Contacts of the strand formed by residues 815 - 819 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ASN* 3.3 46.2 + - + +
82C SER 3.3 6.3 + - - -
83C ASP* 4.3 10.5 + - + +
618C ALA* 3.5 31.8 + - - +
619C GLY* 3.5 21.4 - - - +
692C HIS* 5.7 0.2 - - - -
719C ASN* 3.4 12.9 + - - +
720C GLY* 4.3 5.7 - - - -
721C LEU* 4.3 22.0 + - + +
813C SER* 3.3 12.7 + - - -
814C PRO* 1.3 84.2 - - - +
816C LEU* 1.3 63.3 + - - +
817C GLU* 2.8 35.9 + - + +
826C GLU* 5.2 1.4 + - - -
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Residues in contact with LEU 816 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ALA* 3.8 22.7 - - + +
55C LYS* 3.8 26.5 - - + -
58C GLN* 3.6 29.9 - - - +
80C SER* 3.7 0.5 + - - +
81C ASN* 3.3 3.3 - - - -
82C SER* 2.7 38.7 + - - +
692C HIS* 3.9 24.9 - - + +
813C SER* 3.5 29.6 - - - +
815C ARG* 1.3 75.0 - - - +
817C GLU* 1.3 63.6 + - - +
818C ARG* 5.3 0.2 - - - +
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Residues in contact with GLU 817 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 4.3 1.7 - - - +
80C SER 3.3 8.1 - - - +
81C ASN* 4.6 3.4 - - + +
683C GLU* 4.4 0.3 - - - +
719C ASN 2.8 17.9 - - - +
720C GLY* 4.1 3.5 - - - -
815C ARG* 2.8 42.4 + - - +
816C LEU* 1.3 80.0 - - - +
818C ARG* 1.4 69.8 + - - +
823C PRO* 3.6 4.5 - - - +
824C SER* 3.2 34.9 + - - +
825C MET* 3.3 6.3 - - - -
826C GLU* 2.6 40.3 + - - +
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Residues in contact with ARG 818 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 3.4 37.3 - - - +
62C THR* 4.4 7.4 - - - -
63C GLN* 3.6 32.0 - - - +
66C GLU* 3.0 30.3 + - - +
79C SER* 3.5 5.2 - - - -
80C SER* 2.9 44.7 + - - +
82C SER* 5.6 0.2 - - - -
683C GLU* 5.3 0.2 - - - +
816C LEU 5.3 0.4 - - - +
817C GLU* 1.4 81.0 - - - +
819C TYR* 1.3 61.7 + - - +
820C ASN 4.3 0.2 - - - -
821C GLY 3.2 21.5 + - - -
822C LEU 3.1 15.5 - - - +
823C PRO* 4.3 18.6 - - + +
824C SER* 3.6 6.7 + - - -
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Residues in contact with TYR 819 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR* 3.3 32.1 - + + +
78C MET 3.6 12.3 - - - -
79C SER* 4.1 11.7 - - - -
683C GLU* 3.7 22.7 - - + +
685C ILE* 3.9 25.5 - - + +
818C ARG* 1.3 73.0 - - - +
820C ASN* 1.3 93.8 + - - +
821C GLY 3.1 0.2 - - - -
822C LEU* 2.7 26.4 + - - +
824C SER* 3.6 17.9 - - - +
858C ASP* 3.9 23.1 + - + -
859C TRP 3.5 8.3 + - - -
860C THR* 3.1 38.6 + - - -
864C TYR* 4.6 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
------------------------------------------------------------
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