Contacts of the helix formed by residues 199 - 211 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LEU* 4.0 5.7 - - - +
198B LEU* 1.3 81.0 - - - +
200B PRO* 1.3 74.6 - - - +
201B VAL* 3.1 24.2 + - + +
202B ASP* 2.7 26.6 + - - +
203B VAL* 3.3 15.6 + - - +
745B ASP* 5.3 4.5 + - - +
749B THR* 4.3 7.2 - - - +
790B TYR 3.7 12.1 - - - +
791B VAL* 3.9 4.0 - - + -
792B ARG* 3.6 32.9 + - + +
798B MET* 4.3 2.5 - - + -
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Residues in contact with PRO 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B MET* 3.7 40.3 - - + +
193B LEU* 4.4 7.4 - - + -
199B THR* 1.3 88.1 - - - +
201B VAL* 1.3 55.5 + - - +
203B VAL* 3.1 4.6 + - + +
204B ILE* 2.8 35.0 + - + +
748B THR 4.7 0.4 - - - +
749B THR* 4.0 33.4 - - + +
752B ALA* 4.2 17.5 - - + -
773B VAL* 5.4 0.2 - - - +
789B TRP* 4.1 16.4 - - + -
790B TYR 5.0 2.9 - - - +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B THR* 3.0 12.7 - - - +
200B PRO* 1.3 75.8 - - - +
202B ASP* 1.3 58.7 + - - +
204B ILE* 3.3 10.2 + - + +
205B THR* 2.8 42.6 + - - +
745B ASP* 3.7 41.5 - - - +
748B THR* 3.2 27.1 - - + +
749B THR* 4.1 5.2 - - - +
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Residues in contact with ASP 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LEU* 3.3 18.8 - - + +
199B THR* 2.7 34.0 + - - +
201B VAL* 1.3 78.4 - - - +
203B VAL* 1.3 58.7 + - + +
205B THR* 3.4 6.2 + - - -
206B ALA* 3.0 29.6 + - - +
251B LEU* 3.8 10.1 - - + +
792B ARG* 2.5 36.4 + - - -
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 4.6 5.2 - - + -
188B MET* 4.7 10.3 - - + -
193B LEU* 4.0 19.5 - - + -
198B LEU* 5.7 0.2 - - + -
199B THR 3.5 13.5 - - - +
200B PRO* 3.1 10.7 + - + +
202B ASP* 1.3 76.6 - - + +
204B ILE* 1.3 65.7 + - - +
206B ALA* 3.4 1.6 + - - +
207B ILE* 3.0 38.7 + - + +
251B LEU* 4.0 21.8 - - + -
262B LEU* 3.6 25.8 - - + -
265B VAL* 4.6 2.0 - - + -
773B VAL* 4.2 12.8 - - + -
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Residues in contact with ILE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PRO 2.8 20.6 + - - +
201B VAL* 3.6 11.0 - - + +
203B VAL* 1.3 77.5 - - - +
205B THR* 1.3 66.2 + - - +
207B ILE* 3.2 5.9 + - - +
208B LYS* 3.1 52.2 + - + +
748B THR* 5.3 7.9 - - - +
752B ALA* 4.2 15.3 - - + -
757B SER* 4.3 11.0 - - - +
759B VAL* 3.7 21.3 - - + -
773B VAL* 4.0 22.0 - - + -
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 2.8 35.5 + - - +
202B ASP* 3.7 7.8 - - - -
204B ILE* 1.3 78.1 - - - +
206B ALA* 1.3 63.3 + - - +
208B LYS* 3.4 7.3 + - - +
209B ALA* 3.2 22.9 + - + +
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ASP 3.0 18.5 + - - +
203B VAL 3.8 2.9 - - - +
204B ILE 3.3 0.2 - - - -
205B THR* 1.3 77.9 - - - +
207B ILE* 1.3 56.9 + - + +
209B ALA* 3.2 4.5 + - - +
210B GLN* 3.0 37.8 + - - +
249B ILE* 4.0 16.2 - - + -
250B LEU 4.2 8.7 - - - +
251B LEU* 3.7 22.0 - - + -
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ILE* 3.5 29.2 - - + -
203B VAL* 3.0 34.6 + - + +
204B ILE* 3.8 4.0 - - - +
206B ALA* 1.3 71.5 - - - +
208B LYS* 1.3 66.4 + - - +
211B ASN* 3.1 25.6 + - + +
246B PHE* 4.1 19.1 - - + -
249B ILE* 4.2 13.0 - - + -
262B LEU* 4.1 14.8 - - + -
759B VAL* 3.8 19.7 - - + -
760B ASN* 3.6 11.7 + - - +
771B VAL* 4.2 5.6 - - + -
773B VAL* 4.1 11.0 - - + -
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Residues in contact with LYS 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ILE* 3.1 36.8 + - - +
205B THR* 3.7 6.9 - - - +
207B ILE* 1.3 77.5 - - - +
209B ALA* 1.3 58.6 + - - +
211B ASN 4.0 0.7 - - - +
212B ALA* 3.6 19.6 - - - +
759B VAL* 3.8 28.3 - - + +
760B ASN* 3.6 13.4 + - + +
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B THR* 3.2 18.1 + - + +
206B ALA* 3.7 6.5 - - - +
207B ILE 3.1 0.4 - - - -
208B LYS* 1.3 80.1 - - - +
210B GLN* 1.3 65.6 + - + +
211B ASN 3.5 0.4 - - - -
212B ALA* 4.4 2.5 - - - +
237B GLN* 3.5 13.2 + - - +
733C GLN* 3.3 19.9 + - - +
743C ILE* 6.3 2.5 - - + -
744C ASN* 6.1 0.9 - - - +
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Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ALA* 3.0 19.6 + - - +
207B ILE 4.7 0.4 - - - +
209B ALA* 1.3 80.6 - - + +
211B ASN* 1.3 58.2 + - - +
212B ALA 3.9 1.3 - - - -
237B GLN* 3.9 9.5 + - - +
238B THR 5.1 0.3 - - - +
240B LEU* 3.4 23.4 - - + +
248B LYS 4.7 0.5 - - - +
249B ILE* 3.4 27.1 - - + +
250B LEU* 2.8 52.7 + - - +
733C GLN* 3.6 33.4 + - - +
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Residues in contact with ASN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 3.1 14.6 + - + +
210B GLN* 1.3 76.5 - - - +
212B ALA* 1.3 61.5 + - - +
239B ARG* 3.5 6.2 - - - +
240B LEU* 2.8 44.5 + - + +
246B PHE* 3.9 22.1 - - + -
249B ILE* 5.5 0.2 - - + -
760B ASN* 3.0 32.7 + - - +
761B ASP 2.4 32.1 + - - +
762B PHE* 4.2 1.7 - - - +
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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