Contacts of the strand formed by residues 1595 - 1599 (chain A) in PDB entry 4BHW
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 PHE1595 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1435A ILE 3.8 2.0 - - - -
1436A TRP* 3.5 39.3 - + + -
1485A ASP* 3.2 6.2 - - - -
1486A ILE* 2.9 47.0 + - + -
1507A ASP* 4.3 4.5 - - - -
1508A PHE* 3.3 39.0 - + + -
1509A TRP* 3.4 37.0 - + - -
1591A HIS* 3.4 35.0 - - + -
1592A LYS 3.0 3.7 + - - +
1593A GLU 3.5 0.8 - - - -
1594A VAL* 1.3 86.9 - - + +
1596A PHE* 1.3 62.5 + - - +
1597A VAL* 5.2 0.4 - - + -
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Residues in contact with PHE1596 (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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1434A HIS* 3.4 6.9 + - - +
1435A ILE* 2.9 48.9 + - + +
1437A ALA* 4.2 19.5 - - + -
1464A GLN* 3.7 24.2 - - - -
1467A PHE* 4.0 14.4 - + + -
1468A LYS* 3.9 28.0 - - + -
1471A LEU* 3.5 30.5 - - + -
1483A TYR* 4.1 16.2 - + + -
1484A LYS 4.0 4.9 - - - -
1485A ASP* 4.9 1.1 - - - +
1593A GLU 3.9 20.2 - - - -
1594A VAL 4.4 1.8 - - - -
1595A PHE* 1.3 74.5 - - - +
1597A VAL* 1.3 63.2 + - - +
1598A ILE* 4.1 8.1 - - + -
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Residues in contact with VAL1597 (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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1392A ARG* 5.1 1.8 - - - +
1432A THR* 4.0 18.4 - - + -
1433A GLY 3.6 2.7 - - - -
1434A HIS* 3.4 27.4 - - + +
1483A TYR* 3.3 5.4 - - - +
1484A LYS* 3.0 35.4 + - - +
1486A ILE* 4.4 26.5 - - + -
1489A GLN* 3.9 33.6 - - + +
1595A PHE 4.8 0.4 - - - +
1596A PHE* 1.3 76.0 - - - +
1598A ILE* 1.3 65.3 + - - +
1599A ARG* 4.1 4.6 + - + +
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Residues in contact with ILE1598 (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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1422A LEU* 4.3 12.6 - - + -
1432A THR* 3.2 7.8 - - - -
1433A GLY* 2.8 50.4 + - - +
1435A ILE* 3.7 30.3 - - + -
1471A LEU* 3.5 43.5 - - + -
1480A VAL* 3.7 25.8 - - + -
1482A ASP 3.9 2.5 - - - -
1483A TYR* 4.1 2.5 - - + -
1596A PHE* 4.5 3.6 - - + -
1597A VAL* 1.3 82.3 - - - +
1599A ARG* 1.3 62.6 + - - +
1600A LEU* 3.4 10.5 + - + +
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Residues in contact with ARG1599 (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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1431A THR 4.0 4.5 - - - +
1432A THR* 4.7 11.0 - - + +
1480A VAL* 3.7 1.7 - - - +
1481A HIS* 2.7 48.4 + - + +
1482A ASP* 2.5 55.7 + - - +
1483A TYR* 6.1 0.7 - - - +
1484A LYS* 3.3 15.7 - - - +
1489A GLN* 4.1 23.3 + - - +
1492A GLU* 4.7 7.9 + - - +
1597A VAL* 4.1 4.4 + - + -
1598A ILE* 1.3 69.6 - - - +
1600A LEU* 1.3 56.3 + - - +
1601A ILE 3.6 3.6 - - - +
1602A ALA* 3.6 29.8 - - + +
1603A GLY 4.9 2.8 - - - +
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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