Contacts of the strand formed by residues 873 - 875 (chain D) in PDB entry 4UN0
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 ILE 873 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784D ARG 4.7 0.2 - - - +
785D SER* 2.8 32.3 + - - -
820D LEU* 3.8 24.0 - - + -
839D PHE* 3.6 42.8 - - + +
842D GLN* 3.2 21.6 + - + +
843D LEU* 4.8 10.5 - - + +
865D ILE* 3.8 19.5 - - + -
866D LEU 3.2 2.5 - - - +
867D LEU* 3.7 17.5 - - + -
871D GLY 4.4 4.9 - - - +
872D GLN* 1.3 79.8 - - - +
874D LYS* 1.3 67.5 + - - +
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Residues in contact with LYS 874 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783D HIS 4.0 1.6 + - - -
784D ARG* 2.4 40.6 + - - +
785D SER 3.3 9.0 - - - +
786D VAL 3.8 14.9 + - - +
787D VAL* 3.8 22.9 - - + +
788D ASN* 5.4 2.5 - - - +
814D GLU* 5.1 15.0 - - + +
816D MET* 4.1 28.5 - - + +
843D LEU* 6.0 0.2 - - - -
865D ILE* 3.6 3.7 - - - +
866D LEU* 2.7 45.5 + - + +
872D GLN* 5.6 5.4 - - + -
873D ILE* 1.3 83.4 - - - +
875D LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 875 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785D SER 3.1 14.6 + - - +
786D VAL* 4.0 3.8 - - + -
787D VAL* 3.2 22.3 + - - +
843D LEU* 4.1 24.2 - - + +
846D GLY* 5.6 1.8 - - - -
847D LEU* 4.2 17.7 - - + +
850D CYS* 5.6 2.9 - - - -
857D HIS* 3.4 37.5 - - + +
860D ILE* 4.2 22.4 - - + -
864D ASN* 3.6 12.3 - - + +
865D ILE* 4.1 17.5 - - + +
874D LYS* 1.3 72.1 - - - +
876D ALA* 1.3 65.2 + - - +
878D PHE* 3.9 18.1 - - + -
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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
------------------------------------------------------------
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