Contacts of the strand formed by residues 1546 - 1550 (chain A) in PDB entry 3ZQK
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 VAL1546 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1540A LEU* 4.0 30.3 - - + -
1541A GLN 3.7 3.6 - - - +
1542A TYR* 4.3 4.9 - - + -
1545A MET* 1.3 82.1 - - - +
1547A THR* 1.3 62.9 + - - +
1548A VAL* 4.2 1.7 + - + +
1577A ASN 5.2 0.4 - - - +
1580A LEU* 3.9 20.7 - - + +
1581A ALA* 3.6 35.4 - - + +
1584A TYR* 4.0 32.9 - - + -
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Residues in contact with THR1547 (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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1540A LEU* 3.3 4.2 - - - -
1541A GLN 2.8 33.9 + - - -
1545A MET* 4.0 10.7 - - - +
1546A VAL* 1.3 74.7 + - - +
1548A VAL* 1.3 66.4 + - - +
1549A GLU* 3.2 29.5 + - - +
1571A GLN* 2.7 28.4 + - - +
1507B ASP* 4.2 10.1 - - + +
1572B GLY* 5.8 3.2 - - - -
1573B GLY* 5.3 6.2 + - - +
1574B ASN* 3.9 16.6 - - - +
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Residues in contact with VAL1548 (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 THR* 4.6 1.8 - - - +
1539A VAL 3.8 5.2 - - - +
1540A LEU* 3.6 11.0 - - + -
1546A VAL* 4.2 3.0 + - + +
1547A THR* 1.3 72.5 - - - +
1549A GLU* 1.3 61.4 + - - +
1550A TYR 3.7 26.0 - - - +
1551A PRO* 3.8 17.5 - - + -
1584A TYR* 3.4 42.2 - - + +
1507B ASP* 4.7 0.2 - - - +
1574B ASN* 2.9 28.7 + - - +
4677B NAG 3.8 27.3 + - - +
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Residues in contact with GLU1549 (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 VAL* 2.7 30.6 + - + +
1541A GLN* 3.0 43.1 + - + +
1547A THR* 3.6 24.8 - - - +
1548A VAL* 1.3 73.3 - - - +
1550A TYR* 1.3 59.0 + - - +
1564A ARG* 3.3 28.2 - - - +
1565A LEU* 4.2 9.4 - - + +
1568A ILE* 3.4 25.0 - - + +
1569A ARG 4.5 0.2 - - - +
1571A GLN* 4.5 0.3 - - - +
1507B ASP* 2.6 34.2 - - - +
4677B NAG 4.3 3.1 - - - +
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Residues in contact with TYR1550 (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 VAL 3.9 11.7 - - - -
1538A THR* 2.6 28.5 + - - -
1539A VAL* 3.0 27.7 + - + +
1548A VAL* 3.5 3.9 - - - +
1549A GLU* 1.3 75.7 - - - +
1551A PRO* 1.3 75.6 - - + +
1554A GLU* 3.7 23.0 + - + +
1555A ALA* 2.7 32.1 + - - +
1556A GLN* 3.8 9.9 - - - -
1560A ASP* 3.5 31.1 - - - +
1561A ILE* 3.5 30.7 - - + -
1564A ARG* 3.8 33.2 + - + -
1565A LEU* 4.6 4.9 - - + -
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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