Contacts of the helix formed by residues 782 - 788 (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 LEU 782 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B LEU* 4.1 5.2 - - - -
228B GLN* 4.9 2.5 - - - +
229B GLN* 3.4 30.3 - - - +
230B LEU* 5.2 2.0 - - + -
754C TRP* 3.6 5.9 - - - -
780C ARG 3.7 0.4 - - - -
781C MET* 1.3 91.9 - - + +
783C PRO* 1.3 80.0 - - + +
784C ASP* 3.3 13.5 - - + +
785C ASP* 3.0 38.8 + - - +
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Residues in contact with PRO 783 (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* 4.4 12.6 - - + -
230B LEU* 5.1 6.3 - - + -
727C PHE* 3.8 26.9 - - + -
781C MET 4.6 0.4 - - - +
782C LEU* 1.3 95.9 - - + +
784C ASP* 1.3 67.9 + - - +
785C ASP 3.1 0.2 - - - -
786C ILE* 3.2 25.3 + - + +
807C SER* 5.6 0.4 - - - +
809C TRP* 4.3 26.0 - - + +
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Residues in contact with ASP 784 (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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782C LEU* 4.8 10.7 - - + +
783C PRO* 1.3 84.2 - - - +
785C ASP* 1.3 66.5 + - - +
786C ILE 3.2 1.1 + - - -
787C GLY* 3.6 10.3 + - - -
788C ASP* 3.7 9.2 - - - +
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Residues in contact with ASP 785 (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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754C TRP* 4.1 5.4 - - + -
778C LYS 3.8 11.6 - - - +
779C TYR* 3.7 23.4 - - - +
781C MET* 3.7 8.5 + - - +
782C LEU* 3.0 44.3 + - - +
784C ASP* 1.3 81.2 - - - +
786C ILE* 1.3 65.3 + - - +
787C GLY 3.2 0.7 - - - -
788C ASP* 3.1 31.5 + - - +
789C TRP* 3.4 13.7 + - - -
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Residues in contact with ILE 786 (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* 4.8 4.5 - - + -
727C PHE* 4.3 21.1 - - + -
729C ILE* 4.0 27.1 - - + -
750C LEU* 4.2 14.1 - - + -
754C TRP* 3.5 36.4 - - + +
783C PRO 3.2 19.1 - - - +
784C ASP 3.2 0.4 - - - -
785C ASP* 1.3 77.4 - - - +
787C GLY* 1.3 58.0 + - - +
788C ASP 3.2 4.3 + - - -
789C TRP* 3.3 13.6 + - - +
801C PHE* 3.2 28.1 - - + +
802C SER* 6.0 0.4 - - - -
805C SER* 4.2 9.6 - - - +
807C SER* 5.9 1.1 - - - -
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Residues in contact with GLY 787 (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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784C ASP 3.6 7.2 + - - -
785C ASP 3.2 1.2 - - - -
786C ILE* 1.3 77.7 - - - +
788C ASP* 1.3 64.2 + - - +
789C TRP 3.3 2.6 + - - -
790C TYR* 4.6 3.8 + - - -
800C PRO* 4.0 19.4 - - - +
801C PHE* 4.2 0.2 - - - -
802C SER* 4.1 30.0 + - - -
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Residues in contact with ASP 788 (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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190C PRO* 3.5 26.9 - - + +
191C ASN* 4.5 8.3 - - - +
779C TYR* 4.8 11.6 - - + -
784C ASP 3.7 9.7 - - - +
785C ASP* 3.4 31.0 - - + +
786C ILE 3.1 1.4 - - - -
787C GLY* 1.3 82.5 - - - +
789C TRP* 1.3 61.0 + - + +
790C TYR* 3.5 20.2 - - - -
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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