Contacts of the strand formed by residues 4783 - 4787 (chain C) in PDB entry 5F6K
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 LEU4783 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4775C LEU* 3.9 21.5 - - + -
4776C ALA* 3.6 7.4 - - - +
4777C ARG* 3.8 31.6 - - + +
4778C SER* 3.7 2.7 - - - -
4781C GLN 3.3 1.4 - - - +
4782C GLY* 1.3 75.5 - - - +
4784C GLY* 1.3 58.7 + - - +
4846C TYR* 3.4 34.3 - - + +
4848C ASN* 3.5 1.2 + - - -
5002C SAH 2.5 45.4 + - - +
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Residues in contact with GLY4784 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4775C LEU* 3.3 10.8 - - - +
4776C ALA 2.8 33.7 + - - +
4778C SER* 3.8 3.0 - - - -
4783C LEU* 1.3 75.1 - - - +
4785C LEU* 1.3 62.1 + - - -
4786C TYR* 3.6 6.0 - - - -
4846C TYR 3.3 11.7 - - - -
4848C ASN* 3.7 12.6 - - - -
4881C GLU* 4.0 5.6 - - - -
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Residues in contact with LEU4785 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4773C VAL* 3.9 31.4 - - + -
4774C TYR 3.6 18.2 - - - +
4775C LEU* 4.2 12.8 - - + -
4784C GLY* 1.3 77.0 - - - +
4786C TYR* 1.3 55.1 + - - +
4798C ILE* 4.0 11.0 - - + -
4843C PRO* 3.5 41.7 - - + +
4846C TYR* 3.8 5.2 + - + -
4847C ILE* 3.6 38.5 - - + +
4881C GLU* 3.6 7.8 + - - +
4882C LEU* 2.7 36.4 + - + +
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Residues in contact with TYR4786 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4773C VAL* 3.2 10.9 - - - +
4774C TYR* 3.0 58.2 + + + +
4776C ALA* 3.5 37.7 - - + -
4777C ARG 2.7 21.1 + - - -
4778C SER* 3.2 11.8 - - - -
4779C ARG* 3.4 27.5 + - - +
4784C GLY* 3.6 16.2 - - - -
4785C LEU* 1.3 79.2 - - - +
4787C ALA* 1.3 61.1 + - - +
4879C GLY 3.3 19.1 - - - +
4880C GLU 3.3 4.3 - - - +
4881C GLU* 3.4 29.7 + - + -
4882C LEU* 4.1 4.9 - - - +
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Residues in contact with ALA4787 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4772C ASN 3.4 5.6 - - - -
4774C TYR* 3.5 6.9 - - - -
4786C TYR* 1.3 68.7 - - - +
4788C ALA* 1.3 63.4 + - - +
4789C ARG 3.4 13.4 + - - +
4791C ILE* 4.1 9.0 - - + -
4876C ILE* 3.8 16.8 - - + -
4877C GLN 3.5 22.7 - - - +
4878C LYS* 3.8 0.3 - - - +
4879C GLY 2.9 25.8 + - - -
4880C GLU 2.8 14.9 + - - +
4882C LEU* 4.2 5.4 - - + +
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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