Contacts of the strand formed by residues 953 - 957 (chain A) in PDB entry 4E4N
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 LYS 953 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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872A LYS* 5.6 11.9 - - - +
875A LEU* 4.4 13.5 - - + -
888A LYS* 5.5 2.2 - - - +
890A GLU* 5.0 5.9 + - - -
907A VAL* 3.9 20.2 - - + -
908A LYS 3.4 8.3 - - - +
909A SER* 3.2 30.5 + - - +
922A LEU* 5.0 0.2 - - - -
926A ILE* 4.5 1.1 - - - -
943A ILE* 3.3 11.8 - - - +
944A CYS* 2.7 51.2 + - + +
952A ILE* 1.3 81.0 - - - +
954A LEU* 1.3 59.9 + - - +
955A ILE* 4.4 0.7 - - + -
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Residues in contact with LEU 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A ALA 3.5 1.2 - - - +
907A VAL* 3.3 5.7 - - - -
908A LYS* 2.9 44.2 + - + +
922A LEU* 4.6 5.1 - - + +
925A GLU* 4.2 25.8 - - + +
926A ILE* 3.8 32.0 - - + +
929A LEU* 4.2 11.9 - - + -
940A TYR* 3.7 29.4 - - + -
942A GLY 3.9 3.8 - - - +
953A LYS* 1.3 70.4 - - - +
955A ILE* 1.3 69.3 + - - +
956A MET* 3.9 32.4 - - + +
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Residues in contact with ILE 955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A PHE* 3.9 34.3 - - + -
875A LEU* 3.8 22.0 - - + -
905A VAL* 3.7 31.0 - - + -
906A ALA 3.4 1.6 - - - -
907A VAL* 3.8 26.0 - - + -
941A LYS* 2.9 23.9 + - + -
942A GLY 2.8 34.6 + - - +
943A ILE 4.0 7.2 - - - -
944A CYS* 4.3 7.9 - - + -
953A LYS* 4.4 1.8 - - + +
954A LEU* 1.3 81.2 - - - +
956A MET* 1.3 66.1 + - - +
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Residues in contact with MET 956 (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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889A VAL* 4.6 4.5 - - + -
905A VAL* 3.6 6.9 - - - +
906A ALA* 2.7 42.1 + - + +
908A LYS* 4.1 23.6 - - + +
925A GLU* 6.0 0.4 - - - +
929A LEU* 3.7 32.8 - - + -
938A VAL* 4.3 9.4 - - + -
939A LYS 3.4 10.3 - - - +
940A TYR* 4.7 0.2 - - - -
941A LYS* 3.8 6.5 - - - +
954A LEU* 3.9 23.1 - - + -
955A ILE* 1.3 78.3 - - - +
957A GLU* 1.3 65.4 + - - +
958A PHE 3.5 0.2 + - - -
1020A GLY 4.7 4.9 - - - +
1021A ASP* 6.1 1.1 - - - -
1201A 0NL 3.6 31.2 - - + -
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Residues in contact with GLU 957 (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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904A GLN 5.3 0.7 - - - -
905A VAL* 5.2 0.2 - - - +
938A VAL* 3.5 10.7 - - + +
939A LYS* 3.0 50.8 + - + +
941A LYS* 3.6 19.7 - - + +
956A MET* 1.3 72.1 - - - +
958A PHE* 1.3 60.3 + - - +
959A LEU* 3.5 18.3 - - + +
1012A GLU* 4.3 4.0 - - - +
1018A LYS* 2.7 37.7 + - - +
1201A 0NL 2.8 24.3 + - - -
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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