Contacts of the helix formed by residues 750 - 755 (chain A) in PDB entry 1LVK
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 GLN 750 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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732A ILE* 3.5 25.6 - - + +
733A ASP 4.7 0.9 + - - -
736A GLN* 3.1 40.0 - - + +
746A PHE* 3.4 34.8 - - + -
747A ARG 3.3 16.1 + - - +
748A ALA 3.2 4.6 + - - -
749A GLY* 1.3 75.8 - - - +
751A LEU* 1.3 66.2 + - - +
753A ARG* 2.9 36.7 + - - +
754A ILE* 3.0 17.5 + - + +
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Residues in contact with LEU 751 (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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84A LYS* 5.8 2.5 - - - +
85A PHE* 4.0 24.4 - - + -
93A GLU 4.5 2.5 - - - +
95A SER* 3.5 10.5 + - - +
694A ASN* 4.2 24.2 - - + +
696A ILE* 4.4 14.6 - - + -
701A PHE* 4.4 2.2 - - + -
705A TYR* 3.6 32.3 - - + +
746A PHE* 4.0 27.9 - - + -
747A ARG 4.5 1.0 + - - -
749A GLY 3.4 0.2 - - - -
750A GLN* 1.3 80.0 - - - +
752A ALA* 1.3 56.6 + - - +
754A ILE* 3.4 12.1 + - + -
755A GLU* 2.8 29.2 + - - +
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Residues in contact with ALA 752 (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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82A PRO* 3.6 22.2 - - + +
85A PHE* 4.3 1.6 - - - -
95A SER* 3.0 25.6 + - - +
96A TYR* 3.5 32.5 - - + +
749A GLY 3.6 3.4 - - - +
750A GLN 3.1 0.2 - - - -
751A LEU* 1.3 73.6 - - - +
753A ARG* 1.3 66.9 + - - +
755A GLU* 3.2 4.2 + - - +
756A GLU* 3.0 28.7 + - - +
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Residues in contact with ARG 753 (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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79A GLN* 5.5 1.0 + - - -
96A TYR* 3.9 15.4 + - - +
732A ILE* 6.2 0.7 - - + -
736A GLN* 3.7 17.6 - - - +
748A ALA 4.3 3.2 + - - -
749A GLY* 2.8 33.9 + - - +
750A GLN* 2.9 46.5 + - - +
752A ALA* 1.3 74.3 - - - +
754A ILE* 1.3 56.6 + - - +
756A GLU* 2.7 43.2 + - - +
757A ALA* 3.2 5.5 + - - +
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Residues in contact with ILE 754 (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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701A PHE* 4.4 6.7 - - + -
705A TYR* 3.7 31.4 - - + -
708A LEU* 3.6 11.7 - - + +
727A LEU* 4.6 7.4 - - + -
730A LEU* 4.0 17.3 - - + -
732A ILE* 4.2 14.1 - - + -
746A PHE* 3.7 35.9 - - + -
750A GLN* 3.0 27.9 + - + +
751A LEU* 3.5 12.8 - - + +
753A ARG* 1.3 74.2 - - - +
755A GLU* 1.3 70.1 + - - +
757A ALA* 2.8 23.7 + - - +
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Residues in contact with GLU 755 (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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25A PHE* 3.1 33.6 - - - -
28A THR* 3.9 4.5 + - - -
82A PRO* 4.0 22.7 - - + -
84A LYS* 3.6 17.1 - - + +
85A PHE* 4.1 9.2 - - + -
704A ARG* 2.7 39.5 + - - -
705A TYR* 2.8 34.4 + - - +
751A LEU 2.8 18.1 + - - +
752A ALA* 3.4 10.3 - - - +
754A ILE* 1.3 79.2 - - - +
756A GLU* 1.3 57.6 - - - +
757A ALA 3.1 0.5 + - - -
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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