Contacts of the strand formed by residues 872 - 876 (chain C) in PDB entry 3EI4
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 SER 872 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723C LYS* 4.9 4.0 - - - -
817C VAL* 3.0 14.6 - - - -
870C VAL* 4.1 0.7 - - - +
871C TYR* 1.3 79.3 - - - +
873C MET* 1.3 71.1 + - - +
874C VAL* 5.9 0.2 - - - -
882C ALA* 3.4 0.5 - - - -
883C SER* 3.1 31.2 + - - +
912C LEU 3.6 10.9 + - - -
913C TYR* 4.7 0.7 - - - -
914C LEU* 3.2 40.7 + - - +
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Residues in contact with MET 873 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817C VAL* 3.5 17.4 - - + +
818C SER 5.1 0.9 - - - +
819C CYS* 3.1 37.1 - - - -
830C ILE* 3.2 37.5 - - + +
832C GLY* 3.7 29.8 - - - +
848C ILE* 4.3 9.2 - - - -
870C VAL* 3.8 15.0 - - + -
872C SER* 1.3 82.8 - - - +
874C VAL* 1.3 73.1 + - - +
880C LEU* 4.0 10.3 - - + -
881C LEU 3.1 9.0 - - - +
882C ALA* 4.0 7.9 - - + -
914C LEU* 4.6 0.9 - - - -
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Residues in contact with VAL 874 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819C CYS* 5.0 2.0 - - - -
821C LEU* 5.1 0.4 - - - -
872C SER* 5.9 0.7 - - - -
873C MET* 1.3 81.6 - - - +
875C GLU* 1.3 78.8 + - + +
876C PHE 3.3 0.7 + - - -
879C LYS 3.6 1.0 - - - +
880C LEU* 3.6 7.2 - - - -
881C LEU* 2.9 37.8 + - + +
914C LEU* 4.1 33.9 - - + +
915C LYS* 4.9 2.2 - - + -
916C THR* 3.8 31.0 - - + +
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Residues in contact with GLU 875 (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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819C CYS* 5.5 0.6 - - - -
820C LYS 5.0 3.4 - - - +
821C LEU* 3.6 40.2 - - + +
822C GLY 4.4 5.9 - - - +
874C VAL* 1.3 83.4 - - + +
876C PHE* 1.3 62.2 + - - +
877C ASN* 3.6 8.1 + - - -
878C GLY* 2.6 38.0 + - - -
879C LYS 3.7 4.0 - - - -
916C THR* 4.3 3.6 + - - -
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Residues in contact with PHE 876 (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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874C VAL 4.0 6.5 - - - +
875C GLU* 1.3 75.1 + - - +
877C ASN* 1.3 75.1 + - + +
878C GLY 3.1 0.7 - - - -
879C LYS* 2.7 41.1 + - + +
881C LEU* 4.1 12.8 - - + +
890C LEU* 3.7 25.1 - - + -
916C THR* 3.6 31.2 - - + -
918C GLY 2.9 26.5 - - - -
919C ASP* 3.7 20.0 - - - -
921C ILE* 3.7 23.3 - - + -
935C TYR* 3.8 25.6 - + + -
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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