Contacts of the strand formed by residues 843 - 851 (chain C) in PDB entry 2CKJ
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 PHE 843 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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699C ILE* 5.4 0.2 - - - -
735C ILE 4.1 0.9 - - - +
736C TYR* 2.8 30.9 - - - -
737C ILE* 2.8 38.6 + - + +
841C HIS* 4.2 11.0 - - + -
842C PRO* 1.4 80.4 - - - +
844C LEU* 1.4 56.1 + - - +
845C ALA 4.2 0.4 - - - +
864C HIS* 4.2 18.8 - + + -
865C PHE 3.4 6.3 - - - -
866C SER* 3.5 26.2 - - - -
878C ILE* 5.1 9.0 - - + -
879C MET* 3.8 31.0 - - + -
882C ALA* 4.4 17.7 - - + -
916C GLY* 5.0 3.1 - - - -
919C GLN* 3.6 43.5 - - + -
923C ILE* 5.4 6.3 - - + -
3007C GOL 5.2 1.8 - - - -
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Residues in contact with LEU 844 (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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699C ILE* 4.8 15.7 - - + +
700C GLU* 4.0 25.8 - - - +
703C ILE* 6.2 2.9 - - + -
734C GLU* 4.3 31.4 - - + +
735C ILE 3.4 27.1 - - - +
736C TYR* 3.7 19.7 - - + -
843C PHE* 1.4 70.0 - - - +
845C ALA* 1.3 61.0 + - - +
846C ARG* 4.9 13.2 - - - +
864C HIS* 3.8 0.2 - - - -
865C PHE* 2.6 60.6 + - + +
1296C ARG* 4.8 3.1 - - - +
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Residues in contact with ALA 845 (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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734C GLU* 3.3 3.4 - - - +
735C ILE* 2.9 35.4 + - - +
843C PHE* 4.2 1.3 - - + -
844C LEU* 1.3 75.8 - - - +
846C ARG* 1.4 59.7 + - - +
847C TYR* 4.5 2.6 + - - -
862C VAL* 4.4 3.8 - - + -
863C ASP 3.3 11.2 - - - +
864C HIS* 4.2 9.9 - - - +
923C ILE* 3.3 43.1 - - + -
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Residues in contact with ARG 846 (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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703C ILE* 4.4 20.4 - - - +
733C GLY 3.3 11.7 - - - +
734C GLU* 3.1 29.5 + - + +
844C LEU* 4.9 13.5 - - + +
845C ALA* 1.4 75.1 - - - +
847C TYR* 1.3 60.1 + - - +
861C GLU 4.1 0.2 - - - +
862C VAL* 3.6 4.5 - - - +
863C ASP* 3.1 41.8 + - + +
865C PHE* 4.3 23.1 - - + -
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Residues in contact with TYR 847 (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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731C VAL* 5.2 1.3 - - + -
732C SER* 3.4 7.7 + - - -
733C GLY* 2.8 63.3 + - - +
734C GLU* 3.6 10.0 + - - -
735C ILE* 4.0 17.2 - - + +
845C ALA 4.6 2.2 - - - -
846C ARG* 1.3 76.5 - - - +
848C LYS* 1.3 68.8 + - - +
849C VAL* 5.0 6.3 - - + -
861C GLU 3.3 11.2 - - - +
862C VAL* 4.0 16.6 - - + -
923C ILE* 5.0 10.1 - - + -
926C CYS* 4.2 2.7 - - - -
927C TRP* 3.3 51.6 + + + -
930C GLU* 2.6 29.2 + - - -
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Residues in contact with LYS 848 (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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724C PHE* 3.8 32.0 - - + -
730C VAL* 3.9 15.3 - - + -
731C VAL 3.2 7.2 - - - +
732C SER* 4.2 15.0 - - - +
847C TYR* 1.3 76.3 - - - +
849C VAL* 1.3 64.5 + - - +
860C LEU* 3.6 3.9 - - - +
861C GLU* 3.0 52.5 + - + +
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Residues in contact with VAL 849 (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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730C VAL* 4.1 3.4 - - - -
731C VAL* 2.4 50.6 + - + +
847C TYR* 5.0 7.8 - - + -
848C LYS* 1.3 70.4 - - - +
850C GLY* 1.4 58.8 + - - +
851C PHE* 3.4 9.6 - - + -
857C VAL* 3.9 21.1 - - + -
859C ALA 3.6 9.2 - - - +
860C LEU* 4.6 8.1 - - + -
927C TRP* 4.5 32.5 - - + +
930C GLU* 6.4 0.4 - - + -
931C VAL* 4.1 25.8 - - + -
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Residues in contact with GLY 850 (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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724C PHE* 3.5 20.7 - - - -
727C ALA* 4.3 11.7 - - - -
729C ASN 3.3 9.6 - - - -
730C VAL* 4.1 2.0 - - - -
849C VAL* 1.4 69.4 - - - +
851C PHE* 1.3 63.3 + - - +
857C VAL* 3.5 4.5 - - - +
858C VAL 3.1 21.2 + - - -
859C ALA* 2.9 20.2 + - - -
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Residues in contact with PHE 851 (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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727C ALA* 4.2 3.7 - - - +
728C ASP* 3.4 2.4 - - - +
729C ASN* 3.0 64.1 + - + -
731C VAL* 4.0 16.2 - - + -
849C VAL 3.4 14.4 - - - -
850C GLY* 1.3 77.5 - - - +
852C MET* 1.3 82.9 + - - +
855C GLY* 4.9 1.1 - - - +
856C THR 3.6 13.9 - - - +
857C VAL* 3.8 13.0 - - + +
858C VAL* 4.3 2.5 - - - +
931C VAL* 3.6 37.2 - - + -
934C THR* 3.8 23.3 - - + -
935C CYS* 3.8 22.4 - - - -
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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