23.3 - - + +
1644B VAL 5.6 1.6 - - - +
1645B PHE* 3.5 33.6 - - + -
1646B PRO* 5.0 4.0 - - + -
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Residues in contact with LEU1608 (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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1563B PHE* 3.9 16.2 - - + -
1604B TYR* 2.9 71.3 + - + +
1605B HIS* 4.3 3.8 - - - +
1607B LEU* 1.3 81.0 - - + +
1609B THR* 1.3 61.4 + - - +
1611B LYS* 4.1 15.2 - - + +
1612B PRO* 3.5 16.6 - - - +
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Residues in contact with THR1609 (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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1572B PHE* 3.7 21.3 + - + +
1573B TYR* 4.6 0.7 - - - -
1574B GLN* 4.5 12.1 - - + +
1585B PHE* 3.7 21.6 - - + -
1605B HIS* 2.7 38.7 + - - -
1606B VAL 3.0 5.6 + - - -
1608B LEU* 1.3 78.3 - - - +
1610B LEU* 1.3 61.4 + - - +
1612B PRO* 3.6 9.5 - - - +
1613B TYR* 3.7 14.9 - - - -
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Residues in contact with LEU1610 (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 21.3 - - - -
1572B PHE* 3.8 15.7 - - + -
1585B PHE* 3.5 35.4 - - + -
1606B VAL* 2.8 26.0 + - + +
1607B LEU* 4.1 2.0 - - - +
1609B THR* 1.3 78.4 - - - +
1611B LYS* 1.3 53.1 + - - +
1612B PRO 3.3 1.6 - - - -
1613B TYR* 2.8 26.3 + - + +
1614B TYR* 2.8 28.6 + - + -
1618B TYR* 3.3 42.4 - - + +
1620B ILE* 5.3 0.2 - - + -
1645B PHE* 4.6 7.4 - - + -
1649B ALA* 6.3 0.2 - - + -
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Residues in contact with LYS1611 (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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1607B LEU* 2.8 29.7 + - + +
1608B LEU* 4.3 16.7 - - + +
1610B LEU* 1.3 71.6 - - - +
1612B PRO* 1.3 70.7 - - + +
1613B TYR 3.1 1.0 + - - -
1614B TYR* 3.6 43.8 + - + +
1615B ALA* 5.0 1.2 + - - +
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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