Contacts of the strand formed by residues 916 - 922 (chain O) 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 GLN 916 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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908O TRP* 2.8 33.9 - - - +
909O VAL 3.2 7.2 - - - +
910O GLN* 4.0 25.4 + - + +
911O PHE* 4.7 1.8 - - - -
914O GLY 4.1 5.2 - - - +
915O SER* 1.3 80.0 - - - +
917O LEU* 1.3 61.0 + - - +
918O VAL* 4.9 6.3 - - + +
927P SER 4.2 1.1 - - - -
928P TYR* 3.2 24.5 - - - -
929P THR* 3.1 41.7 + - + +
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Residues in contact with LEU 917 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907O VAL 3.8 1.2 - - - +
908O TRP* 3.6 1.0 - - - -
909O VAL* 2.6 48.8 + - + +
911O PHE* 3.5 34.9 - - + -
916O GLN* 1.3 74.4 - - - +
918O VAL* 1.3 61.5 + - - +
919O VAL* 4.1 8.9 - - + +
926P ILE* 3.6 31.0 - - + -
927P SER 3.3 6.5 - - - +
928P TYR* 4.4 15.0 - - + -
948P ILE* 4.8 11.0 - - + +
951P LYS* 3.9 24.5 - - + +
952P LEU* 4.0 16.2 - - + +
955P LEU* 4.9 2.9 - - + -
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Residues in contact with VAL 918 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906O ALA* 5.4 2.7 - - + -
907O VAL 3.4 11.0 - - - +
908O TRP* 3.8 24.5 - - + -
916O GLN* 4.9 7.9 - - + +
917O LEU* 1.3 78.7 - - - +
919O VAL* 1.3 64.6 + - - +
920O GLN* 4.7 19.2 - - + +
925P SER 3.7 1.7 - - - +
926P ILE* 3.4 5.6 - - - -
927P SER* 2.9 52.9 + - - +
929P THR* 6.4 1.6 - - + -
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Residues in contact with VAL 919 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906O ALA* 3.4 2.6 - - - +
907O VAL* 2.8 51.8 + - + +
909O VAL* 6.2 1.3 - - + -
917O LEU* 5.0 8.3 - - + -
918O VAL* 1.3 78.8 - - - +
920O GLN* 1.3 66.2 + - - +
921O ALA* 4.0 5.3 + - + +
923P VAL* 3.7 35.7 - - + -
925P SER 3.6 2.7 - - - -
926P ILE* 4.5 14.1 - - + -
952P LEU* 4.3 25.4 - - + -
955P LEU* 5.5 6.1 - - + -
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Residues in contact with GLN 920 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901O GLN* 5.4 2.9 + - - -
905O GLY 3.9 5.8 - - - +
906O ALA* 3.6 23.9 - - - +
918O VAL* 4.7 15.6 - - + +
919O VAL* 1.3 73.5 - - - +
921O ALA* 1.3 53.5 + - - +
923P VAL* 3.5 5.5 - - - +
924P SER* 2.6 47.8 + - - +
925P SER* 2.9 28.2 + - - +
937P ARG* 5.0 6.8 - - - +
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Residues in contact with ALA 921 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904O SER* 3.4 5.0 - - - -
905O GLY 2.8 39.4 + - - +
907O VAL* 6.3 2.9 - - + -
919O VAL* 4.0 8.0 + - + +
920O GLN* 1.3 75.6 - - - +
922O GLY* 1.3 58.8 + - - +
921P ALA* 4.5 14.4 - - + -
922P GLY 3.2 15.7 - - - +
923P VAL* 4.5 4.3 - - + -
924P SER* 4.2 3.6 - - - +
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Residues in contact with GLY 922 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903O THR 4.2 0.7 - - - -
904O SER* 4.1 11.2 - - - -
921O ALA* 1.3 75.0 - - - +
923O VAL* 1.3 65.6 + - - -
924O SER* 3.3 0.7 + - - -
940O GLU* 5.9 1.6 - - - -
921P ALA* 3.3 3.0 - - - -
922P GLY* 2.8 34.1 + - - +
924P SER* 4.8 5.6 - - - +
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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