Contacts of the strand formed by residues 904 - 911 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900M THR* 3.7 4.2 - - - -
901M GLN* 2.4 51.1 + - - +
902M LEU 3.6 0.8 - - - -
903M THR* 1.3 83.7 + - - +
905M GLY* 1.3 58.9 + - - +
920M GLN* 6.0 1.1 - - - -
921M ALA 3.3 15.0 - - - -
922M GLY* 4.2 6.3 - - - -
923M VAL* 4.2 4.1 - - - +
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Residues in contact with GLY 905 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899M ALA 3.6 11.9 - - - -
900M THR* 4.0 10.5 - - - -
901M GLN* 3.3 6.4 + - - -
904M SER* 1.3 80.3 - - - +
906M ALA* 1.3 62.0 + - - +
907M VAL* 5.6 1.8 - - - -
920M GLN* 3.7 6.0 - - - +
921M ALA* 2.9 34.5 + - - +
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Residues in contact with ALA 906 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898M TRP* 3.2 6.6 - - - +
899M ALA* 3.1 35.2 + - + +
900M THR* 5.1 1.2 - - - +
901M GLN* 5.2 3.6 - - - +
905M GLY* 1.3 75.0 - - - +
907M VAL* 1.3 63.9 - - - +
908M TRP 4.4 0.2 + - - -
918M VAL* 5.1 6.5 - - + -
919M VAL 3.2 7.2 - - - +
920M GLN* 3.6 30.7 - - - +
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Residues in contact with VAL 907 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896M VAL* 5.7 2.0 - - + -
897M GLY 3.7 8.7 - - - +
898M TRP* 3.8 23.6 - - + -
900M THR* 6.1 1.8 - - + -
905M GLY 5.6 0.7 - - - -
906M ALA* 1.3 80.7 - - - +
908M TRP* 1.3 62.7 + - - +
909M VAL* 3.9 21.7 - - + +
917M LEU 3.5 2.1 - - - +
918M VAL* 3.2 5.4 - - - +
919M VAL* 2.8 50.8 + - + +
955N LEU* 4.6 9.9 - - + -
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Residues in contact with TRP 908 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895M ASN* 3.8 33.2 - - + -
896M VAL* 3.3 14.4 - - - -
897M GLY* 2.8 50.6 + - - +
907M VAL* 1.3 72.4 - - - +
909M VAL* 1.3 74.4 + - - +
910M GLN* 3.7 26.9 - - + -
916M GLN* 2.7 33.2 + - + +
917M LEU 3.3 4.7 - - - -
918M VAL* 3.8 26.0 - - + +
960M LEU* 4.8 5.2 - - + -
962M PHE* 4.4 11.0 - + - -
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Residues in contact with VAL 909 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893M VAL* 3.6 24.7 - - + -
895M ASN 3.5 3.8 - - - -
896M VAL* 3.8 10.5 - - + -
907M VAL* 3.9 11.2 - - + -
908M TRP* 1.3 84.3 + - - +
910M GLN* 1.3 63.8 + - - +
911M PHE* 3.8 27.8 + - + -
916M GLN* 3.2 5.7 - - - +
917M LEU* 2.7 47.9 + - + +
955N LEU* 3.6 36.1 - - + -
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Residues in contact with GLN 910 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893M VAL* 3.8 2.3 - - - +
894M LYS* 2.8 41.7 + - + +
895M ASN* 2.8 43.9 + - + +
908M TRP* 3.7 24.5 - - + -
909M VAL* 1.3 75.6 - - - +
911M PHE* 1.3 64.7 + - - +
914M GLY* 4.2 15.8 + - - +
915M SER 3.5 11.9 - - - +
916M GLN* 4.2 14.5 - - + +
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Residues in contact with PHE 911 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891M VAL* 3.9 14.1 - - + -
892M PHE 3.1 25.6 - - - +
893M VAL* 3.6 24.0 - - + -
894M LYS* 4.3 10.3 + - - +
909M VAL* 3.8 16.8 - - + -
910M GLN* 1.3 81.6 - - - +
912M ASN* 1.3 66.5 + - - +
913M ASP* 3.1 18.8 - - - +
914M GLY* 3.2 12.4 + - - -
915M SER* 3.0 29.2 + - - +
917M LEU* 3.6 31.2 - - + -
928N TYR* 5.7 0.4 - + - -
951N LYS* 3.6 35.0 - - + -
954N CYS* 4.3 8.3 - - + -
955N LEU* 5.1 2.9 - - + -
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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