Contacts of the strand formed by residues 4865 - 4872 (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 GLY4865 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4860C VAL 4.0 0.2 - - - +
4862C PHE* 3.2 30.7 + - - +
4863C GLU 3.1 5.8 - - - -
4864C ARG* 1.3 80.6 - - - +
4866C HIS* 1.3 67.2 + - - -
4867C LYS* 3.8 9.7 + - - +
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Residues in contact with HIS4866 (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* 5.8 0.2 - - - +
4829C MET* 3.7 43.9 - - + +
4830C ASP* 3.5 29.7 + - + +
4859C VAL* 4.0 15.1 - - + +
4860C VAL 3.6 3.1 - - - -
4861C THR* 3.0 43.6 + - + +
4865C GLY* 1.3 73.5 - - - -
4867C LYS* 1.3 70.7 + - - +
342D ASN* 4.2 2.1 + - - -
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Residues in contact with LYS4867 (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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4762C TYR* 3.9 17.6 + - + +
4799C GLU* 3.3 21.7 + - - +
4859C VAL* 3.5 3.2 - - - -
4860C VAL 2.9 36.4 + - - +
4862C PHE* 3.8 24.7 - - + -
4864C ARG* 4.2 28.1 + - - +
4865C GLY* 4.1 9.7 - - - +
4866C HIS* 1.3 83.6 + - - +
4868C ILE* 1.3 65.0 + - - +
4869C ILE* 3.5 18.4 + - + +
341D GLU* 5.4 4.6 - - - +
342D ASN* 4.1 26.6 + - - +
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Residues in contact with ILE4868 (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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4799C GLU* 3.3 9.9 + - - +
4800C TYR* 2.9 53.6 + - + +
4827C PHE* 3.6 44.0 - - + -
4828C ARG 4.2 6.3 - - - +
4829C MET* 4.2 12.1 - - + -
4835C ILE* 3.6 25.5 - - + +
4857C ALA* 4.8 2.0 - - + -
4858C GLU 3.6 4.3 - - - +
4859C VAL* 3.6 31.6 - - + -
4866C HIS 4.4 0.2 + - - -
4867C LYS* 1.3 71.1 - - - +
4869C ILE* 1.3 61.8 + - - +
4870C ILE* 4.7 7.6 - - + -
342D ASN* 5.3 0.4 - - - +
6M THR* 4.8 0.2 - - - +
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Residues in contact with ILE4869 (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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4762C TYR* 3.6 37.7 - - + -
4765C MET* 3.8 10.1 - - + -
4796C MET* 3.7 37.9 - - + -
4798C ILE 3.9 3.4 - - - +
4799C GLU* 4.0 7.2 - - + -
4856C VAL 3.5 2.3 - - - +
4857C ALA* 3.6 1.2 - - - -
4858C GLU* 2.8 41.1 + - + +
4860C VAL* 3.8 28.5 - - + -
4867C LYS* 3.9 8.1 - - + +
4868C ILE* 1.3 81.7 - - - +
4870C ILE* 1.3 67.5 + - - +
4871C SER* 3.8 9.7 + - - +
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Residues in contact with ILE4870 (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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4796C MET* 3.8 0.7 - - - -
4797C VAL* 2.7 36.9 + - + +
4798C ILE* 2.8 35.6 + - + +
4800C TYR* 4.8 10.5 - - + +
4827C PHE* 5.0 1.1 - - + -
4844C ALA* 4.8 4.0 - - + -
4847C ILE* 4.1 20.0 - - + -
4855C CYS* 3.7 30.5 - - + -
4856C VAL 3.5 2.5 - - - +
4857C ALA* 3.7 29.2 - - + -
4868C ILE* 4.7 8.7 - - + -
4869C ILE* 1.3 74.3 - - - +
4871C SER* 1.3 56.2 + - - +
4884C TYR* 4.0 21.5 - - + +
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Residues in contact with SER4871 (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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4794C HIS* 5.1 2.9 - - - -
4795C THR 3.2 13.0 - - - -
4796C MET* 3.5 26.9 + - - +
4797C VAL* 4.4 0.2 - - - -
4855C CYS* 3.1 7.0 - - - -
4856C VAL* 2.6 43.8 + - - +
4858C GLU* 4.2 18.9 + - - -
4869C ILE* 3.8 6.2 + - - +
4870C ILE* 1.3 73.5 - - - +
4872C SER* 1.3 65.6 + - - +
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Residues in contact with SER4872 (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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4791C ILE* 4.2 7.0 - - - -
4792C GLU 2.6 26.3 + - - -
4794C HIS* 3.2 23.4 + - - -
4795C THR* 3.0 20.7 + - - -
4797C VAL* 4.0 3.8 - - - +
4854C ASN 3.4 5.6 - - - -
4855C CYS* 4.2 2.7 - - - +
4856C VAL* 4.8 3.0 - - - +
4871C SER* 1.3 76.0 - - - +
4873C SER* 1.3 60.8 + - - +
4874C ARG 3.5 15.3 - - - -
4876C ILE* 3.7 18.4 - - - -
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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