Contacts of the strand formed by residues 903 - 908 (chain E) in PDB entry 5D6Y
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 903 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898E SER 4.0 5.3 + - - +
899E ILE* 3.3 35.8 - - + +
900E THR* 3.1 43.8 + - - +
901E ALA 3.2 2.2 + - - -
902E GLY* 1.3 77.3 - - - +
904E LYS* 1.3 68.7 + - - +
905E VAL* 4.0 6.3 - - + +
918E GLU* 3.1 4.6 - - - +
919E VAL* 2.7 33.8 + - + +
1005E THR* 4.1 10.9 - - - +
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Residues in contact with LYS 904 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902E GLY 3.8 1.8 + - - +
903E GLN* 1.3 80.5 + - - +
905E VAL* 1.3 65.5 + - - +
916E GLN* 3.8 33.7 - - + +
917E CYS* 3.3 17.9 - - - +
918E GLU* 2.2 48.2 + - + +
1005E THR* 5.8 2.6 - - - -
970F GLY* 4.2 6.5 + - - -
971F GLN* 5.9 0.4 - - - +
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Residues in contact with VAL 905 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899E ILE* 3.8 17.5 - - + -
903E GLN* 3.9 10.7 + - + +
904E LYS* 1.3 78.6 - - - +
906E ILE* 1.3 66.1 + - - +
916E GLN* 3.5 6.5 - - - +
917E CYS* 2.9 49.6 + - - +
919E VAL* 3.5 33.4 - - + -
1003E VAL* 3.6 27.1 - - + -
1004E TYR 3.3 13.7 - - - +
1005E THR* 5.1 2.7 - - - +
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Residues in contact with ILE 906 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905E VAL* 1.3 77.3 - - - +
907E SER* 1.3 65.0 + - - +
914E PHE* 3.5 36.6 - - + -
915E TYR* 3.5 14.1 - - - +
916E GLN* 3.7 22.7 - - + +
1004E TYR* 2.8 51.6 + - + +
1005E THR 6.1 1.8 - - - -
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Residues in contact with SER 907 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906E ILE* 1.3 75.7 - - - +
908E LYS* 1.3 64.2 + - - +
914E PHE* 3.5 9.8 - - - -
915E TYR 3.3 25.0 + - - -
917E CYS* 2.7 29.5 - - - -
988E VAL* 3.4 13.9 - - - +
990E PHE* 3.2 14.3 - - - -
998E VAL* 5.0 3.8 - - - -
1002E ASP 3.4 17.5 - - - -
1003E VAL* 4.2 10.5 - - - -
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Residues in contact with LYS 908 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907E SER* 1.3 76.2 + - - +
909E HIS* 1.3 64.1 + - - +
912E GLY* 4.9 9.2 - - - +
913E ARG 3.9 5.4 - - - +
914E PHE* 4.0 21.9 - - + -
990E PHE* 3.3 6.1 - - - -
996E LEU* 3.2 20.1 - - + +
998E VAL* 5.3 6.5 - - + +
1002E ASP* 4.0 30.3 + - + +
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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