Contacts of the helix formed by residues 199 - 211 (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 199 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C LEU* 4.2 5.4 - - - -
198C LEU* 1.3 80.9 - - - +
200C PRO* 1.3 75.5 - - - +
201C VAL* 3.2 25.1 - - - +
202C ASP* 3.0 23.5 + - - +
203C VAL* 3.3 14.2 + - - +
745C ASP* 5.5 3.5 - - + +
749C THR* 4.1 6.7 - - - -
790C TYR 3.8 2.9 - - - +
791C VAL* 3.7 15.5 - - + -
792C ARG* 3.4 37.0 + - + +
798C MET* 5.0 0.2 - - + -
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Residues in contact with PRO 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C MET* 3.6 37.9 - - + -
193C LEU* 3.9 10.5 - - + -
199C THR* 1.3 87.1 - - - +
201C VAL* 1.3 52.2 + - - +
203C VAL* 3.1 4.4 + - + +
204C ILE* 2.6 44.1 + - + +
748C THR 4.7 0.4 - - - +
749C THR* 3.8 32.8 - - + +
752C ALA* 3.9 20.6 - - + -
773C VAL* 5.4 0.2 - - + -
789C TRP* 4.4 10.3 - - + -
790C TYR 5.0 2.2 - - - +
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Residues in contact with VAL 201 (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* 3.0 16.4 - - - +
200C PRO* 1.3 77.8 - - - +
202C ASP* 1.3 52.3 + - - +
204C ILE* 3.7 7.7 - - + +
205C THR* 2.7 43.9 + - - +
745C ASP* 3.7 36.6 - - - +
748C THR* 3.7 31.2 - - + +
749C THR* 4.3 4.5 - - - +
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Residues in contact with ASP 202 (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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198C LEU* 3.6 22.7 - - + +
199C THR* 3.0 25.9 + - - +
201C VAL* 1.3 77.2 - - - +
203C VAL* 1.3 65.5 + - + +
205C THR* 3.3 6.2 + - - -
206C ALA* 3.1 23.9 + - - +
251C LEU* 4.1 4.9 - - + +
792C ARG* 2.7 46.2 + - - -
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Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ILE* 4.3 12.6 - - + -
188C MET* 4.7 12.3 - - + -
193C LEU* 5.0 10.1 - - + -
198C LEU* 5.3 3.1 - - + -
199C THR 3.5 13.9 - - - +
200C PRO* 3.1 11.4 + - + +
202C ASP* 1.3 80.0 - - + +
204C ILE* 1.3 63.5 + - + +
206C ALA* 3.3 2.6 + - - +
207C ILE* 3.2 44.0 + - + +
251C LEU* 4.1 19.9 - - + +
262C LEU* 3.8 20.4 - - + -
265C VAL* 5.0 6.1 - - + -
266C ALA* 5.6 0.4 - - + -
773C VAL* 4.4 6.3 - - + -
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Residues in contact with ILE 204 (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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200C PRO 2.6 25.6 + - - +
201C VAL* 3.7 4.5 - - - +
203C VAL* 1.3 71.7 - - - +
205C THR* 1.3 65.2 + - - +
207C ILE* 3.1 11.6 + - - +
208C LYS* 3.0 42.3 + - + +
748C THR* 3.6 30.5 - - + -
752C ALA* 4.1 4.7 - - + -
757C SER* 3.9 16.8 - - - +
759C VAL* 3.9 27.1 - - + +
773C VAL* 4.0 18.6 - - + -
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Residues in contact with THR 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C VAL* 2.7 29.2 + - - +
202C ASP* 3.7 6.9 - - - -
203C VAL 3.3 0.2 - - - -
204C ILE* 1.3 78.5 - - - +
206C ALA* 1.3 62.5 + - - +
208C LYS* 3.3 11.2 + - + +
209C ALA* 3.0 24.6 + - + +
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Residues in contact with ALA 206 (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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202C ASP 3.1 9.3 + - - +
203C VAL 3.3 2.7 + - - +
205C THR* 1.3 78.9 - - - +
207C ILE* 1.3 58.9 + - + +
209C ALA* 4.4 2.5 - - - -
210C GLN* 2.8 47.0 + - - +
249C ILE* 3.8 14.8 - - + +
250C LEU 4.3 2.0 - - - +
251C LEU* 3.5 34.5 - - + +
262C LEU* 6.2 0.2 - - + -
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Residues in contact with ILE 207 (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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186C ILE* 3.3 32.8 - - + -
203C VAL* 3.2 30.0 + - + +
204C ILE* 3.1 7.7 + - - +
206C ALA* 1.3 77.8 - - + +
208C LYS* 1.3 59.8 + - - +
211C ASN* 3.0 30.3 + - + +
246C PHE* 4.1 22.4 - - + -
249C ILE* 4.1 18.6 - - + -
262C LEU* 4.6 3.1 - - + -
759C VAL* 3.7 19.3 - - + -
760C ASN* 3.8 8.0 + - - +
771C VAL* 4.3 4.5 - - + -
773C VAL* 4.0 12.1 - - + -
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Residues in contact with LYS 208 (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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204C ILE* 3.0 30.7 + - + +
205C THR* 3.6 10.1 - - - +
207C ILE* 1.3 77.6 - - - +
209C ALA* 1.3 59.4 + - - +
211C ASN 3.7 9.7 - - - +
212C ALA* 3.7 10.4 - - - +
758C TYR 5.7 0.4 + - - -
759C VAL* 3.7 32.7 + - + +
760C ASN* 4.2 12.4 + - - +
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Residues in contact with ALA 209 (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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733A GLN* 4.1 0.3 + - - -
743A ILE* 3.9 28.0 - - + +
744A ASN* 5.6 5.2 - - - +
747A ASN* 5.3 0.2 + - - -
205C THR* 3.0 19.1 + - + +
206C ALA* 3.7 6.5 - - - +
207C ILE 3.1 0.2 - - - -
208C LYS* 1.3 79.4 - - - +
210C GLN* 1.3 66.8 + - + +
211C ASN 3.5 0.2 - - - -
212C ALA* 4.4 2.1 - - - +
237C GLN* 3.1 23.6 + - - +
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Residues in contact with GLN 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A GLN* 3.6 36.7 + - + +
737A GLN* 4.1 9.7 - - - +
206C ALA* 2.8 27.9 + - - +
209C ALA* 1.3 78.9 - - + +
211C ASN* 1.3 56.7 + - - +
237C GLN* 3.3 17.2 - - - +
238C THR 4.6 1.0 - - - +
240C LEU* 3.7 21.5 - - - +
249C ILE* 3.6 20.9 - - + +
250C LEU* 2.9 46.0 + - - +
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Residues in contact with ASN 211 (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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207C ILE* 3.0 23.5 + - + +
208C LYS 3.7 1.7 - - - +
210C GLN* 1.3 75.9 - - - +
212C ALA* 1.3 60.9 + - - +
239C ARG* 3.5 8.7 + - - +
240C LEU* 2.8 45.9 + - + +
246C PHE* 3.7 20.9 - - + -
249C ILE* 5.1 0.2 - - + -
760C ASN* 2.6 52.1 + - - +
761C ASP 2.9 25.8 + - - +
762C PHE* 4.2 0.5 - - - +
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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