Contacts of the helix formed by residues 1611 - 1616 (chain A) in PDB entry 5EK0
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 ARG1611 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1510A ILE* 4.3 1.8 - - - +
1514A ILE* 3.9 21.6 - - + +
1547A PHE* 3.7 26.8 + - - +
1550A GLU* 2.8 31.9 + - - -
1570A PHE* 4.5 11.6 - - + -
1571A ASP* 2.9 42.0 + - - +
1574A VAL* 4.1 17.9 - - + +
1575A VAL* 3.4 24.0 - - - +
1607A GLY 3.3 13.3 + - - +
1608A ARG 3.7 10.5 + - - +
1610A LEU* 1.3 76.6 - - - +
1612A LEU* 1.4 51.5 + - - +
1613A VAL 3.3 0.4 - - - -
1614A THR* 3.2 24.4 + - + +
1615A ALA* 2.8 39.0 + - - +
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Residues in contact with LEU1612 (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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1511A ILE* 5.2 6.5 - - + +
1514A ILE* 3.7 29.8 - - + +
1515A VAL* 3.8 26.2 - - + +
1518A MET* 3.8 34.1 - - + -
1609A ILE 3.2 14.9 + - - +
1610A LEU 3.1 1.6 - - - -
1611A ARG* 1.4 76.4 - - - +
1613A VAL* 1.3 58.3 + - - +
1615A ALA* 4.5 4.0 - - + -
1616A VAL* 3.1 51.4 + - + +
1804A PX4 4.9 9.0 - - + -
1642B LEU* 3.9 22.4 - - + -
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Residues in contact with VAL1613 (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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1610A LEU* 3.4 24.5 + - + +
1612A LEU* 1.3 75.3 - - - +
1614A THR* 1.4 62.2 + - + +
1616A VAL 3.7 0.5 - - - +
1619A MET* 3.4 9.2 - - - +
1620A ARG* 3.2 27.3 + - - -
1623A VAL* 4.1 22.4 - - + -
1639B LEU* 4.2 7.4 - - + -
1642B LEU* 3.6 28.7 - - + -
1643B PHE* 3.5 30.7 - - + -
1646B ILE* 4.5 6.7 - - + -
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Residues in contact with THR1614 (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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1567A TRP* 3.5 36.6 + - - +
1570A PHE* 4.0 21.8 - - + -
1610A LEU 5.0 0.7 - - - +
1611A ARG* 3.2 35.0 - - + +
1613A VAL* 1.4 80.8 - - + +
1615A ALA* 1.3 64.1 + - - +
1620A ARG* 2.8 40.1 + - - +
1623A VAL* 6.0 3.4 - - - -
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Residues in contact with ALA1615 (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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1507A THR* 5.5 1.6 - - - +
1510A ILE* 5.3 4.0 - - + -
1511A ILE* 3.6 22.9 - - + +
1514A ILE* 3.8 24.7 - - + -
1611A ARG* 2.8 27.1 + - - +
1612A LEU* 3.6 3.1 + - - +
1614A THR* 1.3 74.7 - - - +
1616A VAL* 1.4 65.9 + - - +
1617A PRO* 3.5 6.8 - - - +
1620A ARG* 4.3 8.5 + - - +
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Residues in contact with VAL1616 (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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1508A LYS* 6.1 0.9 - - - +
1511A ILE* 3.6 25.5 - - + +
1612A LEU* 3.1 33.7 - - + +
1613A VAL 3.7 2.6 - - - +
1614A THR 4.8 0.2 - - - -
1615A ALA* 1.4 77.2 - - - +
1617A PRO* 1.4 81.4 - - + +
1619A MET* 3.4 34.7 - - + +
1620A ARG* 3.5 8.0 + - - +
1804A PX4 4.9 16.8 - - + -
1642B LEU* 5.1 0.2 - - + -
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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