Contacts of the strand formed by residues 903 - 910 (chain A) in PDB entry 4E5W
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 GLU 903 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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870A PHE* 4.4 11.1 - - - -
893A ARG* 3.5 0.6 - - - -
894A TYR* 2.9 35.4 + - + +
902A GLY* 1.3 71.6 - - - -
904A GLN* 1.3 71.8 + - - +
905A VAL* 3.8 8.8 + - + +
941A LYS* 3.2 37.9 + - - -
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Residues in contact with GLN 904 (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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878A ILE* 4.2 17.6 - - + +
891A LEU* 4.0 13.1 - - + +
892A CYS 3.3 7.0 - - - +
893A ARG* 4.3 26.4 + - + +
902A GLY 3.8 0.2 + - - -
903A GLU* 1.3 78.9 - - - +
905A VAL* 1.3 64.6 + - - +
941A LYS* 5.4 0.7 - - - -
957A GLU* 5.5 0.2 - - - -
958A PHE* 3.7 45.8 + - + +
960A PRO* 5.1 5.3 - - - +
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Residues in contact with VAL 905 (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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870A PHE* 4.5 5.8 - - + -
875A LEU* 3.9 18.2 - - + -
891A LEU* 3.6 4.9 - - - +
892A CYS 2.8 39.3 + - - +
894A TYR* 4.5 7.6 - - + -
903A GLU* 3.8 12.8 - - + +
904A GLN* 1.3 78.2 - - - +
906A ALA* 1.3 58.0 + - - +
907A VAL* 3.8 20.0 - - + -
941A LYS* 3.8 32.1 - - + -
955A ILE* 3.8 15.7 - - + -
956A MET 3.6 7.0 - - - +
958A PHE* 3.9 9.4 - - - +
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Residues in contact with ALA 906 (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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881A LEU* 4.1 7.6 - - + -
889A VAL* 3.9 9.9 - - + -
890A GLU 3.6 4.9 - - - -
905A VAL* 1.3 72.7 - - - +
907A VAL* 1.4 58.3 + - - +
954A LEU 3.6 1.0 - - - +
955A ILE* 3.6 3.5 - - - +
956A MET* 2.8 36.7 + - + +
957A GLU 3.8 5.6 - - - +
958A PHE* 4.0 2.7 - - - +
1201A 0NT 3.2 44.9 - - + +
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Residues in contact with VAL 907 (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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875A LEU* 4.0 8.7 - - + -
888A LYS 3.5 1.9 - - - +
889A VAL* 3.2 4.4 - - - +
890A GLU* 2.8 41.3 + - + +
892A CYS* 3.7 28.3 - - + -
905A VAL* 3.8 17.5 - - + -
906A ALA* 1.4 75.9 - - - +
908A LYS* 1.4 61.2 + - - +
909A SER* 3.9 6.6 + - - +
953A LYS* 3.9 28.0 - - + -
954A LEU 3.4 1.8 - - - -
955A ILE* 3.7 29.8 - - + -
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Residues in contact with LYS 908 (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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884A GLY* 5.4 6.3 - - - -
885A HIS 6.0 0.8 - - - +
887A GLY* 4.5 20.4 - - - +
888A LYS 3.3 9.4 - - - +
889A VAL* 3.8 22.4 - - + -
906A ALA 4.2 0.6 - - - -
907A VAL* 1.4 72.1 - - - +
909A SER* 1.3 62.1 + - - +
922A LEU* 4.1 16.0 - - + +
925A GLU* 2.7 43.6 + - - +
953A LYS* 3.3 5.0 - - - -
954A LEU* 2.8 54.6 + - + +
956A MET* 4.1 7.3 - - + +
1021A ASP* 2.8 33.1 + - - +
1023A GLY* 3.7 5.7 - - - -
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Residues in contact with SER 909 (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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887A GLY* 3.1 3.3 - - - -
888A LYS* 2.9 41.8 + - - +
890A GLU* 5.6 4.3 + - - -
907A VAL* 3.9 6.5 + - - +
908A LYS* 1.3 73.5 - - - +
910A LEU* 1.3 68.1 + - - +
922A LEU* 4.3 7.0 - - - -
952A ILE 4.8 0.9 - - - -
953A LYS* 2.9 42.9 + - - +
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Residues in contact with LEU 910 (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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886A PHE* 3.6 20.0 - - + +
887A GLY* 4.2 0.7 - - - -
888A LYS* 5.0 4.9 - - - +
909A SER* 1.3 80.2 - - - +
911A LYS* 1.3 68.1 + - - +
917A ASN 4.9 4.0 - - - +
918A HIS* 3.5 33.0 - - + +
919A ILE* 3.2 42.2 - - + +
922A LEU* 4.0 27.0 - - + +
952A ILE* 4.9 4.1 + - + +
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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