Contacts of the strand formed by residues 861 - 866 (chain C) in PDB entry 4AY6
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 861 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832C ILE* 3.2 13.0 - - - +
834C TYR* 3.7 22.2 - - - -
855C LEU* 3.2 14.2 + - - +
858C VAL* 2.6 29.1 + - - -
859C PRO 3.2 3.7 + - - +
860C ASN* 1.3 78.1 - - - +
862C VAL* 1.3 69.0 + - - +
889C ARG* 2.9 36.6 + - - -
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Residues in contact with VAL 862 (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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827C LEU* 5.0 2.0 - - + -
828C PRO* 3.9 33.4 - - + -
831C ALA* 4.4 3.1 - - + -
832C ILE 3.0 3.5 + - - +
833C VAL* 3.9 30.7 - - + -
834C TYR* 3.0 27.0 + - - +
855C LEU* 3.8 6.3 - - - -
860C ASN 5.2 0.2 - - - +
861C SER* 1.3 79.4 - - - +
863C LEU* 1.3 63.3 + - - +
888C ASN 4.1 14.8 - - - +
889C ARG* 3.2 16.4 - - - +
891C ILE* 4.4 13.0 - - + -
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Residues in contact with LEU 863 (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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834C TYR* 3.1 30.5 - - + +
835C CYS* 4.5 6.7 - - - +
836C ASN* 5.5 0.7 - - + -
848C LEU* 4.9 2.2 - - + -
851C TRP* 3.6 39.5 - - + -
855C LEU* 3.8 18.9 - - + +
862C VAL* 1.3 75.3 - - - +
864C TRP* 1.3 62.4 + - - +
865C LEU* 4.0 25.6 - - + -
889C ARG 3.1 9.6 + - - +
890C ILE* 3.6 18.9 - - + +
891C ILE* 2.8 31.4 + - - +
912C LEU* 4.0 14.4 - - + -
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Residues in contact with TRP 864 (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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825C TYR* 3.9 24.9 - + + -
827C LEU* 3.7 40.9 - - + +
833C VAL* 3.9 17.7 - - + -
834C TYR 2.6 15.3 + - - +
835C CYS* 3.4 7.6 - - + +
836C ASN 2.9 26.9 + - - +
837C PHE* 3.6 31.4 - + - -
862C VAL* 5.8 0.2 - - + -
863C LEU* 1.3 73.1 - - - +
865C LEU* 1.3 69.5 + - - +
891C ILE* 3.4 15.8 - - + +
893C SER* 3.0 33.7 + - - -
904C ARG* 3.5 41.3 - - + -
907C LEU* 4.2 8.1 - - + -
908C ALA* 4.4 5.8 - - + -
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Residues in contact with LEU 865 (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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836C ASN* 3.3 32.8 - - + +
837C PHE* 5.2 0.4 - - - -
840C LEU* 4.8 6.1 - - + -
843C ILE* 4.8 17.3 - - + -
848C LEU* 5.9 0.4 - - + -
851C TRP* 4.4 9.2 - - + -
863C LEU* 4.0 29.2 - - + -
864C TRP* 1.3 84.2 - - - +
866C LEU* 1.3 73.2 + - - +
876C ILE* 4.4 12.6 - - + -
890C ILE* 4.0 8.5 - - + -
891C ILE 2.8 9.1 + - - +
892C PHE* 3.5 35.7 - - + -
893C SER 3.0 22.5 + - - -
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Residues in contact with LEU 866 (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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836C ASN 4.2 2.6 + - - -
837C PHE* 3.5 47.6 - - + +
838C ASN 4.7 3.5 + - - +
840C LEU* 3.5 23.0 - - - +
865C LEU* 1.3 87.1 - - - +
867C ARG* 1.3 60.2 + - - +
868C PHE* 2.9 25.3 + - + +
892C PHE* 3.9 6.5 - - - -
893C SER* 3.4 21.1 - - - +
894C PRO 4.0 1.3 - - - +
895C VAL* 4.9 4.5 - - + -
904C ARG* 3.3 31.4 - - - +
1200C 12V 3.7 21.8 - - + +
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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