Contacts of the strand formed by residues 1538 - 1542 (chain A) in PDB entry 2V5P
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 PHE1538 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1531A SER 5.3 0.2 - - - -
1532A LEU* 3.3 51.6 - - + -
1534A GLY* 5.0 4.3 - - - -
1536A ALA 4.0 0.4 + - - -
1537A GLY* 1.3 89.2 - - - -
1539A THR* 1.3 65.5 + - - +
1540A ALA 4.0 0.4 - - - -
1549A TYR* 4.0 0.2 - - - -
1550A MET* 2.7 42.3 + - + +
1551A SER* 4.8 0.2 - - - -
1552A ILE* 4.1 12.1 - - + -
1556A ASN* 4.8 0.3 - - - +
1623A ARG* 6.4 0.7 - - + -
1624A PRO* 4.3 17.9 - - + -
1640A TRP* 3.5 30.7 - + + -
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Residues in contact with THR1539 (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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1538A PHE* 1.3 78.4 - - - +
1540A ALA* 1.3 65.3 + - - +
1541A ALA* 3.9 3.3 + - - +
1547A LEU* 4.7 16.1 - - + +
1548A VAL 3.5 4.5 - - - -
1549A TYR* 4.0 30.5 - - + -
1558A ASN* 5.4 3.1 - - - +
1623A ARG* 5.7 4.2 - - - -
1624A PRO* 4.9 4.0 - - - +
1920A GLU* 5.0 11.6 + - - +
1921A SER* 5.5 2.8 + - - -
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Residues in contact with ALA1540 (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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1538A PHE 3.9 1.6 + - - -
1539A THR* 1.3 74.2 - - - +
1541A ALA* 1.3 59.8 + - - +
1546A GLY 4.2 0.2 - - - +
1547A LEU* 4.0 4.2 - - - +
1548A VAL* 2.9 42.4 + - + +
1550A MET* 3.6 28.1 - - - +
1624A PRO* 3.8 19.5 - - - +
1625A MET 5.2 1.1 - - - -
1626A LEU* 5.2 0.7 - - + +
1638A PHE* 3.8 19.3 - - + -
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Residues in contact with ALA1541 (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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1539A THR 3.9 2.0 + - - +
1540A ALA* 1.3 74.5 - - - +
1542A TYR* 1.3 61.2 + - - +
1546A GLY 4.2 4.3 - - - -
1548A VAL* 5.4 0.2 - - - -
1624A PRO 4.5 4.6 + - - -
1625A MET* 5.5 0.9 - - - +
1626A LEU* 3.9 21.3 + - - +
1919A ILE 5.0 4.3 - - - +
1921A SER* 3.7 16.2 - - - +
1922A ARG 3.3 41.5 - - - +
1923A ALA* 4.3 8.8 - - - -
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Residues in contact with TYR1542 (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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1541A ALA* 1.3 75.3 - - - +
1543A SER* 1.3 92.8 + - - +
1544A GLU 4.3 1.2 - - - -
1546A GLY* 3.1 29.9 + - - +
1547A LEU 3.2 22.5 + - - -
1548A VAL* 3.3 30.1 - - + -
1567A PHE* 3.9 21.4 - + - -
1568A GLY* 4.3 11.3 + - - -
1626A LEU* 3.8 23.1 - - + -
1921A SER 5.2 1.7 - - - +
1923A ALA* 4.7 6.2 + - - -
15D ASP* 4.4 9.5 + - - +
18D GLN* 4.1 12.6 + - + +
19D PHE* 3.9 36.8 - + + +
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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