Contacts of the strand formed by residues 895 - 903 (chain D) 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 ILE 895 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715D ILE* 3.7 7.5 - - + +
716D GLU* 3.7 2.3 - - - +
717D LYS* 3.1 44.5 + - + +
720D LEU* 4.7 7.0 - - - +
860D LEU* 3.3 20.6 - - + +
886D MET* 4.2 25.8 - - + -
887D ASP* 5.3 3.1 - - + +
892D ILE* 3.6 30.3 - - + +
893D PRO 5.0 0.9 - - - -
894D ASN* 1.3 76.6 - - - +
896D ARG* 1.3 64.3 + - - +
897D GLY 4.2 0.7 - - - +
955D HIS* 3.8 37.9 - - + +
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Residues in contact with ARG 896 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712D GLU* 3.9 11.1 + - - -
714D LYS* 3.5 31.1 - - + +
715D ILE 3.9 1.6 - - - -
716D GLU* 3.5 29.3 + - + +
720D LEU* 4.4 19.7 - - + -
860D LEU 2.8 11.1 + - - +
861D GLU* 3.3 28.4 - - + +
862D VAL 2.8 28.1 + - - +
863D ASP* 5.2 3.1 + - - +
886D MET* 4.0 2.8 - - - +
895D ILE* 1.3 75.1 - - - +
897D GLY* 1.3 63.4 + - - +
898D THR* 3.9 24.2 - - + +
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Residues in contact with GLY 897 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714D LYS* 3.2 4.0 - - - +
715D ILE* 2.7 41.2 + - - +
862D VAL 3.3 7.9 - - - -
883D LEU* 4.0 8.9 - - - +
886D MET* 3.4 25.0 - - - +
895D ILE* 4.2 0.4 - - - +
896D ARG* 1.3 76.2 - - - +
898D THR* 1.4 60.1 + - - -
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Residues in contact with THR 898 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712D GLU* 3.8 21.3 + - - +
713D LEU 3.2 10.8 - - - -
714D LYS* 3.9 12.1 - - + +
862D VAL 3.3 3.2 + - - -
863D ASP* 2.6 39.2 + - - +
864D HIS* 3.0 28.4 + - - -
883D LEU* 3.4 6.6 - - - +
896D ARG* 3.9 29.2 - - + +
897D GLY* 1.4 73.7 - - - -
899D GLY* 1.3 61.5 + - - +
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Residues in contact with GLY 899 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712D GLU* 3.7 6.2 + - - -
713D LEU* 3.0 37.8 + - - +
864D HIS 3.2 12.3 - - - -
879D MET* 3.6 18.6 - - - -
883D LEU* 5.2 0.2 - - - -
898D THR* 1.3 83.4 - - - +
900D ARG* 1.3 62.3 + - - -
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Residues in contact with ARG 900 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706D ASN* 5.6 1.6 + - - -
708D PHE* 3.1 49.4 + - + -
710D GLY 2.4 33.1 + - - -
711D PRO* 3.3 4.2 - - - +
712D GLU* 2.9 38.2 - - + +
864D HIS 3.1 6.9 + - - -
865D PHE* 3.8 30.0 - - + +
866D SER* 3.5 23.4 - - - -
879D MET* 4.0 1.5 - - - +
899D GLY* 1.3 77.2 - - - -
901D LEU* 1.3 69.6 + - - +
902D CYS* 3.8 2.1 + - - -
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Residues in contact with LEU 901 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708D PHE* 3.0 18.3 + - - +
709D TYR* 3.4 41.7 + - + +
710D GLY 5.4 0.2 + - - -
713D LEU* 5.3 8.1 - - + -
866D SER* 3.6 20.6 - - - +
868D VAL* 3.8 15.3 - - + -
872D GLN* 5.2 6.5 - - + +
875D SER* 3.9 18.6 - - - +
876D GLN* 3.8 36.8 - - + +
879D MET* 4.3 13.7 - - + -
900D ARG* 1.3 83.2 - - - +
902D CYS* 1.3 62.1 + - - +
903D LYS 3.3 1.0 + - - -
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Residues in contact with CYS 902 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699D ILE* 4.2 17.7 - - - -
702D ALA* 3.5 26.0 - - + -
703D ILE* 5.8 0.9 - - - -
708D PHE* 3.5 13.2 - - + -
709D TYR* 4.2 1.8 - - - -
865D PHE* 3.9 27.6 - - - -
866D SER 3.3 21.4 + - - +
867D ASN* 4.1 5.1 - - - -
868D VAL* 3.1 28.6 + - - +
869D GLY 3.9 0.5 + - - -
900D ARG 4.2 2.9 - - - -
901D LEU* 1.3 72.0 - - - +
903D LYS* 1.3 63.3 + - - +
904D THR* 3.6 6.3 + - + +
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Residues in contact with LYS 903 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652D ASP* 6.0 2.2 - - - +
696D ILE* 4.1 6.1 - - + +
702D ALA* 4.5 1.2 - - - +
707D SER* 3.5 17.3 + - - +
708D PHE* 3.6 20.5 - - - +
709D TYR* 3.1 60.5 + - + +
869D GLY 4.7 0.7 - - - +
870D ASN* 5.4 5.3 + - - +
901D LEU 3.3 4.4 + - - -
902D CYS* 1.3 70.0 - - - +
904D THR* 1.3 69.5 + - - +
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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