Contacts of the strand formed by residues 724 - 731 (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 THR 724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580A ALA* 3.6 47.1 - - + +
581A GLY* 4.8 4.7 + - - -
722A GLU 3.6 5.4 + - - +
723A ASP* 1.3 80.1 - - - +
725A PRO* 1.3 79.7 + - + +
726A GLN* 3.8 1.7 - - - +
811A TYR* 3.5 8.2 - - - -
812A GLY 3.0 31.4 + - - +
814A PRO* 4.5 8.8 - - - +
231C ASN 6.1 0.2 - - - -
23E ARG* 5.2 1.1 - - - +
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Residues in contact with PRO 725 (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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581A GLY* 6.0 2.5 - - - -
724A THR* 1.3 96.7 + - - +
726A GLN* 1.3 63.8 + - - +
809A TRP* 4.1 20.2 - - + -
810A GLU 3.3 9.9 - - - +
811A TYR* 3.9 26.5 - - + +
230C LEU* 6.1 1.1 - - + -
231C ASN 4.8 3.6 - - - +
232C ALA* 3.7 20.6 - - + +
233C SER* 4.0 1.6 + - - -
44E ASP* 5.5 1.1 - - - +
46E VAL* 4.4 17.9 - - + -
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Residues in contact with GLN 726 (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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53A ASP* 5.0 4.7 - - - +
724A THR* 3.8 8.3 - - - +
725A PRO* 1.3 82.1 - - - +
727A PHE* 1.3 62.6 + - - +
728A LYS 3.6 0.4 + - - -
809A TRP* 3.3 12.1 - - - -
810A GLU* 2.7 46.5 + - + +
811A TYR 3.6 19.2 + - - -
812A GLY* 3.8 23.2 - - - +
813A SER 4.2 7.4 + - - +
233C SER* 3.4 23.2 - - - +
235C ILE* 3.5 33.0 - - + +
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Residues in contact with PHE 727 (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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726A GLN* 1.3 73.7 - - - +
728A LYS* 1.3 58.3 + - - +
729A ILE* 3.8 17.2 + - + -
783A PRO* 3.6 29.6 - - + -
786A ILE* 3.9 28.3 - - + -
807A SER* 3.4 35.2 - - - -
808A ARG 3.8 4.7 - - - -
809A TRP* 4.0 25.8 - + + -
219C LEU* 3.7 23.8 - - + -
232C ALA* 5.0 0.2 - - + -
233C SER 2.9 9.4 + - - +
234C ILE* 3.4 15.5 - - + -
235C ILE* 2.8 26.7 + - - +
79E LEU* 3.9 11.7 - - + -
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Residues in contact with LYS 728 (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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726A GLN 3.6 1.2 + - - -
727A PHE* 1.3 73.4 - - - +
729A ILE* 1.3 66.6 + - - +
730A ASP* 3.9 18.4 - - - +
807A SER* 3.0 8.0 - - - -
808A ARG* 2.7 67.5 + - + +
810A GLU* 2.9 38.5 + - + +
235C ILE* 3.4 30.5 - - + +
236C ALA 3.7 15.7 + - - +
238C THR* 4.1 17.0 + - - +
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Residues in contact with ILE 729 (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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727A PHE* 4.0 9.9 - - + -
728A LYS* 1.3 75.3 - - - +
730A ASP* 1.3 65.4 + - - +
731A ILE* 4.0 12.5 + - + +
750A LEU* 3.9 25.8 - - + -
786A ILE* 4.1 22.9 - - + -
801A PHE* 5.3 3.1 - - + -
805A SER* 3.8 23.6 - - - +
806A SER 3.3 14.6 - - - +
807A SER* 4.6 4.0 - - - -
234C ILE* 3.7 26.0 - - + -
235C ILE 2.8 14.5 + - - +
236C ALA* 3.6 24.6 - - + -
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Residues in contact with ASP 730 (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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728A LYS* 3.9 15.4 - - - +
729A ILE* 1.3 77.0 - - - +
731A ILE* 1.3 64.7 + - - +
732A ASP* 3.6 1.4 + - - +
805A SER* 3.3 6.1 - - - -
806A SER* 3.0 42.0 + - - +
808A ARG* 2.9 29.9 + - - +
236C ALA 5.5 0.5 - - - +
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Residues in contact with ILE 731 (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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729A ILE* 4.0 12.9 + - + +
730A ASP* 1.3 75.5 - - - +
732A ASP* 1.3 64.2 + - - +
733A GLN* 3.2 20.9 + - - +
736A ALA* 5.0 0.9 - - + -
743A ILE* 4.5 15.7 - - + -
746A ILE* 3.8 46.9 - - + -
747A ASN* 4.8 9.2 - - - +
750A LEU* 5.8 3.6 - - + -
801A PHE* 4.4 11.9 - - + -
804A PHE* 3.7 9.2 - - + +
805A SER* 4.3 16.2 - - - -
236C ALA* 5.6 6.5 - - + -
237C GLN* 5.7 10.8 - - + +
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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