Contacts of the strand formed by residues 724 - 731 (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 THR 724 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580C ALA* 3.4 22.4 - - + -
581C GLY* 4.5 4.0 - - - +
623C ASN* 5.6 3.8 - - - +
722C GLU 3.3 18.2 - - - +
723C ASP* 1.3 75.0 - - - +
725C PRO* 1.3 76.7 + - - +
726C GLN* 3.6 6.2 + - - +
811C TYR* 3.5 7.6 - - - -
812C GLY 2.8 34.1 + - - +
813C SER 4.6 0.2 - - - -
814C PRO* 3.5 23.2 - - + +
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Residues in contact with PRO 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LEU* 5.3 6.7 - - + -
231B ASN 5.7 0.2 - - - +
232B ALA* 3.9 17.2 - - + +
233B SER* 4.3 3.1 + - - -
580C ALA* 4.3 15.3 - - + +
581C GLY* 5.0 10.3 - - - -
724C THR* 1.3 95.0 - - - +
726C GLN* 1.3 62.9 + - - +
809C TRP* 4.1 20.4 - - + -
810C GLU 3.4 7.2 - - - +
811C TYR* 4.1 18.2 - - + -
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Residues in contact with GLN 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B SER* 3.6 23.3 - - - +
235B ILE* 4.0 26.1 - - + +
53C ASP* 4.3 19.5 + - - +
84C SER* 5.4 6.3 - - - -
724C THR* 3.6 14.8 + - - +
725C PRO* 1.3 83.1 - - - +
727C PHE* 1.3 63.8 + - - +
728C LYS 3.7 0.5 + - - -
809C TRP* 3.3 10.7 - - - -
810C GLU* 2.6 49.6 + - + +
811C TYR* 3.8 4.7 + - - +
812C GLY* 3.5 26.4 + - - +
813C SER 5.4 3.8 + - - -
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Residues in contact with PHE 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B LEU* 4.0 17.9 - - + -
232B ALA* 5.2 0.4 - - + -
233B SER 3.0 13.1 + - - +
234B ILE* 3.4 22.6 - - + +
235B ILE* 2.9 26.8 + - - +
726C GLN* 1.3 74.4 - - - +
728C LYS* 1.3 58.4 + - - +
729C ILE* 3.7 7.4 + - + -
783C PRO* 3.8 29.4 - - + -
786C ILE* 4.3 23.3 - - + -
807C SER* 3.3 37.7 - - - -
808C ARG 3.8 7.6 - - - -
809C TRP* 3.6 45.1 - + + -
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Residues in contact with LYS 728 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ILE* 3.3 28.7 - - + +
236B ALA 3.0 22.8 + - - -
237B GLN* 4.9 0.4 - - - +
238B THR* 3.7 19.4 + - - +
726C GLN* 3.7 1.2 + - + -
727C PHE* 1.3 71.0 - - - +
729C ILE* 1.3 60.1 + - - +
730C ASP* 3.8 28.2 + - - +
807C SER* 3.0 5.0 - - - -
808C ARG* 2.6 75.1 + - + +
810C GLU* 3.8 25.9 + - + +
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Residues in contact with ILE 729 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B ILE* 3.4 32.1 - - + -
235B ILE 3.0 5.8 + - - +
236B ALA* 3.5 26.0 - - - +
727C PHE* 4.3 10.3 - - + +
728C LYS* 1.3 75.3 - - - +
730C ASP* 1.3 69.6 + - - +
731C ILE* 4.0 9.9 + - + +
750C LEU* 4.0 24.5 - - + -
786C ILE* 4.0 33.7 - - + -
801C PHE* 4.4 2.7 - - + -
805C SER* 4.1 14.8 - - - +
806C SER 3.4 11.2 - - - +
807C SER* 4.3 8.1 - - - -
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Residues in contact with ASP 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ALA 5.4 1.6 - - - +
237B GLN* 5.6 3.6 - - - +
728C LYS* 3.8 19.9 + - - +
729C ILE* 1.3 72.1 - - - +
731C ILE* 1.3 68.4 + - - +
732C ASP* 3.5 2.5 + - - +
805C SER* 3.5 3.8 - - - -
806C SER* 2.9 40.8 + - - +
808C ARG* 3.4 30.0 + - - +
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Residues in contact with ILE 731 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ALA* 5.7 4.5 - - + -
237B GLN* 6.0 6.5 - - + +
729C ILE* 4.0 17.0 + - + +
730C ASP* 1.3 77.5 + - - +
732C ASP* 1.3 69.6 + - - +
733C GLN* 3.3 13.4 + - + +
743C ILE* 4.6 12.6 - - + -
746C ILE* 3.7 37.5 - - + -
747C ASN* 4.4 9.4 - - - +
750C LEU* 4.4 9.2 - - + -
801C PHE* 3.7 31.6 - - + -
804C PHE* 3.8 9.0 - - + -
805C SER* 4.6 3.1 - - - -
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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
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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