Contacts of the helix formed by residues 742 - 756 (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 SER 742 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740C GLY 4.1 2.0 + - - -
741C VAL* 1.3 73.9 - - - +
743C ILE* 1.3 64.0 + - - +
744C ASN* 3.2 12.3 + - - +
745C ASP* 2.9 45.3 + - - +
746C ILE* 3.1 11.1 + - - +
792C ARG 5.1 0.6 + - - -
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Residues in contact with ILE 743 (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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209B ALA* 6.3 2.5 - - + -
237B GLN* 5.0 0.9 - - - +
731C ILE* 4.6 11.0 - - + -
733C GLN* 3.8 51.8 - - + +
736C ALA* 3.3 35.0 - - + -
737C GLN* 4.8 2.5 - - + +
741C VAL 3.4 9.2 - - - +
742C SER* 1.3 73.3 + - - +
744C ASN* 1.3 60.7 + - - +
746C ILE* 3.3 8.9 + - + +
747C ASN* 2.9 43.7 + - - +
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Residues in contact with ASN 744 (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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209B ALA* 6.1 0.7 - - - +
742C SER* 3.1 8.9 + - - +
743C ILE* 1.3 80.3 - - - +
745C ASP* 1.3 59.4 + - - +
747C ASN* 3.2 10.9 + - - +
748C THR* 2.9 36.0 + - - +
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Residues in contact with ASP 745 (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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199C THR* 5.5 3.4 - - + +
201C VAL* 3.7 31.5 - - + +
742C SER* 2.9 29.4 + - - +
744C ASN* 1.3 82.3 - - - +
746C ILE* 1.3 54.4 + - - +
748C THR* 3.4 1.4 + - - -
749C THR* 2.9 35.3 + - - -
791C VAL* 4.1 16.1 - - + +
792C ARG 4.2 13.2 - - - +
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Residues in contact with ILE 746 (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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731C ILE* 3.7 39.5 - - + -
736C ALA* 3.7 28.9 - - + -
741C VAL* 3.7 9.9 - - + -
742C SER 3.1 6.9 + - - +
743C ILE* 3.5 19.5 - - + +
744C ASN 3.2 0.2 - - - -
745C ASP* 1.3 74.2 - - - +
747C ASN* 1.3 62.8 + - - +
749C THR* 3.0 7.9 + - - -
750C LEU* 2.8 29.4 + - + +
791C VAL* 4.2 9.2 - - + -
801C PHE* 3.8 9.6 - - + -
804C PHE* 3.5 32.3 - - + -
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Residues in contact with ASN 747 (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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209B ALA 6.0 0.2 + - - -
214B VAL* 3.6 42.8 - - + +
215B ALA 4.4 5.9 - - - +
236B ALA* 6.0 0.9 - - - +
237B GLN* 4.9 5.4 + - - +
731C ILE* 4.4 9.5 - - - +
743C ILE* 2.9 36.7 + - - +
744C ASN* 3.2 10.8 + - - +
746C ILE* 1.3 84.9 - - - +
748C THR* 1.3 58.6 + - - +
750C LEU* 4.1 5.5 - - - +
751C GLY* 3.1 24.4 + - - -
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Residues in contact with THR 748 (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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201C VAL* 3.7 23.1 - - + +
204C ILE* 3.6 29.4 - - + -
744C ASN* 2.9 18.8 + - - +
747C ASN* 1.3 76.2 - - - +
749C THR* 1.3 60.7 + - - +
751C GLY* 4.6 0.4 - - - +
752C ALA* 2.8 38.6 + - + +
757C SER* 5.4 2.2 - - - +
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Residues in contact with THR 749 (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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199C THR* 4.1 7.8 - - - -
200C PRO* 3.8 31.3 - - + +
201C VAL* 4.3 2.5 - - - +
745C ASP* 2.9 23.7 + - - +
746C ILE 3.4 4.0 - - - -
748C THR* 1.3 75.3 - - - +
750C LEU* 1.3 65.0 + - - +
752C ALA* 4.1 0.3 - - - +
753C ALA* 3.0 27.7 + - - +
789C TRP* 4.4 17.9 - - + -
790C TYR 4.6 3.8 - - - +
