Contacts of the strand formed by residues 815 - 819 (chain A) in PDB entry 5NC5
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 ARG 815 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 3.7 0.4 - - - +
81A ASN* 3.1 39.1 + - + +
82A SER 3.5 4.7 - - - +
83A ASP* 3.7 25.8 - - + +
617A PHE 5.6 2.0 + - - -
618A ALA* 4.0 22.3 + - - +
692A HIS* 5.6 1.6 - - - -
719A ASN* 4.0 14.2 + - - +
720A GLY* 3.5 15.1 - - - -
721A LEU* 3.7 38.3 + - + +
813A SER* 3.2 16.5 + - - -
814A PRO* 1.4 79.1 - - - +
816A LEU* 1.3 63.8 + - - +
817A GLU* 3.5 32.1 + - - +
826A GLU* 5.4 4.4 + - - -
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Residues in contact with LEU 816 (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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54A ALA* 3.7 16.2 - - + +
55A LYS* 3.7 36.6 - - + +
58A GLN* 3.3 30.5 - - - +
80A SER 3.5 2.9 - - - +
81A ASN* 3.6 1.2 - - - -
82A SER* 2.8 38.8 + - - +
692A HIS* 4.2 23.3 - - + +
813A SER* 3.6 24.7 - - - +
815A ARG* 1.3 73.4 - - - +
817A GLU* 1.3 63.1 + - - +
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Residues in contact with GLU 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 4.8 0.3 - - - +
80A SER 3.4 6.1 - - - +
81A ASN* 4.0 13.5 - - - +
683A GLU* 4.5 0.2 - - - +
719A ASN 5.3 0.7 - - - -
720A GLY* 3.4 28.7 + - - -
721A LEU 4.8 0.2 + - - -
815A ARG* 3.5 21.1 + - - +
816A LEU* 1.3 77.2 - - - +
818A ARG* 1.3 72.3 + - - +
823A PRO* 3.7 2.4 - - - +
824A SER* 2.9 38.6 + - - +
825A MET* 3.8 5.4 - - - +
826A GLU* 3.1 42.3 + - - +
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Residues in contact with ARG 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 3.0 43.9 - - - +
62A THR* 4.3 7.6 - - - -
63A GLN* 3.8 29.2 + - - +
66A GLU* 3.1 31.4 + - - +
79A SER* 3.5 6.8 - - - -
80A SER* 3.1 40.5 + - - +
82A SER* 5.0 0.2 - - - -
816A LEU 4.9 0.7 - - - +
817A GLU* 1.3 84.2 - - - +
819A TYR* 1.3 61.2 + - - +
820A ASN 4.1 1.0 + - - -
821A GLY 3.1 22.0 + - - -
822A LEU* 3.4 11.9 - - - +
823A PRO* 3.3 33.2 - - + +
824A SER* 3.9 4.0 - - - +
766C GLY 4.2 6.9 + - - -
767C ARG* 5.8 0.8 - - - +
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Residues in contact with TYR 819 (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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77A TYR* 3.4 37.6 - + + +
78A MET 3.6 10.3 - - - -
79A SER* 4.3 10.8 - - - -
683A GLU* 3.9 24.9 - - + +
685A ILE* 4.1 21.4 - - + +
818A ARG* 1.3 72.8 - - - +
820A ASN* 1.3 90.2 + - + +
821A GLY 3.1 0.9 + - - -
822A LEU* 2.9 21.4 + - - +
824A SER* 3.6 18.7 - - - +
858A ASP* 3.8 24.9 - - + -
859A TRP 3.2 8.1 + - - -
860A THR* 3.2 37.7 - - + -
864A TYR* 4.7 1.0 - - - -
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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