Contacts of the strand formed by residues 904 - 911 (chain D) in PDB entry 5LHY
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 904 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900D THR* 3.9 3.3 - - - -
901D GLN* 2.4 51.1 + - - +
902D LEU 3.6 0.8 - - - -
903D THR* 1.3 83.8 + - - +
905D GLY* 1.3 59.9 + - - +
920D GLN* 5.9 1.6 - - - -
921D ALA 3.4 15.5 - - - -
922D GLY* 4.4 5.4 - - - -
923D VAL* 4.2 6.1 - - - +
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Residues in contact with GLY 905 (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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899D ALA 3.6 11.2 - - - -
900D THR* 4.0 10.5 - - - -
901D GLN* 3.2 6.0 + - - -
904D SER* 1.3 80.2 - - - +
906D ALA* 1.3 62.1 + - - +
907D VAL* 5.7 0.9 - - - -
920D GLN* 3.7 5.8 - - - +
921D ALA* 2.9 35.0 + - - +
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Residues in contact with ALA 906 (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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898D TRP* 3.2 5.5 - - - +
899D ALA* 2.9 39.9 + - + +
900D THR* 5.0 0.9 - - - +
901D GLN* 5.0 4.9 - - - +
905D GLY* 1.3 75.2 - - - +
907D VAL* 1.3 65.2 + - - +
918D VAL* 5.1 5.6 - - + -
919D VAL 3.2 7.4 - - - +
920D GLN* 3.8 28.7 - - - +
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Residues in contact with VAL 907 (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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955C LEU* 4.3 12.6 - - + -
896D VAL* 5.9 1.3 - - + -
897D GLY 3.5 8.7 - - - +
898D TRP* 3.9 20.6 - - + -
905D GLY 5.7 0.2 - - - -
906D ALA* 1.3 80.3 - - - +
908D TRP* 1.3 61.2 + - - +
909D VAL* 4.0 19.7 - - + +
917D LEU 3.6 1.9 - - - +
918D VAL* 3.3 6.2 - - - +
919D VAL* 2.8 51.5 + - + +
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Residues in contact with TRP 908 (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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895D ASN* 3.8 24.2 - - + -
896D VAL* 3.3 12.1 - - - -
897D GLY* 2.5 59.3 + - - +
898D TRP* 5.6 0.4 - - - -
906D ALA 4.3 0.4 + - - -
907D VAL* 1.3 71.4 - - - +
909D VAL* 1.3 74.7 + - - +
910D GLN* 3.8 25.8 - - + -
916D GLN* 2.8 30.4 - - + +
917D LEU 3.5 2.0 - - - -
918D VAL* 4.0 24.2 - - + +
960D LEU* 3.7 23.1 - - + -
962D PHE* 4.3 11.9 - + - -
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Residues in contact with VAL 909 (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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955C LEU* 3.6 38.6 - - + -
893D VAL* 3.7 25.4 - - + -
895D ASN 3.4 3.8 - - - +
896D VAL* 4.0 9.0 - - + -
907D VAL* 4.0 10.1 - - + -
908D TRP* 1.3 84.7 + - - +
910D GLN* 1.3 64.2 + - - +
911D PHE* 3.7 26.1 - - + -
916D GLN* 3.2 5.7 - - - +
917D LEU* 2.7 48.1 + - + +
919D VAL* 6.3 0.2 - - + -
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Residues in contact with GLN 910 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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893D VAL* 3.9 2.1 - - - +
894D LYS* 2.9 17.8 + - + +
895D ASN* 2.7 63.6 + - + +
908D TRP* 3.8 25.2 - - + -
909D VAL* 1.3 75.8 - - - +
911D PHE* 1.3 71.4 + - - +
914D GLY* 4.2 13.7 + - - +
915D SER 3.4 10.5 - - - +
916D GLN* 4.0 15.6 + - + +
962D PHE* 5.4 0.2 - - - -
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Residues in contact with PHE 911 (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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928C TYR* 5.9 0.2 - + - -
951C LYS* 3.4 41.7 - - + -
954C CYS* 4.5 4.7 - - + -
955C LEU* 5.6 2.0 - - + -
891D VAL* 4.1 11.4 - - + -
892D PHE 3.5 21.5 - - - +
893D VAL* 4.0 20.4 - - + -
894D LYS* 3.8 14.4 + - - +
909D VAL* 3.7 17.9 - - + -
910D GLN* 1.3 79.9 - - - +
912D ASN* 1.3 69.6 + - - +
913D ASP* 3.2 18.4 - - - +
914D GLY* 3.2 12.2 + - - -
915D SER* 2.9 28.4 + - - +
916D GLN 4.7 0.4 - - - -
917D LEU* 3.6 35.7 - - + -
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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