Contacts of the strand formed by residues 918 - 921 (chain A) in PDB entry 4NEN
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 TYR 918 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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916A THR* 3.5 5.6 - - - +
917A LYS* 1.3 92.2 - - + +
919A LEU* 1.3 78.9 + - - +
920A CYS* 3.8 31.0 - - + -
1076A THR* 4.2 1.6 - - - -
1077A VAL* 3.2 23.3 - - + +
1079A GLU* 5.1 9.2 - - - +
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Residues in contact with LEU 919 (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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916A THR* 3.9 16.2 - - + -
918A TYR* 1.3 84.5 - - - +
920A CYS* 1.3 63.2 + - - +
921A PHE* 3.9 3.0 + - - -
930A HIS* 3.5 46.2 - - + +
931A VAL 4.3 0.9 - - - +
932A ALA* 4.4 4.7 - - + -
1032A LEU* 3.8 27.8 - - + -
1034A PHE* 4.3 13.5 - - + -
1076A THR* 4.4 1.6 - - + -
1077A VAL 2.9 7.5 + - - -
1078A LEU* 3.6 27.7 - - + -
1079A GLU 3.0 25.1 + - - +
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Residues in contact with CYS 920 (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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918A TYR* 3.8 28.9 - - + -
919A LEU* 1.3 73.2 - - - +
921A PHE* 1.3 62.9 + - - +
925A GLU* 4.2 3.5 - - - +
1034A PHE* 4.7 4.5 - - - -
1079A GLU* 3.4 23.6 - - - -
1081A TYR* 3.8 26.9 + - + -
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Residues in contact with PHE 921 (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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919A LEU 3.9 4.7 - - - -
920A CYS* 1.3 74.2 - - - +
922A SER* 1.3 74.3 + - - +
923A GLU* 5.7 0.9 - - - -
925A GLU* 3.3 18.6 - - + +
926A GLU* 5.4 5.6 - - + -
1034A PHE* 3.6 55.2 - + + -
1037A VAL* 4.1 26.0 - - + -
1043A LYS 5.5 0.2 - - - -
1078A LEU* 4.0 21.3 - - + -
1079A GLU 3.0 20.8 + - - -
1080A LYS* 3.1 50.1 - - + -
1081A TYR* 3.5 7.2 + - - -
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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