Contacts of the helix formed by residues 1533 - 1540 (chain A) in PDB entry 4W8F
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 GLN1533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1529A ARG 3.9 13.4 + - - +
1530A GLN* 3.5 6.0 + - - +
1531A ARG 3.0 0.8 + - - -
1532A ARG* 1.3 85.9 + - - +
1534A PHE* 1.3 59.3 + - - +
1535A PRO* 4.0 4.7 - - - +
1605A GLN* 3.2 49.6 + - + +
1609A ASN* 5.2 6.9 - - - +
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Residues in contact with PHE1534 (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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1530A GLN 4.0 1.2 + - - -
1531A ARG 2.9 8.8 + - - +
1533A GLN* 1.3 79.5 - - - +
1535A PRO* 1.4 57.7 - - + +
1536A ARG* 2.8 37.1 + - + -
1537A PHE* 2.8 65.1 + + + +
1565A MET* 4.2 12.3 - - - -
1566A PHE* 3.9 15.5 - + - -
1605A GLN* 4.2 10.3 - - - +
1608A LEU* 3.4 44.9 - - + -
1609A ASN* 3.7 25.8 - - + -
1612A ASP* 4.0 11.7 - - + -
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Residues in contact with PRO1535 (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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1531A ARG 3.1 10.4 - - - +
1532A ARG 4.4 7.6 - - - +
1533A GLN 4.0 4.9 - - - +
1534A PHE* 1.4 83.6 - - + +
1536A ARG* 1.3 52.9 + - + +
1537A PHE 2.9 6.1 - - - -
1538A TYR* 2.8 44.0 + - + +
1840A GLN* 3.8 35.0 - - + +
1841A ILE* 3.6 27.9 - - + +
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Residues in contact with ARG1536 (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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1534A PHE* 2.8 36.5 + - + -
1535A PRO* 1.3 78.9 - - + +
1537A PHE* 1.3 56.2 + - - +
1538A TYR 3.0 0.2 - - - -
1539A PHE* 2.9 37.7 + - - +
1540A LEU 4.1 0.5 + - - -
1565A MET* 3.0 39.2 + - + +
1566A PHE* 3.8 31.4 + - - +
1612A ASP* 3.5 29.1 + - - +
1615A ILE* 5.9 0.2 - - - +
1616A LYS* 4.9 4.0 - - - +
1761A GLU* 4.3 29.3 + - - +
1816A VAL* 6.2 0.8 - - - +
1841A ILE* 3.7 36.8 - - + +
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Residues in contact with PHE1537 (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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1530A GLN* 3.8 23.1 - - + -
1531A ARG* 3.5 18.5 + - - -
1534A PHE* 2.8 36.6 + + + +
1536A ARG* 1.3 72.9 - - - +
1538A TYR* 1.3 55.4 + - - +
1539A PHE 2.9 5.8 - - - -
1540A LEU* 2.9 40.0 + - + +
1541A GLY 3.5 3.1 + - - -
1545A LEU* 3.7 26.7 - - + -
1548A ILE* 3.9 29.6 - - + -
1549A ILE* 5.3 4.3 - - + -
1565A MET* 4.1 5.4 - - - -
1604A ALA* 5.2 0.2 - - + -
1605A GLN* 4.3 17.7 - - + -
1608A LEU* 3.4 34.8 - - + -
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Residues in contact with TYR1538 (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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1528A GLU* 3.3 24.4 + - - -
1531A ARG* 3.7 33.4 - - + +
1532A ARG* 2.9 25.3 + - - +
1535A PRO* 2.8 31.4 + - + +
1537A PHE* 1.3 78.0 - - - +
1539A PHE* 1.3 54.9 + - - +
1540A LEU 3.3 0.2 - - - -
1833A ARG* 2.7 58.0 + - + +
1834A LEU* 4.0 1.2 - - - +
1836A VAL* 3.5 10.7 - - + +
1837A GLY* 3.4 27.8 - - - -
1840A GLN* 2.8 42.9 + - - -
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Residues in contact with PHE1539 (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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1536A ARG* 2.9 23.0 + - - +
1538A TYR* 1.3 82.2 - - + +
1540A LEU* 1.3 64.1 + - - +
1564A LYS* 3.5 29.3 - - - +
1565A MET* 3.8 20.6 - - - -
1818A VAL* 3.7 33.2 - - + -
1833A ARG* 3.9 6.0 + - - -
1834A LEU* 3.3 50.5 - - + +
1837A GLY* 4.3 2.0 - - - -
1838A ILE* 4.2 11.7 - - + -
1841A ILE* 3.3 30.7 - - + -
1843A ALA* 5.1 2.2 - - + -
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Residues in contact with LEU1540 (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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1537A PHE* 2.9 23.9 + - + +
1539A PHE* 1.3 82.3 - - - +
1541A GLY* 1.3 68.6 + - - +
1544A ASP* 3.9 17.2 - - + +
1545A LEU* 4.6 11.4 - - + +
1548A ILE* 3.4 35.0 - - + -
1561A PHE* 3.8 27.8 - - + +
1564A LYS* 3.8 34.0 - - + +
1565A MET* 3.8 21.8 - - + +
1833A ARG* 3.6 6.0 + - - -
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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