Contacts of the strand formed by residues 4833 - 4841 (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 HIS4833 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4804C ILE* 3.9 26.8 - - + +
4805C ILE 3.4 10.6 + - - -
4806C ARG* 4.6 12.7 - - + +
4828C ARG* 3.8 0.2 + - - -
4829C MET* 3.1 29.3 + - + -
4830C ASP* 2.7 42.6 + - - +
4832C ASP* 1.3 97.8 + - + +
4834C VAL* 1.3 66.9 + - - +
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Residues in contact with VAL4834 (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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4804C ILE* 3.5 3.0 - - - -
4805C ILE* 2.8 48.3 + - + +
4807C ASN* 3.9 5.6 - - - +
4810C ALA* 4.2 12.8 - - + -
4826C MET* 3.8 37.0 - - + -
4827C PHE 3.8 9.2 - - - +
4828C ARG* 3.3 36.3 - - - +
4829C MET* 4.2 0.4 - - - +
4833C HIS* 1.3 79.6 - - - +
4835C ILE* 1.3 67.1 + - - +
3M THR* 3.9 11.0 - - + -
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Residues in contact with ILE4835 (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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4800C TYR* 3.7 34.2 - - + +
4802C GLY* 3.6 33.4 - - - +
4803C THR 3.7 3.1 - - - -
4804C ILE* 4.6 4.5 - - + +
4825C TYR 3.7 1.2 - - - +
4826C MET* 3.2 5.9 - - - -
4827C PHE 2.7 43.0 + - - +
4829C MET* 3.6 33.4 - - + -
4834C VAL* 1.3 74.6 - - - +
4836C ASP* 1.3 60.2 + - - +
4868C ILE* 3.6 31.0 - - + +
342D ASN* 4.0 9.0 - - - +
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Residues in contact with ASP4836 (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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4802C GLY* 4.3 0.2 - - - -
4803C THR* 2.8 44.9 + - - +
4805C ILE* 3.7 27.2 - - + +
4813C LYS* 4.5 5.0 - - - +
4817C TYR* 2.4 36.2 + - - -
4825C TYR 3.9 1.1 - - - -
4826C MET* 3.7 13.5 - - + +
4834C VAL 3.6 0.8 + - - -
4835C ILE* 1.3 73.3 - - - +
4837C ALA* 1.3 58.9 + - - +
4838C THR* 2.7 28.8 + - - -
4839C LEU* 5.0 1.7 + - - +
4840C THR* 3.4 4.7 + - - +
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Residues in contact with ALA4837 (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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4800C TYR* 3.9 18.8 - - + +
4801C ILE 3.6 22.4 - - - +
4802C GLY* 4.5 0.2 - - - -
4825C TYR* 2.8 18.6 + - - +
4835C ILE 3.8 0.6 + - - -
4836C ASP* 1.3 73.0 - - - +
4838C THR* 1.3 61.9 + - - +
4839C LEU 3.5 2.0 - - - -
4840C THR 3.2 10.1 - - - +
4841C GLY* 4.6 1.1 - - - -
4842C GLY 5.0 0.2 - - - +
4845C ARG* 2.8 43.3 + - + -
336D PHE* 3.6 5.0 - - - -
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Residues in contact with THR4838 (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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4817C TYR* 3.2 43.5 - - + -
4822C ARG* 3.4 33.2 + - + +
4823C GLY 5.1 0.9 + - - +
4825C TYR* 3.5 34.6 + - + +
4826C MET* 4.7 0.5 - - - +
4836C ASP* 2.7 22.8 + - - -
4837C ALA* 1.3 78.8 - - - +
4839C LEU* 1.3 60.4 + - + +
4845C ARG* 3.1 19.1 + - - -
336D PHE* 3.8 3.3 - - - -
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Residues in contact with LEU4839 (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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4813C LYS* 5.0 9.4 - - - +
4817C TYR* 3.8 30.8 + - + +
4822C ARG* 3.8 33.9 - - - +
4836C ASP* 5.0 1.4 + - - +
4838C THR* 1.3 78.2 - - + +
4840C THR* 1.3 68.4 + - + +
336D PHE* 3.1 32.7 - - - +
337D LYS 3.4 1.2 + - - -
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Residues in contact with THR4840 (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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4802C GLY* 3.6 2.9 - - - -
4803C THR* 3.2 24.0 - - - +
4836C ASP 3.4 6.2 - - - +
4837C ALA* 3.2 19.4 - - - -
4838C THR 3.6 1.2 - - - -
4839C LEU* 1.3 88.1 - - + +
4841C GLY* 1.3 58.5 + - - +
336D PHE* 3.7 7.2 - - - -
337D LYS* 2.7 29.8 + - - +
339D LEU* 3.1 23.7 - - + +
343D VAL* 5.6 0.9 - - + -
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Residues in contact with GLY4841 (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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4801C ILE 3.2 17.7 - - - -
4802C GLY* 3.9 2.9 - - - -
4837C ALA* 4.6 2.2 - - - -
4840C THR* 1.3 79.9 + - - +
4842C GLY* 1.3 59.1 + - - -
336D PHE* 3.6 8.3 - - - -
337D LYS 3.2 2.9 + - - +
338D GLU* 2.9 19.3 - - - +
339D LEU* 3.0 27.9 + - - -
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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