Contacts of the strand formed by residues 855 - 858 (chain A) in PDB entry 4N78
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 855 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A ASP* 4.5 1.2 + - - +
792A LEU* 6.5 1.6 - - + -
793A THR* 3.8 17.3 - - - +
850A ASP* 3.8 13.6 + - - -
851A PHE* 3.1 46.0 + + + +
854A ASN* 1.3 82.8 - - - +
856A CYS* 1.3 61.7 + - - +
864A PHE* 3.8 24.0 - - + -
865A VAL* 3.2 24.0 - - - -
866A ARG* 3.2 54.7 + - + +
906A ARG 4.8 2.9 + - - -
907A ASN 5.7 0.6 - - - -
908A PHE* 4.8 4.5 - - - -
909A VAL* 3.8 21.8 - - + -
998A ARG* 3.3 10.8 + - - -
1002A ASN* 2.9 23.6 + - - +
1153A PHE 4.0 0.3 - - - +
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Residues in contact with CYS 856 (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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855A TYR* 1.3 77.5 - - - +
857A TYR* 1.3 63.4 + - - +
858A ASN* 3.7 1.2 + - - +
863A ARG 3.8 0.2 - - - +
864A PHE* 3.3 3.6 - - - -
865A VAL* 2.6 45.6 + - + +
866A ARG 4.1 2.5 - - - -
867A THR* 3.6 21.3 - - - -
998A ARG* 3.6 4.9 - - - -
1150A GLU 4.5 3.4 - - - +
1151A GLN 4.2 6.1 - - - +
1152A CYS 3.2 33.9 - - - -
1153A PHE 3.7 4.9 - - - -
1154A GLY* 3.5 16.4 - - - +
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Residues in contact with TYR 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A TYR 4.2 0.6 + - - -
856A CYS* 1.3 72.2 - - - +
858A ASN* 1.3 62.0 + - - +
859A GLY* 3.4 29.0 + - - -
862A ASN* 2.7 44.9 + - - +
863A ARG 3.8 2.7 - - - -
864A PHE* 3.3 40.4 - + + -
1002A ASN* 4.5 2.5 + - - +
1005A LEU* 3.5 35.7 - - + -
1009A LEU* 3.8 22.7 - - + +
1153A PHE 4.4 0.8 + - - -
1154A GLY* 3.8 6.6 - - - -
1155A ASP* 2.9 38.7 + - + +
1156A GLY 4.4 4.9 - - - +
1159A TRP* 4.6 7.2 - + - -
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Residues in contact with ASN 858 (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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856A CYS 3.7 1.5 + - - +
857A TYR* 1.3 73.4 - - - +
859A GLY* 1.3 53.5 + - - +
860A SER* 3.0 22.4 + - - -
861A THR* 3.3 24.8 + - - +
862A ASN* 2.7 35.3 + - - -
863A ARG 2.8 17.8 + - - +
865A VAL* 5.9 5.6 - - + -
1155A ASP* 3.9 1.8 - - - -
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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