Contacts of the helix formed by residues 1598 - 1611 (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 ASN1598 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1562A GLU* 5.9 1.1 - - - +
1596A GLN 4.2 0.6 - - - -
1597A ILE* 1.3 73.0 - - - +
1599A GLY* 1.3 58.9 + - - +
1600A ASP* 3.2 25.7 - - - +
1601A LEU* 2.7 89.2 + - + +
1602A LEU 3.4 2.9 + - - -
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Residues in contact with GLY1599 (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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1592A PHE* 4.8 6.7 - - - -
1597A ILE 2.8 10.0 + - - -
1598A ASN* 1.3 72.3 + - - +
1600A ASP* 1.3 61.3 + - - +
1602A LEU* 3.2 10.5 + - - +
1603A ILE* 3.3 7.1 + - - +
1637A PHE* 3.0 43.0 - - - -
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Residues in contact with ASP1600 (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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1598A ASN* 3.2 23.8 + - - +
1599A GLY* 1.3 76.8 + - - +
1601A LEU* 1.3 52.8 + - + +
1603A ILE* 3.2 10.9 + - - +
1604A TYR* 2.8 35.1 + - - +
1637A PHE* 5.6 0.9 - - - -
1640A LYS* 4.0 24.4 - - - +
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Residues in contact with LEU1601 (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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1562A GLU* 4.6 19.3 - - + +
1563A PHE* 3.5 40.0 - - + +
1566A LEU* 3.1 26.0 - - + +
1597A ILE* 5.6 0.2 - - + -
1598A ASN* 2.7 57.0 + - + +
1600A ASP* 1.3 72.2 - - + +
1602A LEU* 1.3 57.9 + - - +
1604A TYR* 4.2 8.5 - - + -
1605A HIS* 2.9 22.7 + - - +
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Residues in contact with LEU1602 (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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1566A LEU* 3.5 12.6 - - + +
1571A ILE* 3.7 37.7 - - + -
1587A TYR* 3.9 17.3 - - + +
1592A PHE* 3.4 37.5 - - + -
1597A ILE* 5.0 2.0 - - + -
1598A ASN 3.4 3.3 + - - +
1599A GLY 3.2 9.8 + - - +
1601A LEU* 1.3 77.6 - - - +
1603A ILE* 1.3 58.1 + - - +
1605A HIS* 3.2 6.6 + - + +
1606A VAL* 2.8 46.1 + - + +
1633A PHE* 4.2 7.0 - - + -
1637A PHE* 4.3 3.1 - - + -
1641A TRP* 4.1 20.2 - - + -
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Residues in contact with ILE1603 (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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1599A GLY 3.4 9.4 - - - +
1600A ASP* 3.2 13.2 + - - +
1602A LEU* 1.3 76.3 - - - +
1604A TYR* 1.3 52.4 + - - +
1606A VAL* 3.3 1.6 + - - +
1607A LEU* 2.6 39.0 + - + +
1637A PHE* 3.6 19.7 - - + -
1640A LYS* 4.2 27.6 - - + -
1641A TRP* 3.6 37.5 - - + +
1644A VAL* 3.6 31.0 - - + -
1645A PHE* 4.4 13.3 - - + -
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Residues in contact with TYR1604 (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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1563A PHE* 3.5 28.7 - + + -
1600A ASP 2.8 20.4 + - - +
1601A LEU* 3.8 10.5 - - + +
1603A ILE* 1.3 73.4 - - - +
1605A HIS* 1.3 57.6 + - - +
1607A LEU* 4.0 17.7 - - + -
1608A LEU* 2.9 73.1 + - + +
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Residues in contact with HIS1605 (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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1563A PHE* 3.6 17.0 - - + -
1566A LEU* 3.9 22.2 + - + +
1567A LYS* 3.3 50.0 - - + +
1571A ILE* 5.5 1.7 + - + -
1572A PHE* 3.1 41.0 + - + -
1601A LEU 2.9 17.6 + - - +
1602A LEU* 3.6 10.3 - - + +
1604A TYR* 1.3 77.1 - - - +
1606A VAL* 1.3 54.1 + - + +
1608A LEU* 4.1 2.5 - - - +
1609A THR* 2.4 43.6 + - + +
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Residues in contact with VAL1606 (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 4.0 6.3 - - - +
1572A PHE* 3.8 34.3 - - + -
1587A TYR* 5.4 2.5 - - + -
1602A LEU* 2.8 30.9 + - + +
1603A ILE 3.6 3.1 - - - +
1605A HIS* 1.3 74.5 - - + +
1607A LEU* 1.3 67.5 + - - +
1609A THR* 3.3 9.2 + - - +
1610A LEU* 3.1 42.0 + - + +
1641A TRP* 3.6 31.2 - - + -
1645A PHE* 3.9 7.2 - - + -
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Residues in contact with LEU1607 (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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1603A ILE* 2.6 24.4 + - + +
1604A TYR* 3.6 23.6 - - + +
1606A VAL* 1.3 73.3 - - - +
1608A LEU* 1.3 62.4 + - + +
1610A LEU* 3.1 3.7 + - - +
1611A LYS* 2.9 31.5 + - + +
1614A TYR* 3.7 26.0 - - + +
1644A VAL* 5.3 11.2 - - + +
1645A PHE* 3.5 33.2 - - + -
1646A PRO* 4.7 4.7 - - + -
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Residues in contact with LEU1608 (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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1563A PHE* 3.8 17.7 - - + -
1567A LYS* 6.2 3.8 - - - +
1604A TYR* 2.9 70.4 + - + +
1605A HIS* 4.3 3.6 - - - +
1607A LEU* 1.3 78.6 - - + +
1609A THR* 1.3 59.5 + - - +
1610A LEU 3.7 0.2 + - - -
1611A LYS* 3.9 20.0 - - + +
1612A PRO* 3.7 15.8 - - - +
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Residues in contact with THR1609 (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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1572A PHE* 3.5 25.8 + - + +
1573A TYR* 5.3 0.2 - - - -
1574A GLN* 4.9 7.1 + - - +
1585A PHE* 3.6 21.0 - - - -
1605A HIS* 2.4 46.3 + - + +
1606A VAL* 3.3 18.2 - - - +
1608A LEU* 1.3 75.4 - - - +
1610A LEU* 1.3 60.0 + - - +
1612A PRO* 4.1 6.6 - - - +
1613A TYR* 4.1 7.6 - - - -
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Residues in contact with LEU1610 (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 4.4 11.7 - - - -
1572A PHE* 3.8 12.1 - - + -
1585A PHE* 3.8 37.0 - - + -
1606A VAL* 3.1 35.9 + - + +
1607A LEU 3.9 2.0 - - - +
1609A THR* 1.3 78.2 - - - +
1611A LYS* 1.3 53.7 + - - +
1612A PRO* 3.3 3.6 - - - -
1613A TYR* 2.6 29.1 + - + +
1614A TYR* 2.8 28.1 + - + -
1618A TYR* 3.7 40.4 - - + +
1645A PHE* 4.7 8.7 - - + -
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Residues in contact with LYS1611 (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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1607A LEU* 2.9 17.8 + - + +
1608A LEU* 3.9 22.3 - - + +
1610A LEU* 1.3 74.6 - - - +
1612A PRO* 1.3 70.7 - - + +
1613A TYR 3.2 1.2 + - - -
1614A TYR* 3.4 41.0 + - + +
1615A ALA* 4.9 2.3 + - - +
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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