Contacts of the helix formed by residues 5018 - 5024 (chain y) in PDB entry 3A0B
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 ILE5018 (chain y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6035c CLA 4.9 5.8 - - + -
5011j TRP* 3.4 24.1 - - + +
5035k LEU* 5.4 0.9 - - + -
5038k VAL* 5.2 5.4 - - + -
5039k VAL* 2.9 58.6 - - + -
5042k ALA* 4.1 6.7 - - + -
5014y GLY 4.7 5.8 - - - +
5015y PRO* 3.4 19.9 + - + +
5016y MET 3.1 0.2 - - - -
5017y ILE* 1.3 89.4 - - + +
5019y PHE* 1.3 60.7 + - - +
5020y LEU 3.4 0.2 - - - -
5021y LEU* 3.4 4.4 + - + +
5022y ALA* 3.2 27.5 + - - +
5028y LEU* 3.7 21.6 - - + +
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Residues in contact with PHE5019 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5011j TRP* 3.8 17.0 - + + -
5012j ILE* 4.7 14.6 - - + -
5015y PRO 4.1 0.2 - - - +
5016y MET* 3.3 51.5 - - + +
5017y ILE 3.3 0.2 - - - -
5018y ILE* 1.3 78.4 - - - +
5020y LEU* 1.3 63.7 + - - +
5021y LEU 3.1 1.6 - - - -
5022y ALA* 3.5 1.5 + - + +
5023y VAL* 3.3 38.6 + - + +
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Residues in contact with LEU5020 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5016y MET 3.3 17.0 + - - +
5017y ILE* 3.7 17.0 - - - +
5019y PHE* 1.3 80.2 - - - +
5021y LEU* 1.3 81.3 + - + +
5022y ALA 3.5 0.2 - - - -
5023y VAL* 3.8 8.7 - - - +
5024y ARG* 2.8 44.6 + - + +
5021z ILE* 4.0 22.0 - - + -
5025z VAL* 3.4 20.9 - - + -
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Residues in contact with LEU5021 (chain y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6035c CLA 6.0 3.4 - - + -
5017y ILE* 3.0 29.4 + - + +
5018y ILE* 3.4 10.3 + - + +
5019y PHE 3.1 1.2 - - - -
5020y LEU* 1.3 80.8 - - + +
5022y ALA* 1.3 58.6 + - - +
5024y ARG* 4.4 0.9 - - - -
5025y ARG 2.9 29.0 + - - -
5026y GLY* 3.0 9.0 + - - +
5028y LEU* 4.1 14.2 - - + +
5025z VAL* 3.1 40.2 - - + +
5028z ALA* 3.4 34.8 - - + -
5029z SER* 3.7 22.9 - - - +
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Residues in contact with ALA5022 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5011j TRP* 3.8 26.7 - - + -
5042k ALA* 5.6 0.4 - - + -
5018y ILE 3.2 14.8 + - - +
5019y PHE* 3.5 2.0 + - + +
5020y LEU 3.5 0.2 - - - -
5021y LEU* 1.3 74.3 - - - +
5023y VAL* 1.3 61.6 + - - +
5025y ARG* 3.2 20.7 + - - +
5028y LEU* 4.5 17.5 - - + -
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Residues in contact with VAL5023 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5019y PHE* 3.3 35.2 + - + +
5020y LEU* 3.8 12.1 - - - +
5022y ALA* 1.3 76.1 - - - +
5024y ARG* 1.3 65.1 + - + +
5025y ARG* 3.1 5.5 - - - +
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Residues in contact with ARG5024 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5020y LEU* 2.8 34.5 + - + +
5021y LEU* 4.4 3.4 - - - -
5023y VAL* 1.3 78.9 - - + +
5025y ARG* 1.3 79.0 + - - +
5025z VAL* 5.0 5.8 - - - +
5029z SER* 4.7 12.1 - - - -
5030z PRO* 4.4 3.1 - - - +
5031z GLN* 3.8 46.1 + - - +
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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