Contacts of the strand formed by residues 852 - 860 (chain A) in PDB entry 5J67
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 HIS 852 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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729A GLY* 3.4 5.0 - - - -
730A TYR* 2.8 38.9 + - + +
732A ASN* 3.6 30.2 + - + -
851A SER* 1.3 105.1 + - - +
853A TYR* 1.3 58.5 + - - +
959A VAL* 3.8 34.6 - - + +
960A VAL 3.2 10.8 - - - +
961A PRO* 3.4 36.6 - - + +
962A LEU* 3.6 12.7 - - - +
979A LEU* 5.2 9.4 - - + -
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Residues in contact with TYR 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726A MET 4.9 2.2 - - - +
729A GLY* 4.2 10.8 - - - +
730A TYR 4.5 0.2 - - - +
742A VAL* 4.6 3.6 - - + -
743A PHE* 3.6 36.1 - + + -
817A LEU* 4.3 13.2 - - + -
852A HIS* 1.3 76.1 - - - +
854A ILE* 1.3 73.1 + - - +
855A ALA* 3.5 4.2 + - + -
959A VAL* 3.5 2.7 - - - -
960A VAL* 2.9 76.9 + - + +
961A PRO 4.3 1.6 - - - -
962A LEU* 4.0 15.5 - - + -
964A THR* 4.8 4.2 - - - +
965A LEU* 3.4 33.5 - - + +
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Residues in contact with ILE 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725A GLU* 3.9 26.0 - - + +
726A MET* 3.6 39.6 + - - +
729A GLY* 5.1 1.9 - - - +
730A TYR* 3.9 21.1 - - + +
737A VAL* 4.1 15.0 - - + -
817A LEU* 3.2 17.7 - - - +
853A TYR* 1.3 75.3 - - - +
855A ALA* 1.3 60.3 + - - +
856A GLU 3.6 20.0 - - - +
857A ALA* 3.9 6.1 - - + -
953A LEU* 4.9 3.1 - - + -
956A ILE* 3.7 39.0 - - + -
958A ARG 3.8 3.1 - - - -
959A VAL* 4.6 0.9 - - - -
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Residues in contact with ALA 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726A MET* 3.5 3.0 - - - +
816A LYS* 3.4 23.0 - - - +
817A LEU* 3.4 17.6 + - + +
853A TYR* 3.5 6.8 + - + -
854A ILE* 1.3 72.6 - - - +
856A GLU* 1.3 58.3 + - - +
958A ARG* 2.9 46.7 + - + +
960A VAL* 4.0 19.5 - - + -
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Residues in contact with GLU 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814A ARG* 3.6 30.8 + - - +
815A VAL 3.5 3.8 - - - -
816A LYS* 3.4 33.3 - - + -
854A ILE* 3.6 5.4 - - - +
855A ALA* 1.3 77.9 - - - +
857A ALA* 1.3 65.0 + - - +
957A ASN* 2.9 38.5 + - + +
958A ARG* 3.1 40.4 + - + +
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Residues in contact with ALA 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726A MET* 3.7 23.6 - - - -
814A ARG* 3.6 2.9 - - - -
815A VAL* 2.7 39.1 + - - +
854A ILE* 3.9 7.2 - - + -
856A GLU* 1.3 77.9 - - - +
858A LEU* 1.3 58.7 + - - +
859A TYR* 3.9 4.7 - - + -
953A LEU* 3.8 17.3 - - + -
955A GLU 3.4 13.2 - - - +
956A ILE* 4.5 0.7 - - - -
957A ASN* 3.4 8.7 - - - -
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Residues in contact with LEU 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A LEU* 3.7 31.4 - - + -
809A ARG* 3.4 25.6 - - - +
812A LEU* 4.1 13.5 - - + -
813A TYR 3.6 14.8 - - - +
814A ARG* 3.9 16.2 - - - +
857A ALA* 1.3 72.5 - - - +
859A TYR* 1.3 70.1 + - - +
953A LEU* 3.9 2.3 - - - +
954A LEU* 2.9 27.7 + - + +
955A GLU* 2.9 45.1 + - + +
957A ASN* 3.4 8.1 + - - +
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Residues in contact with TYR 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722A LEU* 5.8 0.9 - - + -
723A PHE* 3.6 41.8 - + + -
725A GLU* 2.6 45.4 + - - +
726A MET* 4.0 9.7 - - - +
812A LEU* 3.2 9.9 - - - +
813A TYR* 2.8 33.6 + - + +
815A VAL* 3.5 28.0 - - + -
854A ILE* 5.9 0.2 - - - +
857A ALA* 3.9 20.9 - - + -
858A LEU* 1.3 78.5 - - - +
860A GLY* 1.3 58.7 + - - +
951A PRO* 3.9 11.7 - - + -
952A VAL 3.2 7.9 - - - +
953A LEU* 3.3 35.1 - - + +
954A LEU* 3.8 4.5 - - - -
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Residues in contact with GLY 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811A ASN* 3.2 22.2 - - - -
812A LEU* 4.1 0.9 - - - -
859A TYR* 1.3 76.5 - - - +
861A SER* 1.3 64.9 + - - -
951A PRO* 3.7 7.4 - - - +
952A VAL* 2.8 36.2 + - - +
954A LEU* 3.7 12.2 - - - +
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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