791C VAL* 3.8 14.8 - - + +
801C PHE* 3.6 24.7 - - + -
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Residues in contact with LEU 750 (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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214B VAL* 6.3 1.8 - - + -
215B ALA 5.5 0.9 - - - +
216B ALA* 4.3 13.9 - - + -
234B ILE* 5.1 3.4 - - + -
236B ALA* 4.4 17.0 - - + -
729C ILE* 4.0 30.1 - - + -
731C ILE* 4.4 10.3 - - + -
746C ILE* 2.8 19.6 + - + +
747C ASN* 4.1 6.7 - - - +
749C THR* 1.3 76.4 - - - +
751C GLY* 1.3 64.9 + - - +
754C TRP* 3.0 54.5 + - + +
786C ILE* 4.2 15.7 - - + -
789C TRP* 6.5 0.4 - - - -
801C PHE* 3.9 20.2 - - + -
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Residues in contact with GLY 751 (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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215B ALA* 3.9 13.0 + - - -
216B ALA* 3.3 16.1 - - - +
747C ASN 3.1 13.9 + - - -
748C THR* 5.2 0.2 - - - -
750C LEU* 1.3 79.4 - - - +
752C ALA* 1.3 58.0 + - - +
755C GLY* 2.9 26.9 + - - -
756C GLY 3.1 10.8 + - - +
757C SER* 5.4 0.2 - - - -
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Residues in contact with ALA 752 (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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188C MET* 4.4 2.2 - - - -
200C PRO* 3.9 21.1 - - + -
204C ILE* 4.1 9.6 - - + -
748C THR* 2.8 26.6 + - + +
751C GLY* 1.3 71.5 - - - +
753C ALA* 1.3 62.3 + - - +
756C GLY* 3.2 15.5 + - - -
757C SER* 3.9 27.1 - - - -
773C VAL* 3.4 6.0 - - + +
774C MET* 3.4 14.9 - - - -
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Residues in contact with ALA 753 (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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188C MET* 4.2 4.2 - - + +
200C PRO* 5.2 0.7 - - + -
749C THR 3.0 18.8 + - - +
750C LEU* 4.9 0.2 - - - -
752C ALA* 1.3 78.9 - - - +
754C TRP* 1.3 68.5 + - + +
774C MET* 3.6 4.5 - - - +
775C SER* 3.0 33.4 + - - +
780C ARG* 3.7 2.9 - - - -
789C TRP* 3.5 45.1 - - + -
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Residues in contact with TRP 754 (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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216B ALA 4.3 5.8 - - - +
217B GLY* 4.0 1.6 - - - -
218B GLN* 3.4 34.9 + - - +
219B LEU* 3.4 26.0 - - + -
221B GLY* 6.2 0.2 - - - -
234B ILE* 3.4 23.3 - - + -
750C LEU* 3.0 35.8 + - + +
753C ALA* 1.3 86.3 - - + +
755C GLY* 1.3 58.7 + - - +
774C MET* 3.8 13.0 - - - +
779C TYR 4.1 6.7 - - - -
780C ARG* 3.6 39.1 + - + +
782C LEU 3.6 21.8 - - - -
785C ASP* 4.1 4.3 - - + -
786C ILE* 3.5 37.4 - - + +
789C TRP* 3.7 19.6 - - - +
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Residues in contact with GLY 755 (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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216B ALA 3.3 13.8 + - - -
217B GLY* 3.7 8.3 - - - -
218B GLN* 6.2 0.4 - - - -
751C GLY 2.9 10.0 + - - -
754C TRP* 1.3 77.6 - - - +
756C GLY* 1.3 66.2 + - - +
772C TYR* 6.0 0.2 - - - -
774C MET* 4.0 11.9 - - - +
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Residues in contact with GLY 756 (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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185C ARG* 5.4 0.4 - - - -
751C GLY 3.1 11.9 + - - +
752C ALA 3.2 9.7 + - - -
754C TRP 3.7 0.8 - - - -
755C GLY* 1.3 85.5 - - - +
757C SER* 1.3 61.5 + - - -
758C TYR 4.2 0.2 - - - -
772C TYR* 4.9 7.9 - - - -
773C VAL 3.2 15.0 - - - -
774C MET* 3.8 13.7 - - - +
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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